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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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combine problem reading RI_MakeTablePIR.R #114

Closed mponcecic closed 1 year ago

mponcecic commented 1 year ago

Hi!

I have recently run vast-align on my RNA-seq data which run perfectly fine. This RNA-seq presents around 65 million reads per sample, is paired end 151 bps and mouse genome was used in this mapping. Afterwards, I run vast-combine and the process was finished but if we take a look at the error file and error turned out. I do believe that this error does not really affects the output of the final table but affects the capability of the vast-combine to arise a syntax error when the commands are not correct, as it is indicated in the RI_MakeTablePIR.R.

My command: ./vast-tools/vast-tools combine -o /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results -sp Mm2 --cores 6 --IR_version 2 --keep_raw_reads --extra_eej 5 -C

Error: 

[vast combine error]: in call /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R --verbose 1 -s /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/VASTDB/Mm2 --IR_version 2 -c /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/to_combine -q /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/to_combine/Coverage_key_v2-Mm240.IRQ -o /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/raw_incl
/vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R: line 18: syntax error near unexpected token `('
/vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R: line 18: `argv <- commandArgs(trailingOnly = FALSE)'

Error file:

[vast combine]: VAST-TOOLS v2.5.1
[vast combine]: Species assembly: mm10, VASTDB Species key: Mm2
[vast combine]: Using VASTDB -> /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/VASTDB/Mm2
[vast combine]: VASTDB Version: vastdb.mm2.23.06.20
[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 quality score table for intron retention (version 2)
[vast combine IR]:    S_01: found to_combine/S_01.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_02: found to_combine/S_02.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_03: found to_combine/S_03.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_04: found to_combine/S_04.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_05: found to_combine/S_05.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_06: found to_combine/S_06.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_07: found to_combine/S_07.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_08: found to_combine/S_08.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_09: found to_combine/S_09.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_10: found to_combine/S_10.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_11: found to_combine/S_11.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_12: found to_combine/S_12.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_13: found to_combine/S_13.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_14: found to_combine/S_14.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_15: found to_combine/S_15.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_16: found to_combine/S_16.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_17: found to_combine/S_17.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_18: found to_combine/S_18.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_19: found to_combine/S_19.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_20: found to_combine/S_20.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_21: found to_combine/S_21.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_22: found to_combine/S_22.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_23: found to_combine/S_23.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_24: found to_combine/S_24.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_25: found to_combine/S_25.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_26: found to_combine/S_26.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_27: found to_combine/S_27.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_28: found to_combine/S_28.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_29: found to_combine/S_29.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_30: found to_combine/S_30.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_31: found to_combine/S_31.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_32: found to_combine/S_32.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_33: found to_combine/S_33.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_34: found to_combine/S_34.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_35: found to_combine/S_35.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_36: found to_combine/S_36.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_37: found to_combine/S_37.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_38: found to_combine/S_38.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_39: found to_combine/S_39.info. Sample will be treated as being strand-specific.
[vast combine IR]:    S_40: found to_combine/S_40.info. Sample will be treated as being strand-specific.

[vast combine error]: in call /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R --verbose 1 -s /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/VASTDB/Mm2 --IR_version 2 -c /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/to_combine -q /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/to_combine/Coverage_key_v2-Mm240.IRQ -o /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/raw_incl
/vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R: line 18: syntax error near unexpected token `('
/vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/RI_MakeTablePIR.R: line 18: `argv <- commandArgs(trailingOnly = FALSE)'

[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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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]:    S_01: found to_combine/S_01.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_02: found to_combine/S_02.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_03: found to_combine/S_03.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_04: found to_combine/S_04.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_05: found to_combine/S_05.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_06: found to_combine/S_06.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_07: found to_combine/S_07.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_08: found to_combine/S_08.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_09: found to_combine/S_09.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_10: found to_combine/S_10.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_11: found to_combine/S_11.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_12: found to_combine/S_12.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_13: found to_combine/S_13.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_14: found to_combine/S_14.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_15: found to_combine/S_15.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_16: found to_combine/S_16.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_17: found to_combine/S_17.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_18: found to_combine/S_18.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_19: found to_combine/S_19.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_20: found to_combine/S_20.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_21: found to_combine/S_21.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_22: found to_combine/S_22.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_23: found to_combine/S_23.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_24: found to_combine/S_24.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_25: found to_combine/S_25.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_26: found to_combine/S_26.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_27: found to_combine/S_27.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_28: found to_combine/S_28.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_29: found to_combine/S_29.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_30: found to_combine/S_30.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_31: found to_combine/S_31.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_32: found to_combine/S_32.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_33: found to_combine/S_33.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_34: found to_combine/S_34.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_35: found to_combine/S_35.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_36: found to_combine/S_36.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_37: found to_combine/S_37.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_38: found to_combine/S_38.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_39: found to_combine/S_39.info. Sample will be treated as being strand-specific.
[vast combine annot]:    S_40: found to_combine/S_40.info. Sample will be treated as being strand-specific.
[vast combine annot]: Quantifying PSIs

[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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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]:    S_01: found to_combine/S_01.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_02: found to_combine/S_02.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_03: found to_combine/S_03.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_04: found to_combine/S_04.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_05: found to_combine/S_05.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_06: found to_combine/S_06.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_07: found to_combine/S_07.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_08: found to_combine/S_08.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_09: found to_combine/S_09.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_10: found to_combine/S_10.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_11: found to_combine/S_11.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_12: found to_combine/S_12.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_13: found to_combine/S_13.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_14: found to_combine/S_14.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_15: found to_combine/S_15.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_16: found to_combine/S_16.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_17: found to_combine/S_17.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_18: found to_combine/S_18.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_19: found to_combine/S_19.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_20: found to_combine/S_20.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_21: found to_combine/S_21.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_22: found to_combine/S_22.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_23: found to_combine/S_23.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_24: found to_combine/S_24.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_25: found to_combine/S_25.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_26: found to_combine/S_26.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_27: found to_combine/S_27.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_28: found to_combine/S_28.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_29: found to_combine/S_29.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_30: found to_combine/S_30.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_31: found to_combine/S_31.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_32: found to_combine/S_32.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_33: found to_combine/S_33.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_34: found to_combine/S_34.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_35: found to_combine/S_35.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_36: found to_combine/S_36.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_37: found to_combine/S_37.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_38: found to_combine/S_38.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_39: found to_combine/S_39.info. Sample will be treated as being strand-specific.
[vast combine combi]:    S_40: found to_combine/S_40.info. Sample will be treated as being strand-specific.
[vast combine combi]: Quantifying PSIs

[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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff   Length: 50
[vast combine alt5]: Loading: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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]:    S_01: found to_combine/S_01.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_02: found to_combine/S_02.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_03: found to_combine/S_03.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_04: found to_combine/S_04.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_05: found to_combine/S_05.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_06: found to_combine/S_06.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_07: found to_combine/S_07.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_08: found to_combine/S_08.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_09: found to_combine/S_09.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_10: found to_combine/S_10.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_11: found to_combine/S_11.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_12: found to_combine/S_12.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_13: found to_combine/S_13.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_14: found to_combine/S_14.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_15: found to_combine/S_15.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_16: found to_combine/S_16.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_17: found to_combine/S_17.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_18: found to_combine/S_18.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_19: found to_combine/S_19.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_20: found to_combine/S_20.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_21: found to_combine/S_21.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_22: found to_combine/S_22.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_23: found to_combine/S_23.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_24: found to_combine/S_24.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_25: found to_combine/S_25.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_26: found to_combine/S_26.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_27: found to_combine/S_27.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_28: found to_combine/S_28.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_29: found to_combine/S_29.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_30: found to_combine/S_30.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_31: found to_combine/S_31.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_32: found to_combine/S_32.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_33: found to_combine/S_33.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_34: found to_combine/S_34.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_35: found to_combine/S_35.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_36: found to_combine/S_36.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_37: found to_combine/S_37.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_38: found to_combine/S_38.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_39: found to_combine/S_39.info. Sample will be treated as being strand-specific.
[vast combine alt5]:    S_40: found to_combine/S_40.info. Sample will be treated as being 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: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/VASTDB/Mm2/FILES/Mm2_COMBI-M-50-gDNA.eff   Length: 50
[vast combine alt3]: Loading: /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/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]:    S_01: found to_combine/S_01.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_02: found to_combine/S_02.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_03: found to_combine/S_03.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_04: found to_combine/S_04.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_05: found to_combine/S_05.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_06: found to_combine/S_06.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_07: found to_combine/S_07.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_08: found to_combine/S_08.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_09: found to_combine/S_09.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_10: found to_combine/S_10.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_11: found to_combine/S_11.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_12: found to_combine/S_12.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_13: found to_combine/S_13.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_14: found to_combine/S_14.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_15: found to_combine/S_15.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_16: found to_combine/S_16.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_17: found to_combine/S_17.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_18: found to_combine/S_18.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_19: found to_combine/S_19.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_20: found to_combine/S_20.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_21: found to_combine/S_21.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_22: found to_combine/S_22.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_23: found to_combine/S_23.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_24: found to_combine/S_24.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_25: found to_combine/S_25.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_26: found to_combine/S_26.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_27: found to_combine/S_27.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_28: found to_combine/S_28.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_29: found to_combine/S_29.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_30: found to_combine/S_30.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_31: found to_combine/S_31.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_32: found to_combine/S_32.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_33: found to_combine/S_33.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_34: found to_combine/S_34.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_35: found to_combine/S_35.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_36: found to_combine/S_36.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_37: found to_combine/S_37.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_38: found to_combine/S_38.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_39: found to_combine/S_39.info. Sample will be treated as being strand-specific.
[vast combine alt3]:    S_40: found to_combine/S_40.info. Sample will be treated as being strand-specific.
[vast combine alt3]: Starting PSI quantification

[vast combine]: Combining results into a single table
Smartmatch is experimental at /vols/GPArkaitz_bigdata/DATA_shared/NewCluster_Software/vast-tools/bin/Add_to_FULL.pl line 191.
cat: raw_incl/INCLUSION_LEVELS_IR-Mm240.tab: No such file or directory
[vast combine]: Final table saved as: /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/INCLUSION_LEVELS_FULL-mm10-40.tab
[vast combine]: Deleting raw_incl/ folder
[vast combine]: Completed Fri May 26 14:49:26 2023

Thank you!

María

mirimia commented 1 year ago

Hi Maria,

Thank you for the message. I'm tagging @UBrau, who can hopefully take a look (thanks!).

Best Manu

mponcecic commented 1 year ago

Hi Manu!

Thank you very much for your fast response. I hope we can find a solution to this issue.

María

UBrau commented 1 year ago

Hi Maria,

Would you mind sharing some of the files with me? I would like to see: /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/VTS_LOG_commands.txt /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/to_combine/Coverage_key_v2-Mm240.IRQ

and the final /vols/GPArkaitz_bigdata/mponce/AC62/02_VAST_TOOLS/Results/INCLUSION_LEVELS_FULL-...

I can send you an upload link.

Ulrich

mponcecic commented 1 year ago

Hi Ulrich!

Yes! I can send you the files. Just send me the link and I will upload the files you just asked.

Thanks!

María

UBrau commented 1 year ago

Please use https://www.dropbox.com/scl/fo/s13ihdhklhgorj2eqa1tz/h?dl=0&rlkey=iytee6yahvxid1s4hzxk0prkr

Also, please do an ls -l of the _tocombine subfolder.

mponcecic commented 1 year ago

Hi Ulrich!

Each file is now available in the link. In addition, the output of the ls -l ./to_combine is saved as to_combine_files_and_folders.txt.

Do not hesitate to reach me if you need something else.

Thanks, María

UBrau commented 1 year ago

Hi Maria,

It seems that the error happened when a script was started that collects the intron retention information from the different samples into a single table. This script is in R, and it seems your system is trying to interpret it using the bash interpreter, which of course fails and produces the error message line 18: syntax error near unexpected token `(' etc. vast-tools combine then proceeds without the intron retention events, and they are missing in the final output.

Can you verify that you have R installed as per the requirements, and that your system runs the R interpreter when you start an R script, not using

Rscript

but just invoking a script as in

myscript.R -h

and the script has the header line #!/usr/bin/env Rscript

mponcecic commented 1 year ago

Hi Ulrich,

First of all, sorry for the late replay. I am running vast-tools in a cluster which might be the reason of this environment issue. At this point, we are working together with the cluster technician to solve this problem because we were able to work this program in other cluster without a issue.

I hope we can solve this problem fast.

Best regards, María

UBrau commented 1 year ago

Hi Maria,

Thanks for letting us know!

Ulrich

On Jun 6, 2023, at 05:23, mponcecic @.***> wrote:



Hi Ulrich,

First of all, sorry for the late replay. I am running vast-tools in a cluster which might be the reason of this environment issue. At this point, we are working together with the cluster technician to solve this problem because we were able to work this program in other cluster without a issue.

I hope we can solve this problem fast.

Best regards, María

— Reply to this email directly, view it on GitHubhttps://github.com/vastgroup/vast-tools/issues/114#issuecomment-1578277870, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB4HSWTVAB4I47KMJUCDAB3XJ3ZJTANCNFSM6AAAAAAYSOKZ34. You are receiving this because you were assigned.Message ID: @.***>

mponcecic commented 1 year ago

Hi Ulrich

I am glad to let you know that we solved the problem! The encoding of the file RI_MakeTablePIR.R was not in UNIX format (LF), instead it was in Windows (CRLF) and the line break was not appropiate. After changing the codification of the file to UNIX format, the cluster was able to run the program without failing. In addition, we add the R source path to the script due to some specifications of the clustes.

Thank you for your fast and detail answers,

Best regards, María Ponce,

UBrau commented 1 year ago

Thanks for letting us know!