[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/SRR5264040_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264040_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264040_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/vast_out/tmp!
# reads processed: 500000
# reads with at least one reported alignment: 256785 (51.36%)
# reads that failed to align: 199886 (39.98%)
# reads with alignments suppressed due to -m: 43329 (8.67%)
Reported 256785 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4894 / 0.5106
# reads processed: 500000
# reads with at least one reported alignment: 253193 (50.64%)
# reads that failed to align: 204460 (40.89%)
# reads with alignments suppressed due to -m: 42347 (8.47%)
Reported 253193 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4959 / 0.5041
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 13879118
[vast trim]: Total valid fwd reads: 13879118
# reads processed: 13879118
# reads with at least one reported alignment: 8033497 (57.88%)
# reads that failed to align: 4233844 (30.51%)
# reads with alignments suppressed due to -m: 1611777 (11.61%)
Reported 8033497 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 13879118
[vast trim]: Total valid fwd reads: 13879118
[vast trim]: Total valid rev reads: 13879118
[vast align]: Doing genome subtraction
# reads processed: 83274708
# reads with at least one reported alignment: 48926000 (58.75%)
# reads that failed to align: 15779805 (18.95%)
# reads with alignments suppressed due to -m: 18568903 (22.30%)
Reported 48926000 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 15779805
# reads with at least one reported alignment: 4602807 (29.17%)
# reads that failed to align: 10975910 (69.56%)
# reads with alignments suppressed due to -m: 201088 (1.27%)
Reported 4602807 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 15779805
# reads with at least one reported alignment: 747291 (4.74%)
# reads that failed to align: 15024748 (95.22%)
# reads with alignments suppressed due to -m: 7766 (0.05%)
Reported 747291 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 15779805
# reads with at least one reported alignment: 992293 (6.29%)
# reads that failed to align: 14765967 (93.58%)
# reads with alignments suppressed due to -m: 21545 (0.14%)
Reported 992293 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 15779805
# reads with at least one reported alignment: 89973 (0.57%)
# reads that failed to align: 15669697 (99.30%)
# reads with alignments suppressed due to -m: 20135 (0.13%)
Reported 89973 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 83274708
# reads with at least one reported alignment: 6706687 (8.05%)
# reads that failed to align: 76300754 (91.63%)
# reads with alignments suppressed due to -m: 267267 (0.32%)
Reported 6706687 alignments to 1 output stream(s)
# reads processed: 83274708
# reads with at least one reported alignment: 1096885 (1.32%)
# reads that failed to align: 81379910 (97.72%)
# reads with alignments suppressed due to -m: 797913 (0.96%)
Reported 1096885 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264040_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264040_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 18:25:55 2022