[vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-0_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-0_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-B-0_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 362437 (72.49%) # reads that failed to align: 116645 (23.33%) # reads with alignments suppressed due to -m: 20918 (4.18%) Reported 362437 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0061 / 0.9939 # reads processed: 500000 # reads with at least one reported alignment: 359590 (71.92%) # reads that failed to align: 119851 (23.97%) # reads with alignments suppressed due to -m: 20559 (4.11%) Reported 359590 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9934 / 0.0066 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-0_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_cSKM877S/D-B-0_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 94131748 [vast trim]: Total valid fwd reads: 94131748 # reads processed: 94131748 # reads with at least one reported alignment: 69828395 (74.18%) # reads that failed to align: 20372341 (21.64%) # reads with alignments suppressed due to -m: 3931012 (4.18%) Reported 69828395 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 94131748 [vast trim]: Total valid fwd reads: 94131748 [vast trim]: Total valid rev reads: 94131748 [vast align]: Doing genome subtraction # reads processed: 753053984 # reads with at least one reported alignment: 481863211 (63.99%) # reads that failed to align: 113838137 (15.12%) # reads with alignments suppressed due to -m: 157352636 (20.90%) Reported 481863211 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 113838137 # reads with at least one reported alignment: 64162450 (56.36%) # reads that failed to align: 46956260 (41.25%) # reads with alignments suppressed due to -m: 2719427 (2.39%) Reported 64162450 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 113838137 # reads with at least one reported alignment: 10277183 (9.03%) # reads that failed to align: 103478627 (90.90%) # reads with alignments suppressed due to -m: 82327 (0.07%) Reported 10277183 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 113838137 # reads with at least one reported alignment: 12989371 (11.41%) # reads that failed to align: 100615470 (88.38%) # reads with alignments suppressed due to -m: 233296 (0.20%) Reported 12989371 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 113838137 # reads with at least one reported alignment: 1347414 (1.18%) # reads that failed to align: 112384736 (98.72%) # reads with alignments suppressed due to -m: 105987 (0.09%) Reported 1347414 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 753053984 # reads with at least one reported alignment: 87563204 (11.63%) # reads that failed to align: 663640366 (88.13%) # reads with alignments suppressed due to -m: 1850414 (0.25%) Reported 87563204 alignments to 1 output stream(s) # reads processed: 753053984 # reads with at least one reported alignment: 6934296 (0.92%) # reads that failed to align: 743822212 (98.77%) # reads with alignments suppressed due to -m: 2297476 (0.31%) Reported 6934296 alignments to 1 output stream(s) [vast align]: Cleaning D-B-0_1-50.fa.gz files! [vast align]: Cleaning up D-B-0_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 07:56:15 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-1_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-1_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-B-1_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 341297 (68.26%) # reads that failed to align: 135127 (27.03%) # reads with alignments suppressed due to -m: 23576 (4.72%) Reported 341297 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0104 / 0.9896 # reads processed: 500000 # reads with at least one reported alignment: 337639 (67.53%) # reads that failed to align: 138877 (27.78%) # reads with alignments suppressed due to -m: 23484 (4.70%) Reported 337639 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9878 / 0.0122 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-1_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_MV7MyOpp/D-B-1_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 89151822 [vast trim]: Total valid fwd reads: 89151822 # reads processed: 89151822 # reads with at least one reported alignment: 62786234 (70.43%) # reads that failed to align: 22766397 (25.54%) # reads with alignments suppressed due to -m: 3599191 (4.04%) Reported 62786234 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 89151822 [vast trim]: Total valid fwd reads: 89151822 [vast trim]: Total valid rev reads: 89151822 [vast align]: Doing genome subtraction # reads processed: 713214576 # reads with at least one reported alignment: 437973361 (61.41%) # reads that failed to align: 114772126 (16.09%) # reads with alignments suppressed due to -m: 160469089 (22.50%) Reported 437973361 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 114772126 # reads with at least one reported alignment: 57565561 (50.16%) # reads that failed to align: 54750856 (47.70%) # reads with alignments suppressed due to -m: 2455709 (2.14%) Reported 57565561 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 114772126 # reads with at least one reported alignment: 9177654 (8.00%) # reads that failed to align: 105521438 (91.94%) # reads with alignments suppressed due to -m: 73034 (0.06%) Reported 9177654 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 114772126 # reads with at least one reported alignment: 11579456 (10.09%) # reads that failed to align: 102984663 (89.73%) # reads with alignments suppressed due to -m: 208007 (0.18%) Reported 11579456 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 114772126 # reads with at least one reported alignment: 1208756 (1.05%) # reads that failed to align: 113468939 (98.86%) # reads with alignments suppressed due to -m: 94431 (0.08%) Reported 1208756 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 713214576 # reads with at least one reported alignment: 79004292 (11.08%) # reads that failed to align: 632541982 (88.69%) # reads with alignments suppressed due to -m: 1668302 (0.23%) Reported 79004292 alignments to 1 output stream(s) # reads processed: 713214576 # reads with at least one reported alignment: 6212839 (0.87%) # reads that failed to align: 704893360 (98.83%) # reads with alignments suppressed due to -m: 2108377 (0.30%) Reported 6212839 alignments to 1 output stream(s) [vast align]: Cleaning D-B-1_1-50.fa.gz files! [vast align]: Cleaning up D-B-1_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 06:02:23 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-6_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-6_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-B-6_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 352806 (70.56%) # reads that failed to align: 127296 (25.46%) # reads with alignments suppressed due to -m: 19898 (3.98%) Reported 352806 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0052 / 0.9948 # reads processed: 500000 # reads with at least one reported alignment: 348525 (69.70%) # reads that failed to align: 132317 (26.46%) # reads with alignments suppressed due to -m: 19158 (3.83%) Reported 348525 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9945 / 0.0055 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-B-6_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_stHk2tVx/D-B-6_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 95858477 [vast trim]: Total valid fwd reads: 95858477 # reads processed: 95858477 # reads with at least one reported alignment: 69229518 (72.22%) # reads that failed to align: 22670028 (23.65%) # reads with alignments suppressed due to -m: 3958931 (4.13%) Reported 69229518 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 95858477 [vast trim]: Total valid fwd reads: 95858477 [vast trim]: Total valid rev reads: 95858477 [vast align]: Doing genome subtraction # reads processed: 766867816 # reads with at least one reported alignment: 494213570 (64.45%) # reads that failed to align: 122532248 (15.98%) # reads with alignments suppressed due to -m: 150121998 (19.58%) Reported 494213570 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 122532248 # reads with at least one reported alignment: 65309265 (53.30%) # reads that failed to align: 54393033 (44.39%) # reads with alignments suppressed due to -m: 2829950 (2.31%) Reported 65309265 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 122532248 # reads with at least one reported alignment: 10457761 (8.53%) # reads that failed to align: 111991807 (91.40%) # reads with alignments suppressed due to -m: 82680 (0.07%) Reported 10457761 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 122532248 # reads with at least one reported alignment: 13140756 (10.72%) # reads that failed to align: 109154629 (89.08%) # reads with alignments suppressed due to -m: 236863 (0.19%) Reported 13140756 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 122532248 # reads with at least one reported alignment: 1377655 (1.12%) # reads that failed to align: 121050925 (98.79%) # reads with alignments suppressed due to -m: 103668 (0.08%) Reported 1377655 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 766867816 # reads with at least one reported alignment: 87793934 (11.45%) # reads that failed to align: 677093749 (88.29%) # reads with alignments suppressed due to -m: 1980133 (0.26%) Reported 87793934 alignments to 1 output stream(s) # reads processed: 766867816 # reads with at least one reported alignment: 7443678 (0.97%) # reads that failed to align: 757089363 (98.72%) # reads with alignments suppressed due to -m: 2334775 (0.30%) Reported 7443678 alignments to 1 output stream(s) [vast align]: Cleaning D-B-6_1-50.fa.gz files! [vast align]: Cleaning up D-B-6_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 14:01:45 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-0_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-0_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-C-0_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 356835 (71.37%) # reads that failed to align: 124273 (24.85%) # reads with alignments suppressed due to -m: 18892 (3.78%) Reported 356835 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0040 / 0.9960 # reads processed: 500000 # reads with at least one reported alignment: 347086 (69.42%) # reads that failed to align: 134681 (26.94%) # reads with alignments suppressed due to -m: 18233 (3.65%) Reported 347086 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9961 / 0.0039 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-0_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_f6TQmtNT/D-C-0_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 95609128 [vast trim]: Total valid fwd reads: 95609128 # reads processed: 95609128 # reads with at least one reported alignment: 68747860 (71.91%) # reads that failed to align: 23128735 (24.19%) # reads with alignments suppressed due to -m: 3732533 (3.90%) Reported 68747860 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 95609128 [vast trim]: Total valid fwd reads: 95609128 [vast trim]: Total valid rev reads: 95609128 [vast align]: Doing genome subtraction # reads processed: 764873024 # reads with at least one reported alignment: 480126266 (62.77%) # reads that failed to align: 141989387 (18.56%) # reads with alignments suppressed due to -m: 142757371 (18.66%) Reported 480126266 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 141989387 # reads with at least one reported alignment: 66436066 (46.79%) # reads that failed to align: 72743021 (51.23%) # reads with alignments suppressed due to -m: 2810300 (1.98%) Reported 66436066 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 141989387 # reads with at least one reported alignment: 10635099 (7.49%) # reads that failed to align: 131261144 (92.44%) # reads with alignments suppressed due to -m: 93144 (0.07%) Reported 10635099 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 141989387 # reads with at least one reported alignment: 13410881 (9.44%) # reads that failed to align: 128340076 (90.39%) # reads with alignments suppressed due to -m: 238430 (0.17%) Reported 13410881 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 141989387 # reads with at least one reported alignment: 1395380 (0.98%) # reads that failed to align: 140481260 (98.94%) # reads with alignments suppressed due to -m: 112747 (0.08%) Reported 1395380 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 764873024 # reads with at least one reported alignment: 89612141 (11.72%) # reads that failed to align: 673432190 (88.04%) # reads with alignments suppressed due to -m: 1828693 (0.24%) Reported 89612141 alignments to 1 output stream(s) # reads processed: 764873024 # reads with at least one reported alignment: 6626883 (0.87%) # reads that failed to align: 755804232 (98.81%) # reads with alignments suppressed due to -m: 2441909 (0.32%) Reported 6626883 alignments to 1 output stream(s) [vast align]: Cleaning D-C-0_1-50.fa.gz files! [vast align]: Cleaning up D-C-0_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 17:10:26 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-1_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-1_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-C-1_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 362121 (72.42%) # reads that failed to align: 118242 (23.65%) # reads with alignments suppressed due to -m: 19637 (3.93%) Reported 362121 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0038 / 0.9962 # reads processed: 500000 # reads with at least one reported alignment: 353265 (70.65%) # reads that failed to align: 127739 (25.55%) # reads with alignments suppressed due to -m: 18996 (3.80%) Reported 353265 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9962 / 0.0038 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-1_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_O6DMoooK/D-C-1_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 118005680 [vast trim]: Total valid fwd reads: 118005680 # reads processed: 118005680 # reads with at least one reported alignment: 86120610 (72.98%) # reads that failed to align: 27089623 (22.96%) # reads with alignments suppressed due to -m: 4795447 (4.06%) Reported 86120610 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 118005680 [vast trim]: Total valid fwd reads: 118005680 [vast trim]: Total valid rev reads: 118005680 [vast align]: Doing genome subtraction # reads processed: 944045440 # reads with at least one reported alignment: 596756651 (63.21%) # reads that failed to align: 167753119 (17.77%) # reads with alignments suppressed due to -m: 179535670 (19.02%) Reported 596756651 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 167753119 # reads with at least one reported alignment: 81992003 (48.88%) # reads that failed to align: 82288980 (49.05%) # reads with alignments suppressed due to -m: 3472136 (2.07%) Reported 81992003 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 167753119 # reads with at least one reported alignment: 13077296 (7.80%) # reads that failed to align: 154561567 (92.14%) # reads with alignments suppressed due to -m: 114256 (0.07%) Reported 13077296 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 167753119 # reads with at least one reported alignment: 16435567 (9.80%) # reads that failed to align: 151024226 (90.03%) # reads with alignments suppressed due to -m: 293326 (0.17%) Reported 16435567 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 167753119 # reads with at least one reported alignment: 1734792 (1.03%) # reads that failed to align: 165880590 (98.88%) # reads with alignments suppressed due to -m: 137737 (0.08%) Reported 1734792 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 944045440 # reads with at least one reported alignment: 111025859 (11.76%) # reads that failed to align: 830744410 (88.00%) # reads with alignments suppressed due to -m: 2275171 (0.24%) Reported 111025859 alignments to 1 output stream(s) # reads processed: 944045440 # reads with at least one reported alignment: 8302977 (0.88%) # reads that failed to align: 932724800 (98.80%) # reads with alignments suppressed due to -m: 3017663 (0.32%) Reported 8302977 alignments to 1 output stream(s) [vast align]: Cleaning D-C-1_1-50.fa.gz files! [vast align]: Cleaning up D-C-1_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 19:05:41 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-6_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-6_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-C-6_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 362511 (72.50%) # reads that failed to align: 117896 (23.58%) # reads with alignments suppressed due to -m: 19593 (3.92%) Reported 362511 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0039 / 0.9961 # reads processed: 500000 # reads with at least one reported alignment: 355169 (71.03%) # reads that failed to align: 125725 (25.14%) # reads with alignments suppressed due to -m: 19106 (3.82%) Reported 355169 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9960 / 0.0040 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-C-6_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_ckBfo0r8/D-C-6_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 114891650 [vast trim]: Total valid fwd reads: 114891650 # reads processed: 114891650 # reads with at least one reported alignment: 84059608 (73.16%) # reads that failed to align: 26175215 (22.78%) # reads with alignments suppressed due to -m: 4656827 (4.05%) Reported 84059608 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 114891650 [vast trim]: Total valid fwd reads: 114891650 [vast trim]: Total valid rev reads: 114891650 [vast align]: Doing genome subtraction # reads processed: 919133200 # reads with at least one reported alignment: 591906431 (64.40%) # reads that failed to align: 159816821 (17.39%) # reads with alignments suppressed due to -m: 167409948 (18.21%) Reported 591906431 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 159816821 # reads with at least one reported alignment: 81745472 (51.15%) # reads that failed to align: 74542980 (46.64%) # reads with alignments suppressed due to -m: 3528369 (2.21%) Reported 81745472 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 159816821 # reads with at least one reported alignment: 13090707 (8.19%) # reads that failed to align: 146611777 (91.74%) # reads with alignments suppressed due to -m: 114337 (0.07%) Reported 13090707 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 159816821 # reads with at least one reported alignment: 16304856 (10.20%) # reads that failed to align: 143218005 (89.61%) # reads with alignments suppressed due to -m: 293960 (0.18%) Reported 16304856 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 159816821 # reads with at least one reported alignment: 1736983 (1.09%) # reads that failed to align: 157946417 (98.83%) # reads with alignments suppressed due to -m: 133421 (0.08%) Reported 1736983 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 919133200 # reads with at least one reported alignment: 109082402 (11.87%) # reads that failed to align: 807716541 (87.88%) # reads with alignments suppressed due to -m: 2334257 (0.25%) Reported 109082402 alignments to 1 output stream(s) # reads processed: 919133200 # reads with at least one reported alignment: 8397873 (0.91%) # reads that failed to align: 907913882 (98.78%) # reads with alignments suppressed due to -m: 2821445 (0.31%) Reported 8397873 alignments to 1 output stream(s) [vast align]: Cleaning D-C-6_1-50.fa.gz files! [vast align]: Cleaning up D-C-6_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 18:55:32 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-0_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-0_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-D-0_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 354087 (70.82%) # reads that failed to align: 124113 (24.82%) # reads with alignments suppressed due to -m: 21800 (4.36%) Reported 354087 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0066 / 0.9934 # reads processed: 500000 # reads with at least one reported alignment: 349271 (69.85%) # reads that failed to align: 129411 (25.88%) # reads with alignments suppressed due to -m: 21318 (4.26%) Reported 349271 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9928 / 0.0072 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-0_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_aUQ19_4X/D-D-0_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 92396084 [vast trim]: Total valid fwd reads: 92396084 # reads processed: 92396084 # reads with at least one reported alignment: 67135153 (72.66%) # reads that failed to align: 21315568 (23.07%) # reads with alignments suppressed due to -m: 3945363 (4.27%) Reported 67135153 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 92396084 [vast trim]: Total valid fwd reads: 92396084 [vast trim]: Total valid rev reads: 92396084 [vast align]: Doing genome subtraction # reads processed: 739168672 # reads with at least one reported alignment: 460795298 (62.34%) # reads that failed to align: 120645503 (16.32%) # reads with alignments suppressed due to -m: 157727871 (21.34%) Reported 460795298 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 120645503 # reads with at least one reported alignment: 62277905 (51.62%) # reads that failed to align: 55709203 (46.18%) # reads with alignments suppressed due to -m: 2658395 (2.20%) Reported 62277905 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 120645503 # reads with at least one reported alignment: 9937128 (8.24%) # reads that failed to align: 110618682 (91.69%) # reads with alignments suppressed due to -m: 89693 (0.07%) Reported 9937128 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 120645503 # reads with at least one reported alignment: 12469761 (10.34%) # reads that failed to align: 107953598 (89.48%) # reads with alignments suppressed due to -m: 222144 (0.18%) Reported 12469761 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 120645503 # reads with at least one reported alignment: 1287598 (1.07%) # reads that failed to align: 119258098 (98.85%) # reads with alignments suppressed due to -m: 99807 (0.08%) Reported 1287598 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 739168672 # reads with at least one reported alignment: 85035532 (11.50%) # reads that failed to align: 652304324 (88.25%) # reads with alignments suppressed due to -m: 1828816 (0.25%) Reported 85035532 alignments to 1 output stream(s) # reads processed: 739168672 # reads with at least one reported alignment: 6392431 (0.86%) # reads that failed to align: 730706035 (98.86%) # reads with alignments suppressed due to -m: 2070206 (0.28%) Reported 6392431 alignments to 1 output stream(s) [vast align]: Cleaning D-D-0_1-50.fa.gz files! [vast align]: Cleaning up D-D-0_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sat Feb 26 17:34:25 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-1_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-1_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-D-1_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 362363 (72.47%) # reads that failed to align: 113139 (22.63%) # reads with alignments suppressed due to -m: 24498 (4.90%) Reported 362363 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0065 / 0.9935 # reads processed: 500000 # reads with at least one reported alignment: 358153 (71.63%) # reads that failed to align: 117927 (23.59%) # reads with alignments suppressed due to -m: 23920 (4.78%) Reported 358153 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9927 / 0.0073 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-1_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_soZ_2ywF/D-D-1_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 94417426 [vast trim]: Total valid fwd reads: 94417426 # reads processed: 94417426 # reads with at least one reported alignment: 70032914 (74.17%) # reads that failed to align: 19814241 (20.99%) # reads with alignments suppressed due to -m: 4570271 (4.84%) Reported 70032914 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 94417426 [vast trim]: Total valid fwd reads: 94417426 [vast trim]: Total valid rev reads: 94417426 [vast align]: Doing genome subtraction # reads processed: 755339408 # reads with at least one reported alignment: 461558340 (61.11%) # reads that failed to align: 117619237 (15.57%) # reads with alignments suppressed due to -m: 176161831 (23.32%) Reported 461558340 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 117619237 # reads with at least one reported alignment: 62919638 (53.49%) # reads that failed to align: 52020819 (44.23%) # reads with alignments suppressed due to -m: 2678780 (2.28%) Reported 62919638 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 117619237 # reads with at least one reported alignment: 10011347 (8.51%) # reads that failed to align: 107514135 (91.41%) # reads with alignments suppressed due to -m: 93755 (0.08%) Reported 10011347 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 117619237 # reads with at least one reported alignment: 12392921 (10.54%) # reads that failed to align: 104998959 (89.27%) # reads with alignments suppressed due to -m: 227357 (0.19%) Reported 12392921 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 117619237 # reads with at least one reported alignment: 1325036 (1.13%) # reads that failed to align: 116184733 (98.78%) # reads with alignments suppressed due to -m: 109468 (0.09%) Reported 1325036 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 755339408 # reads with at least one reported alignment: 89228144 (11.81%) # reads that failed to align: 664235715 (87.94%) # reads with alignments suppressed due to -m: 1875549 (0.25%) Reported 89228144 alignments to 1 output stream(s) # reads processed: 755339408 # reads with at least one reported alignment: 6442211 (0.85%) # reads that failed to align: 746872480 (98.88%) # reads with alignments suppressed due to -m: 2024717 (0.27%) Reported 6442211 alignments to 1 output stream(s) [vast align]: Cleaning D-D-1_1-50.fa.gz files! [vast align]: Cleaning up D-D-1_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sun Feb 27 06:49:53 2022 [vast align]: VAST-TOOLS v2.5.1 [vast align]: Species assembly: mm10, VASTDB Species key: Mm2 [vast align]: VASTDB Version: vastdb.mm2.23.06.20 [vast align]: Input RNA-seq file(s): /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-6_1.fq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-6_2.fq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 125 (100.00%) and 125 (100.00%) [vast align]: Sample name: D-D-6_1 [vast align]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast align]: Setting output directory to vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp! # reads processed: 500000 # reads with at least one reported alignment: 356687 (71.34%) # reads that failed to align: 121902 (24.38%) # reads with alignments suppressed due to -m: 21411 (4.28%) Reported 356687 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.0053 / 0.9947 # reads processed: 500000 # reads with at least one reported alignment: 352957 (70.59%) # reads that failed to align: 126170 (25.23%) # reads with alignments suppressed due to -m: 20873 (4.17%) Reported 352957 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.9947 / 0.0053 [vast align]: reverse-complementing reads from /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/D-D-6_1.fq.gz; writing into /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/tmp/tmpfqs_FxccNyxi/D-D-6_1.fq.gz [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs [vast trim]: Total processed reads: 136007557 [vast trim]: Total valid fwd reads: 136007557 # reads processed: 136007557 # reads with at least one reported alignment: 98978986 (72.77%) # reads that failed to align: 31040245 (22.82%) # reads with alignments suppressed due to -m: 5988326 (4.40%) Reported 98978986 alignments to 1 output stream(s) [vast align]: Trimming RNAseq reads to 50 nt sequences [vast trim]: Total processed reads: 136007557 [vast trim]: Total valid fwd reads: 136007557 [vast trim]: Total valid rev reads: 136007557 [vast align]: Doing genome subtraction # reads processed: 1088060456 # reads with at least one reported alignment: 695189531 (63.89%) # reads that failed to align: 173804325 (15.97%) # reads with alignments suppressed due to -m: 219066600 (20.13%) Reported 695189531 alignments to 1 output stream(s) [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... # reads processed: 173804325 # reads with at least one reported alignment: 95342185 (54.86%) # reads that failed to align: 74312877 (42.76%) # reads with alignments suppressed due to -m: 4149263 (2.39%) Reported 95342185 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... # reads processed: 173804325 # reads with at least one reported alignment: 15222656 (8.76%) # reads that failed to align: 158445378 (91.16%) # reads with alignments suppressed due to -m: 136291 (0.08%) Reported 15222656 alignments to 1 output stream(s) [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... # reads processed: 173804325 # reads with at least one reported alignment: 18908144 (10.88%) # reads that failed to align: 154555800 (88.93%) # reads with alignments suppressed due to -m: 340381 (0.20%) Reported 18908144 alignments to 1 output stream(s) [vast align]: Mapping reads to microexon EEJ library and Analyzing... # reads processed: 173804325 # reads with at least one reported alignment: 1977474 (1.14%) # reads that failed to align: 171678193 (98.78%) # reads with alignments suppressed due to -m: 148658 (0.09%) Reported 1977474 alignments to 1 output stream(s) [vast align]: Mapping reads to intron retention library (version 2)... # reads processed: 1088060456 # reads with at least one reported alignment: 129111859 (11.87%) # reads that failed to align: 956038717 (87.87%) # reads with alignments suppressed due to -m: 2909880 (0.27%) Reported 129111859 alignments to 1 output stream(s) # reads processed: 1088060456 # reads with at least one reported alignment: 10346411 (0.95%) # reads that failed to align: 1074538467 (98.76%) # reads with alignments suppressed due to -m: 3175578 (0.29%) Reported 10346411 alignments to 1 output stream(s) [vast align]: Cleaning D-D-6_1-50.fa.gz files! [vast align]: Cleaning up D-D-6_1-50-e.fa.gz! [vast align]: Deleting temporary files with reverse-complemented reads. [vast align]: Completed Sun Feb 27 21:36:35 2022 [vast combine]: VAST-TOOLS v2.5.1 [vast combine]: Species assembly: mm10, VASTDB Species key: Mm2 [vast combine]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2 [vast combine]: VASTDB Version: vastdb.mm2.23.06.20 [vast combine]: Building Table for COMBI (splice-site based pipeline) [vast combine combi]: Loading strand-unspecific mappability for each EEJ and length: [vast combine combi]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff Length: 50 [vast combine combi]: Loading strand-specific mappability for each EEJ and length: [vast combine combi]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff Length: 50 [vast combine combi]: Parsing Template file [vast combine combi]: Loading EEJ read counts data [vast combine combi]: D-B-0_1: found to_combine/D-B-0_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-B-1_1: found to_combine/D-B-1_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-B-6_1: found to_combine/D-B-6_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-C-0_1: found to_combine/D-C-0_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-C-1_1: found to_combine/D-C-1_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-C-6_1: found to_combine/D-C-6_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-D-0_1: found to_combine/D-D-0_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-D-1_1: found to_combine/D-D-1_1.info. Sample will be treated as being strand-specific. [vast combine combi]: D-D-6_1: found to_combine/D-D-6_1.info. Sample will be treated as being strand-specific. [vast combine combi]: Quantifying PSIs [vast combine]: Building Table for EXSK (transcript-based pipeline, single) [vast combine apr]: Loading and parsing data for each sample for EXSK [vast combine apr]: Parsing info and getting Quality scores (Q) for EXSK [vast combine]: Building Table for MULTI (transcript-based pipeline, multiexon) [vast combine apr]: Loading and parsing data for each sample for MULTI [vast combine apr]: Parsing info and getting Quality scores (Q) for MULTI [vast combine]: Building Table for MIC (microexon pipeline) [vast combine]: Building Table for ANNOT (annotation-based pipeline) [vast combine annot]: Loading strand-unspecific mappability for each EEJ and length: [vast combine annot]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff Length: 50 [vast combine annot]: Loading strand-unspecific mappability for each EEJ and length: [vast combine annot]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff Length: 50 [vast combine annot]: Parsing Template file [vast combine annot]: Loading EEJ read counts data [vast combine annot]: D-B-0_1: found to_combine/D-B-0_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-B-1_1: found to_combine/D-B-1_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-B-6_1: found to_combine/D-B-6_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-C-0_1: found to_combine/D-C-0_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-C-1_1: found to_combine/D-C-1_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-C-6_1: found to_combine/D-C-6_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-D-0_1: found to_combine/D-D-0_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-D-1_1: found to_combine/D-D-1_1.info. Sample will be treated as being strand-specific. [vast combine annot]: D-D-6_1: found to_combine/D-D-6_1.info. Sample will be treated as being strand-specific. [vast combine annot]: Quantifying PSIs [vast combine]: Building quality score table for intron retention (version 2) [vast combine IR]: D-B-0_1: found to_combine/D-B-0_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-B-1_1: found to_combine/D-B-1_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-B-6_1: found to_combine/D-B-6_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-C-0_1: found to_combine/D-C-0_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-C-1_1: found to_combine/D-C-1_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-C-6_1: found to_combine/D-C-6_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-D-0_1: found to_combine/D-D-0_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-D-1_1: found to_combine/D-D-1_1.info. Sample will be treated as being strand-specific. [vast combine IR]: D-D-6_1: found to_combine/D-D-6_1.info. Sample will be treated as being strand-specific. [vast combine]: Building Table for intron retention (version 2) Trying to load required package: optparse Merging IR of 9 sample(s)... D-B-0_1 D-B-1_1 D-B-6_1 D-C-0_1 D-C-1_1 D-C-6_1 D-D-0_1 D-D-1_1 D-D-6_1 used (Mb) gc trigger (Mb) max used (Mb) Ncells 1668685 89.2 2637877 140.9 2637877 140.9 Vcells 13339370 101.8 26657243 203.4 26633418 203.2 ... done. [vast combine]: Building Table for Alternative 5'ss choice events [vast combine alt5]: Parsing Template file [vast combine alt5]: Loading mappability files (strand-unspecific and strand-specific): [vast combine alt5]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff Length: 50 [vast combine alt5]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff Length: 50 [vast combine alt5]: Loading EEJ data for ALT5 [vast combine alt5]: D-B-0_1: found to_combine/D-B-0_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-B-1_1: found to_combine/D-B-1_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-B-6_1: found to_combine/D-B-6_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-C-0_1: found to_combine/D-C-0_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-C-1_1: found to_combine/D-C-1_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-C-6_1: found to_combine/D-C-6_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-D-0_1: found to_combine/D-D-0_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-D-1_1: found to_combine/D-D-1_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: D-D-6_1: found to_combine/D-D-6_1.info. Sample will be treated as being strand-specific. [vast combine alt5]: Starting PSI quantifications [vast combine]: Building Table for Alternative 3'ss choice events [vast combine alt3]: Parsing Template file [vast combine alt3]: Loading mappability files (strand-unspecific and strand-specific): [vast combine alt3]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff Length: 50 [vast combine alt3]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff Length: 50 [vast combine alt3]: Loading EEJ data for ALT3 [vast combine alt3]: D-B-0_1: found to_combine/D-B-0_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-B-1_1: found to_combine/D-B-1_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-B-6_1: found to_combine/D-B-6_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-C-0_1: found to_combine/D-C-0_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-C-1_1: found to_combine/D-C-1_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-C-6_1: found to_combine/D-C-6_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-D-0_1: found to_combine/D-D-0_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-D-1_1: found to_combine/D-D-1_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: D-D-6_1: found to_combine/D-D-6_1.info. Sample will be treated as being strand-specific. [vast combine alt3]: Starting PSI quantification [vast combine]: Combining results into a single table [vast combine]: Final table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/INCLUSION_LEVELS_FULL-mm10-9.tab [vast combine]: Combining cRPKMs into a single table [vast combine]: Final cRPKM table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/cRPKM-mm10-9.tab [vast combine]: Final cRPKM and COUNTS table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/03_vtools_BCD/vast_out/cRPKM_AND_COUNTS-mm10-9.tab [vast combine]: Deleting raw_incl/ folder [vast combine]: Deleting raw_reads/ folder [vast combine]: Completed Sun Feb 27 22:21:33 2022