[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/SRR5264067_1.fastq.gz and /nfs/no_backup/jvalcarcel/emancini/anieto/SRR5264067_2.fastq.gz
[vast align]: Most common read lengths detected for fq1 & fq2: 101 (100.00%) and 101 (100.00%)
[vast align]: Sample name: SRR5264067_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: 178466 (35.69%)
# reads that failed to align: 307135 (61.43%)
# reads with alignments suppressed due to -m: 14399 (2.88%)
Reported 178466 alignments to 1 output stream(s)
[vast align]:    fraction of first reads mapping to fwd / rev strand : 0.4931 / 0.5069
# reads processed: 500000
# reads with at least one reported alignment: 176071 (35.21%)
# reads that failed to align: 309902 (61.98%)
# reads with alignments suppressed due to -m: 14027 (2.81%)
Reported 176071 alignments to 1 output stream(s)
[vast align]:    fraction of second reads mapping to fwd / rev strand : 0.4980 / 0.5020
[vast align]: Mapping RNAseq reads against mRNA sequences
[vast align]: Calculating cRPKMs
[vast trim]: Total processed reads: 11776499
[vast trim]: Total valid fwd reads: 11776499
# reads processed: 11776499
# reads with at least one reported alignment: 5933628 (50.39%)
# reads that failed to align: 5199294 (44.15%)
# reads with alignments suppressed due to -m: 643577 (5.46%)
Reported 5933628 alignments to 1 output stream(s)
[vast align]: Trimming RNAseq reads to 50 nt sequences
[vast trim]: Total processed reads: 11776499
[vast trim]: Total valid fwd reads: 11776499
[vast trim]: Total valid rev reads: 11776499
[vast align]: Doing genome subtraction
# reads processed: 70658994
# reads with at least one reported alignment: 37043704 (52.43%)
# reads that failed to align: 24311041 (34.41%)
# reads with alignments suppressed due to -m: 9304249 (13.17%)
Reported 37043704 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
# reads processed: 24311041
# reads with at least one reported alignment: 2890228 (11.89%)
# reads that failed to align: 21289035 (87.57%)
# reads with alignments suppressed due to -m: 131778 (0.54%)
Reported 2890228 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing...
# reads processed: 24311041
# reads with at least one reported alignment: 472299 (1.94%)
# reads that failed to align: 23833869 (98.04%)
# reads with alignments suppressed due to -m: 4873 (0.02%)
Reported 472299 alignments to 1 output stream(s)
[vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing...
# reads processed: 24311041
# reads with at least one reported alignment: 610940 (2.51%)
# reads that failed to align: 23686386 (97.43%)
# reads with alignments suppressed due to -m: 13715 (0.06%)
Reported 610940 alignments to 1 output stream(s)
[vast align]: Mapping reads to microexon EEJ library and Analyzing...
# reads processed: 24311041
# reads with at least one reported alignment: 58949 (0.24%)
# reads that failed to align: 24237255 (99.70%)
# reads with alignments suppressed due to -m: 14837 (0.06%)
Reported 58949 alignments to 1 output stream(s)
[vast align]: Mapping reads to intron retention library (version 2)...
# reads processed: 70658994
# reads with at least one reported alignment: 4098709 (5.80%)
# reads that failed to align: 66375705 (93.94%)
# reads with alignments suppressed due to -m: 184580 (0.26%)
Reported 4098709 alignments to 1 output stream(s)
# reads processed: 70658994
# reads with at least one reported alignment: 762087 (1.08%)
# reads that failed to align: 69225993 (97.97%)
# reads with alignments suppressed due to -m: 670914 (0.95%)
Reported 762087 alignments to 1 output stream(s)
[vast align]: Cleaning SRR5264067_1-50.fa.gz files!
[vast align]: Cleaning up SRR5264067_1-50-e.fa.gz!
[vast align]: Deleting temporary files with reverse-complemented reads.
[vast align]: Completed Sat Jan 29 18:16:31 2022