binom.test error: 'x' must be nonnegative and integer

[ferngonz]

Hello, I'm running combine tool, but I get error when using optparse package. I'm running R/4.2.0. Also, is this error related to the INCLUSION_LEVELS_ALT3-Mm24-n.tab not being found?

Thank you for all your help! Below is full output message with error.

[vast combine]: VAST-TOOLS v2.5.1 [vast combine]: Species assembly: mm10, VASTDB Species key: Mm2 [vast combine]: Using VASTDB -> /scratch/users/ferngonz/vast-tools/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: /scratch/users/ferngonz/vast-tools/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: /scratch/users/ferngonz/vast-tools/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]: AKO1: found to_combine/AKO1.info. Sample will be treated as being strand-specific. [vast combine combi]: AKO2: found to_combine/AKO2.info. Sample will be treated as being strand-specific. [vast combine combi]: WT1: found to_combine/WT1.info. Sample will be treated as being strand-specific. [vast combine combi]: WT2: found to_combine/WT2.info. Sample will be treated as being 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: /scratch/users/ferngonz/vast-tools/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: /scratch/users/ferngonz/vast-tools/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]: AKO1: found to_combine/AKO1.info. Sample will be treated as being strand-specific. [vast combine annot]: AKO2: found to_combine/AKO2.info. Sample will be treated as being strand-specific. [vast combine annot]: WT1: found to_combine/WT1.info. Sample will be treated as being strand-specific. [vast combine annot]: WT2: found to_combine/WT2.info. Sample will be treated as being strand-specific. [vast combine annot]: Quantifying PSIs

[vast combine]: Building quality score table for intron retention (version 2) [vast combine IR]: AKO1: found to_combine/AKO1.info. Sample will be treated as being strand-specific. [vast combine IR]: AKO2: found to_combine/AKO2.info. Sample will be treated as being strand-specific. Use of uninitialized value $temp[4] in sprintf at /scratch/users/ferngonz/vast-tools/bin/RI_MakeCoverageKey_v2.pl line 110, line 144190. Use of uninitialized value $temp[4] in sprintf at /scratch/users/ferngonz/vast-tools/bin/RI_MakeCoverageKey_v2.pl line 110, line 144190. [vast combine IR]: WT1: found to_combine/WT1.info. Sample will be treated as being strand-specific. [vast combine IR]: WT2: found to_combine/WT2.info. Sample will be treated as being strand-specific.

[vast combine error]: in call /scratch/users/ferngonz/vast-tools/bin/RI_MakeTablePIR.R --verbose 1 -s /scratch/users/ferngonz/vast-tools/Mm2 --IR_version 2 -c /scratch/users/ferngonz/vast-tools/vast_out/to_combine -q /scratch/users/ferngonz/vast-tools/vast_out/to_combine/Coverage_key_v2-Mm24.IRQ -o /scratch/users/ferngonz/vast-tools/vast_out/raw_incl Trying to load required package: optparse Merging IR of 4 sample(s)... AKO1 AKO2 Error in binom.test(x = x[1], n = x[2], p = 1/3.5, alternative = "less") : 'x' must be nonnegative and integer Calls: apply -> FUN -> binom.test Execution halted

[vast combine]: Combining results into a single table Smartmatch is experimental at /scratch/users/ferngonz/vast-tools/bin/Add_to_FULL.pl line 191. cat: raw_incl/INCLUSION_LEVELS_ALT3-Mm24-n.tab: No such file or directory cat: raw_incl/INCLUSION_LEVELS_ALT5-Mm24-n.tab: No such file or directory cat: raw_incl/INCLUSION_LEVELS_IR-Mm24.tab: No such file or directory [vast combine]: Final table saved as: /scratch/users/ferngonz/vast-tools/vast_out/INCLUSION_LEVELS_FULL-mm10-4.tab [vast combine]: Deleting raw_incl/ folder [vast combine]: Deleting raw_reads/ folder [vast combine]: Completed Thu Oct 12 17:21:13 2023

[mirimia]

Hello,

This is a strange error. I think it's likely due to a previous issue running align. Could you please:

• send me the command you use for combine.
• do an ls -lsh in the to_combine folder and copy paste the print out?

Thanks!

[ferngonz]

You were right! I reran vast-tools align function and it fixed the error. Thank you!

[mirimia]

Great!