[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/SRR5264060_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264060_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264060_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: 205691 (41.14%)
# reads that failed to align: 263958 (52.79%)
# reads with alignments suppressed due to -m: 30351 (6.07%)
Reported 205691 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4927 / 0.5073
# reads processed: 500000
# reads with at least one reported alignment: 203102 (40.62%)
# reads that failed to align: 267224 (53.44%)
# reads with alignments suppressed due to -m: 29674 (5.93%)
Reported 203102 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4943 / 0.5057
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 19264945
[vast trim]: Total valid fwd reads: 19264945
# reads processed: 19264945
# reads with at least one reported alignment: 9882473 (51.30%)
# reads that failed to align: 7606266 (39.48%)
# reads with alignments suppressed due to -m: 1776206 (9.22%)
Reported 9882473 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 19264945
[vast trim]: Total valid fwd reads: 19264945
[vast trim]: Total valid rev reads: 19264945
[vast align]: Doing genome subtraction
# reads processed: 115589670
# reads with at least one reported alignment: 65690015 (56.83%)
# reads that failed to align: 29068649 (25.15%)
# reads with alignments suppressed due to -m: 20831006 (18.02%)
Reported 65690015 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 29068649
# reads with at least one reported alignment: 5131913 (17.65%)
# reads that failed to align: 23714221 (81.58%)
# reads with alignments suppressed due to -m: 222515 (0.77%)
Reported 5131913 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 29068649
# reads with at least one reported alignment: 836446 (2.88%)
# reads that failed to align: 28223493 (97.09%)
# reads with alignments suppressed due to -m: 8710 (0.03%)
Reported 836446 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 29068649
# reads with at least one reported alignment: 1171045 (4.03%)
# reads that failed to align: 27872960 (95.89%)
# reads with alignments suppressed due to -m: 24644 (0.08%)
Reported 1171045 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 29068649
# reads with at least one reported alignment: 98514 (0.34%)
# reads that failed to align: 28958788 (99.62%)
# reads with alignments suppressed due to -m: 11347 (0.04%)
Reported 98514 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 115589670
# reads with at least one reported alignment: 7594175 (6.57%)
# reads that failed to align: 107625810 (93.11%)
# reads with alignments suppressed due to -m: 369685 (0.32%)
Reported 7594175 alignments to 1 output stream(s)
# reads processed: 115589670
# reads with at least one reported alignment: 1596038 (1.38%)
# reads that failed to align: 112736743 (97.53%)
# reads with alignments suppressed due to -m: 1256889 (1.09%)
Reported 1596038 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264060_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264060_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 19:11:00 2022