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DCC crashes with -fg set and -M unset #42
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Hi tjakobi, |
Dear @Yaoyinghhao, I've looked into the DCC code for some more insights. If you are using the latest DCC version on GitHub than line 356 in the main script is as follows:
That means this code should only be executed when neither -M or -fg is specified. Therefore this line should never be run if you specify -fg or -M in the command line. However, you wrote that the command line you used contains the -fg parameter. Could you please verify that you indeed used -fg and not -M in the command line? If possible you may upload the DCC log file that contains the complete command line. Cheers, |
Dear Tobias,
According to your reply, I noticed the GTF file that I used is not correctly formated. So, I re-downloaded the lasted version of GTF file and run DCC again. But I still got wrong message.
Attached file are the first 100 lines of GTF file that I used in the second run and corresponding log file.
Thank you.
Yinghao
At 2017-08-28 01:11:59, "Tobias Jakobi" <notifications@github.com> wrote:
Dear @Yaoyinghhao,
I've looked into the DCC code for some more insights. If you are using the latest DCC version on GitHub than line 356 in the main script is as follows:
if not options.chrM and not options.filterbygene:
filt.sortOutput(options.tmp_dir + "tmp_unsortedWithChrM", output_circ_counts,
output_coordinates, samplelist)
That means this code should only be executed when neither -M or -fg is specified. Therefore this line should never be run if you specify -fg or -M in the command line.
However, you wrote that the command line you used contains the -fg parameter. Could you please verify that you indeed used -fg and not -M in the command line? If possible you may upload the DCC log file that contains the complete command line.
Cheers,
Tobias
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2017-08-28 08:39:43,163 DCC 0.4.4 started
2017-08-28 08:39:43,163 DCC command line: /home/yaoyh//.local/bin/DCC @samplesheet -mt1 @mate1 -mt2 @mate2 -T 16 -D -an /data/yaoyh/circRNA/GTF_file/gencode.v26.annotation.gtf -Pi -M -F -fg -G -Nr 1 1 -A /data/yaoyh/circRNA/Homo_sapiens.GRCh38.dna.primary_assembly.fa
2017-08-28 08:39:43,164 Input file names have duplicates, add number suffix in input order to output files for distinction
2017-08-28 08:39:43,242 Starting to detect circRNAs
2017-08-28 08:39:43,242 Stranded data mode
2017-08-28 08:39:43,242 Please make sure that the read pairs have been mapped both, combined and on a per mate basis
2017-08-28 08:39:43,243 Collecting chimera information from mates-separate mapping
2017-08-28 08:40:03,298 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.CP85IG
2017-08-28 08:40:03,299 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.ML4PVW
2017-08-28 08:40:03,300 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.HJDR5I
2017-08-28 08:40:03,301 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.JW8Y8E
2017-08-28 08:40:03,302 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.3AKSF5
2017-08-28 08:40:03,302 started circRNA detection from file _tmp_DCC/Chimeric.out.junction.6ZF9ND
2017-08-28 08:44:29,310 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.HJDR5I
2017-08-28 08:45:16,387 Read 96907264.-.96907748.SRR5398218.24236944 has more than 2 count.
2017-08-28 08:45:16,396 Read 96907264.-.96907748.SRR5398218.24236944 has more than 2 count.
2017-08-28 08:46:12,574 Read 96907264.-.96907748.SRR5398218.24236944 has more than 2 count.
2017-08-28 08:49:00,789 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.CP85IG
2017-08-28 08:53:50,006 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.6ZF9ND
2017-08-28 08:54:51,829 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.3AKSF5
2017-08-28 09:04:59,162 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.ML4PVW
2017-08-28 10:48:46,647 finished circRNA detection from file _tmp_DCC/Chimeric.out.junction.JW8Y8E
2017-08-28 10:48:46,650 Combining individual circRNA read counts
2017-08-28 10:50:07,721 Write in annotation
2017-08-28 10:50:07,722 Select gene features in Annotation file
2017-08-28 11:00:42,871 Filtering started
2017-08-28 11:00:42,871 Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
2017-08-28 11:00:48,336 Filtering by read counts
2017-08-28 11:00:50,976 Deleting circRNA candidates from mitochondrial chromosome
|
Dear @Yaoyinghhao, I can only see the attached log file and no GTF file. What error message are you receiving? Is it still the one from circAnnotate.py / HTSeq? Cheers, |
Dear Tobias,
The attached file is GTF file I used. The error message I got is printed in the following picture.
Cheers,
Yinghao
At 2017-08-28 14:46:15, "Tobias Jakobi" <notifications@github.com> wrote:
Dear @Yaoyinghhao,
I can only see the attached log file and no GTF file. What error message are you receiving? Is it still the one from circAnnotate.py / HTSeq?
Cheers,
Tobias
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|
Dear @Yaoyinghhao, Are you sure you attached screenshot and GTF file? Neither within GitHub nor the GitHub notification I can see any attachments. You may want to try an upload service like https://www.file.io/ instead. Cheers, |
Can you see them now? |
Yes, thank you for providing the files. However, I am not yet able to reproduce the error. I will post any updates here. |
Dear @Yaoyinghhao, sorry for the delay. I'm still having a hard time reproducing your error. Just to make sure we're on the same page:
Cheers, |
Actually this error should have been fixed in #33 . Closing for now. |
DCC crashes when using the following command line:
The following error is thrown:
![1](https://user-images.githubusercontent.com/1384800/29450432-f596daaa-83fe-11e7-8cfd-d2aef70f089d.png)
The issues seems to be related to the -M and -fg filter flags.
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