Comments (5)
STAR
I encountered this problem before, but had no time to fix it yet. The problem is that the iGenomes STAR index is not compatible with the STAR version used in the pipeline. A workaround is setting manually setting star = null
, which prevents usage of iGenomes and thus forces the pipeline to build an own index. Opened #91 for this.
CIRIquant
This is most probably due to missing escape characters in nextflow scripts, will be fixed via #83
DCC
Could potentially also be fixed via #83
What can you do now?
I expect #83 to be merged into dev
within the next days, if you want to try it faster, you can use the caching
branch of the pipeline (nextflow run -r caching ...
). Keep me posted, in case something is working better then. If the problems (especially with DCC) persist, you could also try to fix the scripts yourself and open a PR.
from circrna.
Hi, just letting you know I ran with the merged bug fix #83, and also got a similar DCC error.
ValueError: invalid literal for int() with base 10: '2"'
details:
-[nf-core/circrna] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC (control_1)'
Caused by:
Process `NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC (control_1)` terminated with an error exit status (1)
Command executed:
sed -i 's/^chr//g' gencode.v44.chr_patch_hapl_scaff.annotation.gtf
mkdir control_1 && mv control_1.Chimeric.out.junction control_1 && printf "control_1/control_1.Chimeric.out.junction" > samplesheet
mkdir control_1_mate1 && mv control_1_mate1.Chimeric.out.junction control_1_mate1 && printf "control_1_mate1/control_1_mate1.Chimeric.out.junction" > mate1file
mkdir control_1_mate2 && mv control_1_mate2.Chimeric.out.junction control_1_mate2 && printf "control_1_mate2/control_1_mate2.Chimeric.out.junction" > mate2file
DCC @samplesheet -mt1 @mate1file -mt2 @mate2file -D -an gencode.v44.chr_patch_hapl_scaff.annotation.gtf -Pi -ss -F -M -Nr 1 1 -fg -A GRCh38.p14.genome.fa -N -T 12
awk '{print $6}' CircCoordinates >> strand
paste CircRNACount strand | tail -n +2 | awk -v OFS="\t" '{print $1,$2,$3,$5,$4}' >> control_1.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC":
dcc: $(DCC --version)
END_VERSIONS
Command exit status:
1
Command output:
Output folder ./ already exists, reusing
DCC 0.5.0 started
24 CPU cores available, using 12
WARNING: non-stranded data, the strand of circRNAs guessed from the strand of host genes
Please make sure that the read pairs have been mapped both, combined and on a per mate basis
Collecting chimera information from mates-separate mapping
Combining individual circRNA read counts
Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
Filtering by read counts
Remove ChrM
Count CircSkip junctions
started circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
=> separating duplicates [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> locating small circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> locating circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> merging circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> sorting circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
finished circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
Command error:
Unable to find image 'quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0' locally
1.2.1--pyh7cba7a3_0: Pulling from biocontainers/circtools
73349e34840e: Already exists
acab339ca1e8: Already exists
425fd6205dc3: Pulling fs layer
425fd6205dc3: Download complete
425fd6205dc3: Pull complete
Digest: sha256:7317627874031c4c9924d40b76602662a2d400c9ee4c1c626998c287e5e7bd65
Status: Downloaded newer image for quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0
Output folder ./ already exists, reusing
DCC 0.5.0 started
24 CPU cores available, using 12
Traceback (most recent call last):
File "/usr/local/bin/DCC", line 10, in <module>
WARNING: non-stranded data, the strand of circRNAs guessed from the strand of host genes
Please make sure that the read pairs have been mapped both, combined and on a per mate basis
Collecting chimera information from mates-separate mapping
Combining individual circRNA read counts
Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
Filtering by read counts
Remove ChrM
Count CircSkip junctions
sys.exit(main())
File "/usr/local/lib/python3.10/site-packages/DCC/main.py", line 490, in main
CircSkipfiles = findCircSkipJunction(output_coordinates, options.tmp_dir,
File "/usr/local/lib/python3.10/site-packages/DCC/main.py", line 679, in findCircSkipJunction
circStartAdjacentExons, circStartAdjacentExonsIv = CCEM.findcircAdjacent(circStartExons, Custom_exon_id2Iv,
File "/usr/local/lib/python3.10/site-packages/DCC/Circ_nonCirc_Exon_Match.py", line 281, in findcircAdjacent
interval = Custom_exon_id2Iv[self.getAdjacent(ids, start=start)]
File "/usr/local/lib/python3.10/site-packages/DCC/Circ_nonCirc_Exon_Match.py", line 222, in getAdjacent
exon_number = int(custom_exon_id.split(':')[1]) - 1
ValueError: invalid literal for int() with base 10: '2"'
started circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
=> separating duplicates [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> locating small circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> locating circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> merging circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
=> sorting circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
finished circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
Work dir:
/Users/marieke/Documents/work/66/1152ceffd34d8324ab17adcbacdcf6
from circrna.
Related Issues (20)
- Problems with scripts referenced using the ${workflow.projectDir} variable HOT 1
- To Do before release HOT 1
- [nf-core/circrna] error: Your FASTQ files do not have the appropriate extension HOT 19
- pipeline won't start without filling ref-genome bwa, bowtie, etc... HOT 2
- old version of /opt/conda/envs HOT 1
- Test workflow not working HOT 2
- Release Preparation Checklist HOT 1
- DSL2 modules HOT 1
- conda recepies HOT 8
- Not a valid path value: 'null' HOT 1
- Wrong BWA index directory in references HOT 7
- Issues generating, and pointing to, genome reference data lead to early crashes during configuration (w/ fix(?)) HOT 3
- Not all samples are used in analysis resulting in pipeline failur HOT 7
- Problem in running circrna HOT 2
- Limitted input length. HOT 2
- Fix problems with outdated STAR indices in iGenomes HOT 1
- Implement coding potential analysis
- mapsplice error when input fasta file contains multiple fields in the header
- Implement improved annotation of hits also in the DIFFERENTIAL_EXPRESSION:PARENT_GENE process HOT 1
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from circrna.