combine error with --IR_version 1

[UBrau]

Hi guys,

Hong just ran three mouse samples (PE, stranded) with --IR_version 1 and align failed with the error below. There is a bug with the {} in RI_MakeCoverageKey.pl, lines 70, 71, 74 and 76. I'm fixing it.

Command line for combine: vast-tools combine -o . -sp Mmu --IR_version 1 --dbDir ~/2018_RNASeq_Pipeline/vast-tools/VASTDB/ -C

Combine output:

## Wed Jul 25 13:32:32 2018 #################################################################

==> 27977682.bc.ccbr.utoronto.ca.OU

==> Run command    : vast-tools combine -o . -sp Mmu --IR_version 1 --dbDir /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/ -C

==> Execution host : grendel.ccbr.utoronto.ca

[vast combine]: Using VASTDB -> /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu

[vast combine]: Building Table for COMBI (a posteriori pipeline)

[vast combine combi]: Loading strand-unspecific mappability for each EEJ and length:

[vast combine combi]: Loading: /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu/FILES/Mmu_COMBI-M-50-gDNA.eff    Length: 50

[vast combine combi]: Loading strand-specific mappability for each EEJ and length:

[vast combine combi]: Loading: /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu/FILES/Mmu_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]:    Blencowe_1_A01_S110_R1_001: found to_combine/Blencowe_1_A01_S110_R1_001.info. Sample will be treated as being strand-specific.

[vast combine combi]:    Blencowe_2_A02_S111_R1_001: found to_combine/Blencowe_2_A02_S111_R1_001.info. Sample will be treated as being strand-specific.

[vast combine combi]:    Blencowe_3_A03_S112_R1_001: found to_combine/Blencowe_3_A03_S112_R1_001.info. Sample will be treated as being strand-specific.

[vast combine combi]: Quantifying PSIs

[vast combine]: Building Table for EXSK (a priori 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 (a priori 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 (microexons)

[vast combine]: Building Table for ANNOT (annotated pipeline)

[vast combine annot]: Loading strand-unspecific mappability for each EEJ and length:

[vast combine annot]: Loading: /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu/FILES/Mmu_COMBI-M-50-gDNA.eff    Length: 50

[vast combine annot]: Loading strand-unspecific mappability for each EEJ and length:

[vast combine annot]: Loading: /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu/FILES/Mmu_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]:    Blencowe_1_A01_S110_R1_001: found to_combine/Blencowe_1_A01_S110_R1_001.info. Sample will be treated as being strand-specific.

[vast combine annot]:    Blencowe_2_A02_S111_R1_001: found to_combine/Blencowe_2_A02_S111_R1_001.info. Sample will be treated as being strand-specific.

[vast combine annot]:    Blencowe_3_A03_S112_R1_001: found to_combine/Blencowe_3_A03_S112_R1_001.info. Sample will be treated as being strand-specific.

[vast combine annot]: Quantifying PSIs

[vast combine]: Building quality score table for intron retention (version 1)

Do not find to_combine/{Blencowe_1_A01_S110_R1_001}.info. You might need to run vast-tools align again. at /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/bin/RI_MakeCoverageKey.pl line 70.

[vast combine error]: /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/bin/RI_MakeCoverageKey.pl -sp Mmu -dbDir /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/VASTDB/Mmu /home/blencowe/blencowe1/honghan/NovaSeq20180719/test/test_vast_out/to_combine Failed in RunDBS_2.pl! at /home/blencowe/blencowe1/honghan/2018_RNASeq_Pipeline/vast-tools/bin/RunDBS_2.pl line 53.

==> Resources used : cput=00:06:26,mem=1489344kb,vmem=2111208kb,walltime=00:06:33

==> Exit status    : 2