[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/SRR5264043_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264043_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264043_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: 223237 (44.65%)
# reads that failed to align: 258669 (51.73%)
# reads with alignments suppressed due to -m: 18094 (3.62%)
Reported 223237 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4937 / 0.5063
# reads processed: 500000
# reads with at least one reported alignment: 220195 (44.04%)
# reads that failed to align: 261987 (52.40%)
# reads with alignments suppressed due to -m: 17818 (3.56%)
Reported 220195 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4939 / 0.5061
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 14624720
[vast trim]: Total valid fwd reads: 14624720
# reads processed: 14624720
# reads with at least one reported alignment: 8812324 (60.26%)
# reads that failed to align: 4867479 (33.28%)
# reads with alignments suppressed due to -m: 944917 (6.46%)
Reported 8812324 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 14624720
[vast trim]: Total valid fwd reads: 14624720
[vast trim]: Total valid rev reads: 14624720
[vast align]: Doing genome subtraction
# reads processed: 87748320
# reads with at least one reported alignment: 45828371 (52.23%)
# reads that failed to align: 27899856 (31.80%)
# reads with alignments suppressed due to -m: 14020093 (15.98%)
Reported 45828371 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 27899856
# reads with at least one reported alignment: 4714549 (16.90%)
# reads that failed to align: 22978821 (82.36%)
# reads with alignments suppressed due to -m: 206486 (0.74%)
Reported 4714549 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 27899856
# reads with at least one reported alignment: 761169 (2.73%)
# reads that failed to align: 27130530 (97.24%)
# reads with alignments suppressed due to -m: 8157 (0.03%)
Reported 761169 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 27899856
# reads with at least one reported alignment: 1021134 (3.66%)
# reads that failed to align: 26856957 (96.26%)
# reads with alignments suppressed due to -m: 21765 (0.08%)
Reported 1021134 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 27899856
# reads with at least one reported alignment: 92350 (0.33%)
# reads that failed to align: 27787814 (99.60%)
# reads with alignments suppressed due to -m: 19692 (0.07%)
Reported 92350 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 87748320
# reads with at least one reported alignment: 6815617 (7.77%)
# reads that failed to align: 80649115 (91.91%)
# reads with alignments suppressed due to -m: 283588 (0.32%)
Reported 6815617 alignments to 1 output stream(s)
# reads processed: 87748320
# reads with at least one reported alignment: 971344 (1.11%)
# reads that failed to align: 85987069 (97.99%)
# reads with alignments suppressed due to -m: 789907 (0.90%)
Reported 971344 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264043_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264043_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 19:26:14 2022