Nextflow 23.10.0 is available - Please consider updating your version to it
N E X T F L O W ~ version 22.10.7
Launching `./main.nf` [silly_galileo] DSL1 - revision: 35281af540
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============You are running MeRIPseqPipe with the following parameters===============
Checking parameters ...
===================================Pipeline summary=============================
Max Resources : 100 GB memory, 20 cpus, 10d time per job
Container : docker - kingzhuky/meripseqpipe:dev
Output dir : results_mr231028/
Launch dir : /home/wuqy/bin/MeRIPseqPipe
Working dir : /home/wuqy/bin/MeRIPseqPipe/work
Script dir : /home/wuqy/bin/MeRIPseqPipe
User : root
Config Profile : docker
=====================================Reads types================================
SingleEnd : Paired-End
Stranded : no
gzip : true
====================================Mode selected==============================
aligners : star
peakCalling_mode : independence
peakMerged_mode : rank
expression_analysis_mode : DESeq2
methylation_analysis_mode : QNB
==================================Input files selected==========================
Reads Path : false
fasta file : ref/TAIR10_chr_all.fasta
Gtf file : ref/Araport11_GTF_genes_transposons.Oct2023.gtf
Design file : mr231028/mr231028_designfile_paired.tsv
Compare file : mr231028/mr231028_comparefile.txt
==================================Skip model selected==========================
Skip samtools sort : false
Skip expression analysis : false
Skip peakCalling : false
Skip diffpeakCalling : false
Skip annotation : false
Skip qc : false
executor > local (4)
[e4/d87b9a] process > CheckDesignCompare [100%] 1 of 1 ✔
[20/62b06d] process > makeBED12 (gtf2bed12) [ 0%] 0 of 1
[e6/20c208] process > makechromesize (gtf2bed12) [ 0%] 0 of 1
[- ] process > MakeTophat2Index -
[- ] process > MakeHisat2Index -
[- ] process > MakeBWAIndex -
executor > local (4)
[e4/d87b9a] process > CheckDesignCompare [100%] 1 of 1 ✔
[20/62b06d] process > makeBED12 (gtf2bed12) [100%] 1 of 1, failed: 1 ✘
[e6/20c208] process > makechromesize (gtf2bed12) [ 0%] 0 of 1
[- ] process > MakeTophat2Index -
[- ] process > MakeHisat2Index -
[- ] process > MakeBWAIndex -
[68/681c8a] process > MakeStarIndex (star_index) [100%] 1 of 1 ✔
executor > local (4)
[e4/d87b9a] process > CheckDesignCompare [100%] 1 of 1 ✔
[20/62b06d] process > makeBED12 (gtf2bed12) [100%] 1 of 1, failed: 1 ✘
[e6/20c208] process > makechromesize (gtf2bed12) [100%] 1 of 1 ✔
[- ] process > MakeTophat2Index -
[- ] process > MakeHisat2Index -
[- ] process > MakeBWAIndex -
[68/681c8a] process > MakeStarIndex (star_index) [100%] 1 of 1 ✔
[- ] process > MakerRNAindex -
One more CTRL+C to force exit [ 0%] 0 of 4
executor > local (4)
[e4/d87b9a] process > CheckDesignCompare [100%] 1 of 1 ✔
[20/62b06d] process > makeBED12 (gtf2bed12) [100%] 1 of 1, failed: 1 ✘
[e6/20c208] process > makechromesize (gtf2bed12) [100%] 1 of 1 ✔
[- ] process > MakeTophat2Index -
[- ] process > MakeHisat2Index -
[- ] process > MakeBWAIndex -
[68/681c8a] process > MakeStarIndex (star_index) [100%] 1 of 1 ✔
[- ] process > MakerRNAindex -
[- ] process > Fastp [ 0%] 0 of 4
[- ] process > Fastqc -
[- ] process > Tophat2Align -
[- ] process > Hisat2Align -
[- ] process > BWAAlign -
[- ] process > StarAlign -
[- ] process > SortRename -
[- ] process > RSeQC -
[- ] process > CreateBedgraph -
[- ] process > multiqc -
[- ] process > FeatureCount -
[- ] process > DESeq2 -
[- ] process > EdgeR -
[- ] process > Metpeak -
[- ] process > Macs2 -
[- ] process > MATKpeakCalling -
[- ] process > MeyerPrepration -
[- ] process > Meyer -
[- ] process > PeakMerge -
[- ] process > BedAnnotated -
[- ] process > MotifSearching -
[- ] process > PeaksMotifReport -
[- ] process > PeaksQuantification -
[- ] process > diffm6APeak -
[- ] process > SingleNucleotidePrediction -
[- ] process > DiffReport -
[- ] process > CreateIGVjs -
[- ] process > get_software_versions [ 0%] 0 of 1
Error executing process > 'makeBED12 (gtf2bed12)'
Caused by:
Process `makeBED12 (gtf2bed12)` terminated with an error exit status (255)
Command executed:
gtf_file=Araport11_GTF_genes_transposons.Oct2023.gtf
gtfToGenePred -genePredExt -geneNameAsName2 $gtf_file ${gtf_file/.gtf/.tmp}
genePredToBed ${gtf_file/.gtf/.tmp} ${gtf_file/.gtf/.bed}
Command exit status:
255
Command output:
(empty)
Command error:
no exons defined for group AT1G01010, feature gene (perhaps try -ignoreGroupsWithoutExons)
Work dir:
/home/wuqy/bin/MeRIPseqPipe/work/20/62b06de331ba54b9654d8afede57d9
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
I downloaded the gtf and chromosome fasta from TAIR official site. It seems like something going wrong with gene definition starting from the first gene.
It mentioned to try -ignoreGroupsWithoutExons, but im not sure where to put this parameter since it does not show in the parameter docs. And it seems not working in the initial command line.
The problem is fixed by editing the .gtf file of Arabidopsis thaliana. I think there will be no error for other species gtf file. The miRNA without exons in the gtf file may also causes this issue, just simply added -ignoreGroupsWithoutExons at line 382 of main.nf.
The test run of Nextflow worked well. But something goes wrong when using my own data.
I have two pairs of input and two pairs of ip. The sample is Arabidopsis thaliana. Following is my command and the pop-ups in Ubuntu:
sudo NXF_VER=22.10.7 nextflow run . -profile docker --designfile mr231028/mr231028_designfile_paired.tsv --comparefile mr231028/mr231028_comparefile.txt --fasta ref/TAIR10_chr_all.fasta --gtf ref/Araport11_GTF_genes_transposons.Oct2023.gtf --outdir results_mr231028/I downloaded the gtf and chromosome fasta from TAIR official site. It seems like something going wrong with gene definition starting from the first gene.
It mentioned to try -ignoreGroupsWithoutExons, but im not sure where to put this parameter since it does not show in the parameter docs. And it seems not working in the initial command line.
It would be thankful if anyone can fix this.
============================================================
The problem is fixed by editing the .gtf file of Arabidopsis thaliana. I think there will be no error for other species gtf file. The miRNA without exons in the gtf file may also causes this issue, just simply added -ignoreGroupsWithoutExons at line 382 of main.nf.