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egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
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scons: *** [samples/S4/processings/circRNAs/tophat_out/accepted_hits.bam] Error 1 #20

Open npont opened 9 months ago

npont commented 9 months ago

Hello, I have the following error: scons: *** [samples/S4/processings/circRNAs/tophat_out/accepted_hits.bam] Error 1 which appears during the tophat process.

Indeed I have the following:

[2023-10-11 15:12:46] Reporting output tracks [FAILED] Error running path/softwares/circompara2/tools/tophat-2.1.0.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir samples/S4/processings/circRNAs/tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 --fusion-search --fusion-anchor-length 20 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p4 --gtf-annotations path/softwares/circompara2/test_circompara/annotation/CFLAR_HIPK3.gtf --gtf-juncs samples/S4/processings/circRNAs/tophat_out/tmp/CFLAR_HIPK3.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header samples/S4/processings/circRNAs/tophat_out/tmp/CFLAR_HIPK3_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=pathsoftwares/circompara2/tools/tophat-2.1.0.Linux_x86_64/samtools_0.1.18 --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 path/softwares/circompara2/test_circompara/analysis_fl/dbs/indexes/indexes/bowtie/CFLAR_HIPK3.fa samples/S4/processings/circRNAs/tophat_out/junctions.bed samples/S4/processings/circRNAs/tophat_out/insertions.bed samples/S4/processings/circRNAs/tophat_out/deletions.bed samples/S4/processings/circRNAs/tophat_out/fusions.out samples/S4/processings/circRNAs/tophat_out/tmp/accepted_hits samples/S4/processings/circRNAs/tophat_out/tmp/left_kept_reads.bam Loaded 74 GFF junctions from samples/S4/processings/circRNAs/tophat_out/tmp/CFLAR_HIPK3.juncs.

It is hard to understand as the logs do not provide much more info. I am trying to run circompara2 on my data (it was working with the test data you provide). Any idea on what could be the problem?

Thanks a bunch!

npont commented 9 months ago

It did not create the accepted_hits.bam (samples/S4/processings/circRNAs/tophat_out/accepted_hits.bam)