Closed gabee-chan closed 2 years ago
tjakobi
commented
5 years ago Hi @gabee-chan,
do you provide any BAM files via -B? You are trying to run host gene counting (-G) but I cannot see the BAM files required for that step. There might be a check for the argument BAM missing at that stage of DCC.
Cheers, Tobias
gabee-chan
commented
5 years ago Hi!
I added the -B parameter but I still get the same error.
DCC 0.4.7 started
4 CPU cores available, using 2
started circRNA detection from file SCZ_2016-793_BA46_60F_CAUCChimeric.out.junction
=> locating circRNAs (stranded mode) [SCZ_2016-793_BA46_60F_CAUCChimeric.out.junction]
=> sorting circRNAs (stranded mode) [SCZ_2016-793_BA46_60F_CAUCChimeric.out.junction]
finished circRNA detection from file SCZ_2016-793_BA46_60F_CAUCChimeric.out.junction
Combining individual circRNA read counts
Traceback (most recent call last):
File "/share/ClusterShare/biodata/contrib/gabrod/anaconda2/bin/DCC", line 11, in
The command I used is:
DCC [STAR_output]Chimeric.out.junction -D -R Repeat_hg19.gtf -an hg19_ens.gtf -F -M -Nr 5 6 -fg -G -A hg19.fa -B [file].bam
tjakobi
commented
5 years ago Dear @gabee-chan,
just to rule out that at some point no circRNAs are found, could you set the filter parameter to -Nr 2 2 and try again.
Cheers, Tobias
xiaowufeiying
commented
4 years ago I got the same IndexError
Output folder ./ already exists, reusing
Temporary folder emp already exists, reusing
DCC 0.4.8 started
6 CPU cores available, using 2
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
WARNING: File ./circRNA/mate2, line 1 does not contain all features.
WARNING: ./circRNA/mate2 is probably corrupt.
WARNING: Offending line: /Users/tao/Desktop/circRNA/DCC-test/SRR2185851/mate2_mapping/Chimeric.out.junction
Traceback (most recent call last):
File "/Users/tao/.local/bin/DCC", line 11, in
The command I use: DCC ./circRNA/samplesheet -mt1 ./circRNA/mate1 -mt2 ./circRNA/mate2 -D -an ./data\ analysis/GenCode_PRI/gencode.vM25.primary_assembly.annotation.gtf -M -Nr 2 1 -fg -temp -ss -F -Pi -L 20 -A ./data\ analysis/GenCode_PRI/GRCm38.primary_assembly.genome.fa
tjakobi
commented
4 years ago Dear @gabee-chan,
could you please attach the file /Users/tao/Desktop/circRNA/DCC-test/SRR2185851/mate2_mapping/Chimeric.out.junction ? There seems to be something wrong with that file that breaks the parser.
The first 100 lines would probably also be okay if the file is too large.
Cheers, Tobias
xiaowufeiying
commented
4 years ago Dear @gabee-chan,
could you please attach the file
/Users/tao/Desktop/circRNA/DCC-test/SRR2185851/mate2_mapping/Chimeric.out.junction? There seems to be something wrong with that file that breaks the parser.The first 100 lines would probably also be okay if the file is too large.
Cheers, Tobias
Chimeric.out.junction.100.txt Dear Tobias, Attached, please find the first 100 lines of the Chimeric.out.junction file. best
tjakobi
commented
4 years ago Dear @xiaowufeiying,
I see you used DCC version 0.4.7.
Could you try to directly install DCC from the master branch? There was a recent fix that might fix this issue.
Cheers, Tobias
Hi I am trying to run DCC and get this error.
load_entry_point('DCC==0.4.7', 'console_scripts', 'DCC')() File "build/bdist.linux-x86_64/egg/DCC/main.py", line 269, in main File "build/bdist.linux-x86_64/egg/DCC/CombineCounts.py", line 42, in comb_coor File "build/bdist.linux-x86_64/egg/DCC/CombineCounts.py", line 96, in sortBed IndexError: list index out of range
I installed DCC clonning the git, so I expect is the latest version
The command I use to run DCC is
DCC [STAR_output]Chimeric.out.junction -D -R Repeat.gtf -an hg19_ens.gtf -F -M -Nr 5 6 -fg -G -A hg19.fa
My numpy version is the '1.16.4'
Thanks before handed.