Error message from test run

[dataMaster-Kris]

After a bunch of warning and OK messages, monkey threw the following error:

[WARNING] The filename 'CC_WT_R2_1.fq.gz' had text in it that made it look like a second-of-a-pair paired-end file (like '.R1' or '.pair1'), but it was listed as either single-end of as the first file in a pair. Double check that this file is really NOT a second-mate-pair paired-end file! at /wynton/group/gladstone/biocore/monkey/bananas_agw.pm line 549, line 55.
[WARNING] The filename 'CC_KO_R2_1.fq.gz' had text in it that made it look like a second-of-a-pair paired-end file (like '.R1' or '.pair1'), but it was listed as either single-end of as the first file in a pair. Double check that this file is really NOT a second-mate-pair paired-end file! at /wynton/group/gladstone/biocore/monkey/bananas_agw.pm line 549, line 57.
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/hg19_ensembl_igenome_with_chr_and_ercc/bwa.hg19.chr_and_ERCC92', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/hg19_ensembl_igenome_with_chr_and_ercc/hg19.chr_and_ERCC92', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/hg19_ensembl_igenome_with_chr_and_ercc/hg19.chr_and_ERCC92.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/hg19_ensembl_igenome_with_chr_and_ercc/hg19.chr_and_ERCC92.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/hg19_ensembl_igenome_with_chr_and_ercc/STAR_index_hg19.chr_and_ERCC92', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg19_ERCC' '/wynton/group/gladstone/references/rseqc_bed_files/hg19_Ensembl.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/hg38.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/hg38.chr.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/hg38.chr.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/hg38_per_chr_fasta_dir', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/bwa.hg38.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/wynton/group/gladstone/references/hg38_ncbi_igenome/STAR_index_hg38.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/bwa.mm9.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/mm9.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/mm9.chr.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/mm9.chr.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/mm9.chr_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/mm9_ensembl_igenome_with_chr/STAR_index_mm9.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/wynton/group/gladstone/references/rseqc_bed_files/mm9_NCBI37_Ensembl.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/bwa.mm10.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/mm10.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/mm10.chr.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/mm10.chr.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/mm10.chr_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/mm10_ensembl_igenome_with_chr/STAR_index_mm10.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/wynton/group/gladstone/references/rseqc_bed_files/mm10_Ensembl80.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/bwa.rn6.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/rn6.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/rn6.chr.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/rn6.chr.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/rn6.chr_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/STAR_index_rn6.chr', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' '/wynton/group/gladstone/references/galGal4_ensembl_igenome_ucsc/galGal4_ucsc', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' '/wynton/group/gladstone/references/galGal4_ensembl_igenome_ucsc/galGal4_ucsc.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' '/wynton/group/gladstone/references/galGal4_ensembl_igenome_ucsc/galGal4_ucsc.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' '/wynton/group/gladstone/references/galGal4_ensembl_igenome_ucsc/galGal4_ucsc_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'galGal4' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/wynton/group/gladstone/references/danRer7_ensembl_igenome_ucsc/danRer7_ucsc', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/wynton/group/gladstone/references/danRer7_ensembl_igenome_ucsc/danRer7_ucsc.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/wynton/group/gladstone/references/danRer7_ensembl_igenome_ucsc/danRer7_ucsc.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/wynton/group/gladstone/references/danRer7_ensembl_igenome_ucsc/danRer7_ucsc_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/wynton/group/gladstone/references/rseqc_bed_files/danRer7_Ensembl.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/drosophila_dm3_BDGP5_ensembl_igenome_with_chr/dm3_ucsc', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/drosophila_dm3_BDGP5_ensembl_igenome_with_chr/dm3_ucsc.gtf', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/drosophila_dm3_BDGP5_ensembl_igenome_with_chr/dm3_ucsc.fa', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/drosophila_dm3_BDGP5_ensembl_igenome_with_chr/dm3_ucsc_chromosome_fastas/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/drosophila_dm3_BDGP5_ensembl_igenome_with_chr/STAR_index_dm3_ucsc/', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/wynton/group/gladstone/references/rseqc_bed_files/dm3_Ensembl.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' 'NA', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'hg38' '/data/applications/monkey/poo/hg38_chrom.sizes', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_chrom.sizes', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_genomicBins.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_genomicBinsID.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_ucsc_geneWindows.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_symbolXref.txt', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm9' '/data/applications/monkey/poo/mm9_repeatMask.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_chrom.sizes', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_genomicBins.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_genomicBinsID.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_ensemblGeneWindows.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_symbolXref.txt', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'mm10' '/data/applications/monkey/poo/mm10_repeatMask.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'rn6' '/wynton/group/gladstone/references/rn6_ensembl_igenome_with_chr/rn6.chr.chrom.sizes.txt', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/data/applications/monkey/poo/danRer7_chrom.sizes', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/data/applications/monkey/poo/danRer7_genomicBins.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/data/applications/monkey/poo/danRer7_genomicBinsID.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/data/applications/monkey/poo/danRer7_symbolXref.txt', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'danRer7' '/data/applications/monkey/poo/danRer7_repeatMask.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_chrom.sizes', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_genomicBins.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_genomicBinsID.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_geneWindows.bed', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_symbolXref.txt', since that is not the current species (which is 'hg19').
[OK] Skipping a key for species 'dm3' '/data/applications/monkey/poo/dm3_repeatMask.bed', since that is not the current species (which is 'hg19').

System call >>>>> mkdir -p "z.test_rsync_permissions.tmpdir"; rsync --chmod=u+rx,g+rx,o+rx --perms --dirs z.test_rsync_permissions.tmpdir /wynton/group/gladstone/biocore/rna_seq_test_for_porting_monkey/browser//
(Returned exit code 0)
System call >>>>> /bin/rmdir "z.test_rsync_permissions.tmpdir"
(Returned exit code 0)
Can't locate bananas_agw.pm in @inc (@inc contains: /data/work/Code/alexgw/monkey_agw /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /wynton/group/gladstone/biocore/monkey/bin/02.filter.pl line 8.
BEGIN failed--compilation aborted at /wynton/group/gladstone/biocore/monkey/bin/02.filter.pl line 8.
[ERROR in syntax checking while setting up qsub jobs]: Looks like perl was not able to parse the syntax of the script </wynton/group/gladstone/biocore/monkey/bin/02.filter.pl> (in other words, perl -c /wynton/group/gladstone/biocore/monkey/bin/02.filter.pl FAILED to return exit code zero. That script probably has an error that needs to be fixed at /wynton/group/gladstone/biocore/monkey/bananas_agw.pm line 496.
bananas_agw::validateScriptOrDie('/wynton/group/gladstone/biocore/monkey/bin/02.filter.pl', 'HASH(0x24c7a68)') called at /wynton/group/gladstone/biocore/monkey/bananas_agw.pm line 1092
bananas_agw::setJobInfo('HASH(0x24c7a68)', 's02_filter', 'CC_WT_con.3', 'HASH(0x2bf92e0)', 'HASH(0x2bf9370)', '/wynton/group/gladstone/biocore/monkey/bin', '02.filter.pl') called at /wynton/group/gladstone/biocore/monkey/bananas_agw.pm line 1199
bananas_agw::buildJobSubmissionList('HASH(0x24c7a68)') called at /wynton/group/gladstone/biocore/monkey/monkey_agw line 72

[wmaguire-gladstone]

Did you specify the path /wynton/group/gladstone/references/ somewhere? I don't see that in the code.

Also the bin files weren't the updated ones from the wynton_sge branch. I've corrected that, which also means the path for monkey is under: /wynton/group/gladstone/biocore/MonkeyPipeline

[dataMaster-Kris]

Yes, that path is in the config file that Monkey takes as input when submitting the job.

[dataMaster-Kris]

I tried to test the new Monkey path that you have specified by asking Monkey to display the help documentation. It threw a compilation error. Can you please look into it? Thanks.

syntax error at /wynton/group/gladstone/biocore/MonkeyPipeline/bananas_agw.pm line 58, near ","
BEGIN not safe after errors--compilation aborted at /wynton/group/gladstone/biocore/MonkeyPipeline/bananas_agw.pm line 391.
Compilation failed in require at /wynton/group/gladstone/biocore/MonkeyPipeline/monkey_agw line 20.
BEGIN failed--compilation aborted at /wynton/group/gladstone/biocore/MonkeyPipeline/monkey_agw line 20.