[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/SRR5264057_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264057_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264057_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: 203280 (40.66%)
# reads that failed to align: 274996 (55.00%)
# reads with alignments suppressed due to -m: 21724 (4.34%)
Reported 203280 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4924 / 0.5076
# reads processed: 500000
# reads with at least one reported alignment: 200396 (40.08%)
# reads that failed to align: 278445 (55.69%)
# reads with alignments suppressed due to -m: 21159 (4.23%)
Reported 200396 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4965 / 0.5035
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 10097414
[vast trim]: Total valid fwd reads: 10097414
# reads processed: 10097414
# reads with at least one reported alignment: 4970173 (49.22%)
# reads that failed to align: 4423003 (43.80%)
# reads with alignments suppressed due to -m: 704238 (6.97%)
Reported 4970173 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 10097414
[vast trim]: Total valid fwd reads: 10097414
[vast trim]: Total valid rev reads: 10097414
[vast align]: Doing genome subtraction
# reads processed: 60584484
# reads with at least one reported alignment: 35176288 (58.06%)
# reads that failed to align: 15284784 (25.23%)
# reads with alignments suppressed due to -m: 10123412 (16.71%)
Reported 35176288 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 15284784
# reads with at least one reported alignment: 2579747 (16.88%)
# reads that failed to align: 12589922 (82.37%)
# reads with alignments suppressed due to -m: 115115 (0.75%)
Reported 2579747 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 15284784
# reads with at least one reported alignment: 418998 (2.74%)
# reads that failed to align: 14861287 (97.23%)
# reads with alignments suppressed due to -m: 4499 (0.03%)
Reported 418998 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 15284784
# reads with at least one reported alignment: 569219 (3.72%)
# reads that failed to align: 14703101 (96.19%)
# reads with alignments suppressed due to -m: 12464 (0.08%)
Reported 569219 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 15284784
# reads with at least one reported alignment: 50134 (0.33%)
# reads that failed to align: 15228229 (99.63%)
# reads with alignments suppressed due to -m: 6421 (0.04%)
Reported 50134 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 60584484
# reads with at least one reported alignment: 4000830 (6.60%)
# reads that failed to align: 56362506 (93.03%)
# reads with alignments suppressed due to -m: 221148 (0.37%)
Reported 4000830 alignments to 1 output stream(s)
# reads processed: 60584484
# reads with at least one reported alignment: 854768 (1.41%)
# reads that failed to align: 58943636 (97.29%)
# reads with alignments suppressed due to -m: 786080 (1.30%)
Reported 854768 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264057_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264057_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 18:17:42 2022