[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/SRR5264054_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264054_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264054_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: 204187 (40.84%)
# reads that failed to align: 254690 (50.94%)
# reads with alignments suppressed due to -m: 41123 (8.22%)
Reported 204187 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4922 / 0.5078
# reads processed: 500000
# reads with at least one reported alignment: 201268 (40.25%)
# reads that failed to align: 258717 (51.74%)
# reads with alignments suppressed due to -m: 40015 (8.00%)
Reported 201268 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4955 / 0.5045
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 15194345
[vast trim]: Total valid fwd reads: 15194345
# reads processed: 15194345
# reads with at least one reported alignment: 7802125 (51.35%)
# reads that failed to align: 5547097 (36.51%)
# reads with alignments suppressed due to -m: 1845123 (12.14%)
Reported 7802125 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 15194345
[vast trim]: Total valid fwd reads: 15194345
[vast trim]: Total valid rev reads: 15194345
[vast align]: Doing genome subtraction
# reads processed: 91166070
# reads with at least one reported alignment: 50168841 (55.03%)
# reads that failed to align: 21705221 (23.81%)
# reads with alignments suppressed due to -m: 19292008 (21.16%)
Reported 50168841 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 21705221
# reads with at least one reported alignment: 3973793 (18.31%)
# reads that failed to align: 17559417 (80.90%)
# reads with alignments suppressed due to -m: 172011 (0.79%)
Reported 3973793 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 21705221
# reads with at least one reported alignment: 650138 (3.00%)
# reads that failed to align: 21047874 (96.97%)
# reads with alignments suppressed due to -m: 7209 (0.03%)
Reported 650138 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 21705221
# reads with at least one reported alignment: 914163 (4.21%)
# reads that failed to align: 20770758 (95.69%)
# reads with alignments suppressed due to -m: 20300 (0.09%)
Reported 914163 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 21705221
# reads with at least one reported alignment: 79276 (0.37%)
# reads that failed to align: 21617466 (99.60%)
# reads with alignments suppressed due to -m: 8479 (0.04%)
Reported 79276 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 91166070
# reads with at least one reported alignment: 5883073 (6.45%)
# reads that failed to align: 85003345 (93.24%)
# reads with alignments suppressed due to -m: 279652 (0.31%)
Reported 5883073 alignments to 1 output stream(s)
# reads processed: 91166070
# reads with at least one reported alignment: 1186794 (1.30%)
# reads that failed to align: 89163892 (97.80%)
# reads with alignments suppressed due to -m: 815384 (0.89%)
Reported 1186794 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264054_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264054_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 18:35:46 2022