[vast combine]: VAST-TOOLS v2.5.1
[vast combine]: Species assembly: mm10, VASTDB Species key: Mm2
[vast combine]: Using VASTDB -> /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2
[vast combine]: VASTDB Version: vastdb.mm2.23.06.20
[vast combine]: Building Table for COMBI (splice-site based pipeline)
[vast combine combi]: Loading strand-unspecific mappability for each EEJ and length:
[vast combine combi]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff	Length: 50
[vast combine combi]: Loading strand-specific mappability for each EEJ and length:
[vast combine combi]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff	Length: 50
[vast combine combi]: Parsing Template file
[vast combine combi]: Loading EEJ read counts data
[vast combine combi]:    SRR5264037_1: found to_combine/SRR5264037_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264040_1: found to_combine/SRR5264040_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264043_1: found to_combine/SRR5264043_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264054_1: found to_combine/SRR5264054_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264057_1: found to_combine/SRR5264057_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264060_1: found to_combine/SRR5264060_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264067_1: found to_combine/SRR5264067_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264070_1: found to_combine/SRR5264070_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]:    SRR5264073_1: found to_combine/SRR5264073_1.info. Sample will be treated as being not strand-specific.
[vast combine combi]: Quantifying PSIs

[vast combine]: Building Table for EXSK (transcript-based pipeline, single)
[vast combine apr]: Loading and parsing data for each sample for EXSK
[vast combine apr]: Parsing info and getting Quality scores (Q) for EXSK

[vast combine]: Building Table for MULTI (transcript-based pipeline, multiexon)
[vast combine apr]: Loading and parsing data for each sample for MULTI
[vast combine apr]: Parsing info and getting Quality scores (Q) for MULTI

[vast combine]: Building Table for MIC (microexon pipeline)

[vast combine]: Building Table for ANNOT (annotation-based pipeline)
[vast combine annot]: Loading strand-unspecific mappability for each EEJ and length:
[vast combine annot]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff	Length: 50
[vast combine annot]: Loading strand-unspecific mappability for each EEJ and length:
[vast combine annot]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff	Length: 50
[vast combine annot]: Parsing Template file
[vast combine annot]: Loading EEJ read counts data
[vast combine annot]:    SRR5264037_1: found to_combine/SRR5264037_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264040_1: found to_combine/SRR5264040_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264043_1: found to_combine/SRR5264043_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264054_1: found to_combine/SRR5264054_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264057_1: found to_combine/SRR5264057_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264060_1: found to_combine/SRR5264060_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264067_1: found to_combine/SRR5264067_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264070_1: found to_combine/SRR5264070_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]:    SRR5264073_1: found to_combine/SRR5264073_1.info. Sample will be treated as being not strand-specific.
[vast combine annot]: Quantifying PSIs

[vast combine]: Building quality score table for intron retention (version 2)
[vast combine IR]:    SRR5264037_1: found to_combine/SRR5264037_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264040_1: found to_combine/SRR5264040_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264043_1: found to_combine/SRR5264043_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264054_1: found to_combine/SRR5264054_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264057_1: found to_combine/SRR5264057_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264060_1: found to_combine/SRR5264060_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264067_1: found to_combine/SRR5264067_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264070_1: found to_combine/SRR5264070_1.info. Sample will be treated as being not strand-specific.
[vast combine IR]:    SRR5264073_1: found to_combine/SRR5264073_1.info. Sample will be treated as being not strand-specific.

[vast combine]: Building Table for intron retention (version 2)
Trying to load required package: optparse
Merging IR of 9 sample(s)...
SRR5264037_1 
SRR5264040_1 
SRR5264043_1 
SRR5264054_1 
SRR5264057_1 
SRR5264060_1 
SRR5264067_1 
SRR5264070_1 
SRR5264073_1 
           used (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  1234216 66.0    2164898 115.7  2164898 115.7
Vcells 11619033 88.7   26657121 203.4 26652649 203.4
... done.

[vast combine]: Building Table for Alternative 5'ss choice events
[vast combine alt5]: Parsing Template file
[vast combine alt5]: Loading mappability files (strand-unspecific and strand-specific):
[vast combine alt5]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff	Length: 50
[vast combine alt5]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff	Length: 50
[vast combine alt5]: Loading EEJ data for ALT5
[vast combine alt5]:    SRR5264037_1: found to_combine/SRR5264037_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264040_1: found to_combine/SRR5264040_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264043_1: found to_combine/SRR5264043_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264054_1: found to_combine/SRR5264054_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264057_1: found to_combine/SRR5264057_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264060_1: found to_combine/SRR5264060_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264067_1: found to_combine/SRR5264067_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264070_1: found to_combine/SRR5264070_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]:    SRR5264073_1: found to_combine/SRR5264073_1.info. Sample will be treated as being not strand-specific.
[vast combine alt5]: Starting PSI quantifications

[vast combine]: Building Table for Alternative 3'ss choice events
[vast combine alt3]: Parsing Template file
[vast combine alt3]: Loading mappability files (strand-unspecific and strand-specific):
[vast combine alt3]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff	Length: 50
[vast combine alt3]: Loading: /nfs/users/mirimia/projects/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA-SS.eff	Length: 50
[vast combine alt3]: Loading EEJ data for ALT3
[vast combine alt3]:    SRR5264037_1: found to_combine/SRR5264037_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264040_1: found to_combine/SRR5264040_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264043_1: found to_combine/SRR5264043_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264054_1: found to_combine/SRR5264054_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264057_1: found to_combine/SRR5264057_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264060_1: found to_combine/SRR5264060_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264067_1: found to_combine/SRR5264067_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264070_1: found to_combine/SRR5264070_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]:    SRR5264073_1: found to_combine/SRR5264073_1.info. Sample will be treated as being not strand-specific.
[vast combine alt3]: Starting PSI quantification

[vast combine]: Combining results into a single table
[vast combine]: Final table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/vast_out/INCLUSION_LEVELS_FULL-mm10-9.tab
[vast combine]: Combining cRPKMs into a single table
[vast combine]: Final cRPKM table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/vast_out/cRPKM-mm10-9.tab
[vast combine]: Final cRPKM and COUNTS table saved as: /nfs/no_backup/jvalcarcel/emancini/anieto/vast_out/cRPKM_AND_COUNTS-mm10-9.tab
[vast combine]: Deleting raw_incl/ folder
[vast combine]: Deleting raw_reads/ folder
[vast combine]: Completed Sat Jan 29 20:34:03 2022