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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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output files #71

Closed Anbupalam closed 4 years ago

Anbupalam commented 4 years ago

Hi DCC was run with the following commands for two samples.

python /data2/DCC/DCC/main.py @samplesheet -mt1 @mate1 -mt2 @mate2 -D -R /data2/Refgenome/UCSC_grch38_repeats.gtf -an /data2/Refgenome/Homo_sapiens.GRCh38.97.gtf -Pi -F -M -Nr 5 6 -fg -G -A Homo_sapiens.GRCh38.dna.primary_assembly.fa

The program completed normally but the output files are only in the temporary folder "_tmp_DCC"

-rw-rw-r-- 1 user1 user1 101234720 Nov 7 07:47 1137ROI1_S92_R.Chimeric.out.junction.H3XX33
-rw-rw-r-- 1 user1 user1 4311935 Nov 7 09:52 1137ROI1_S92_R.Chimeric.out.junction.H3XX33.circRNA
-rw-rw-r-- 1 user1 user1 7326316 Nov 7 09:52 1137ROI1_S92_R.Chimeric.out.junction.H3XX33.circRNAmapped
-rw-rw-r-- 1 user1 user1 107940938 Nov 7 07:48 22704ROI1_S78_R.Chimeric.out.junction.0QXV72
-rw-rw-r-- 1 user1 user1 4941834 Nov 7 08:50 22704ROI1_S78_R.Chimeric.out.junction.0QXV72.circRNA
-rw-rw-r-- 1 user1 user1 7323560 Nov 7 09:52 22704ROI1_S78_R.Chimeric.out.junction.0QXV72.circRNAmapped
-rw-rw-r-- 1 user1 user1 6823054 Nov 7 09:52 tmp_circCount
-rw-rw-r-- 1 user1 user1 8456137 Nov 7 09:59 tmp_coordinates
-rw-rw-r-- 1 user1 user1 5877569 Nov 7 09:51 tmp_duplicates.GWY7MD
-rw-rw-r-- 1 user1 user1 3609301 Nov 7 08:50 tmp_duplicates.XN8OXV
-rw-rw-r-- 1 user1 user1 13040015 Nov 7 09:51 tmp_findcirc.GWY7MD
-rw-rw-r-- 1 user1 user1 9278707 Nov 7 08:50 tmp_findcirc.XN8OXV
-rw-rw-r-- 1 user1 user1 582692510 Nov 7 09:59 tmp_Homo_sapiens.GRCh38.97.gtf.exon.sorted
-rw-rw-r-- 1 user1 user1 87642483 Nov 7 07:47 tmp_merged
-rw-rw-r-- 1 user1 user1 49071549 Nov 7 09:51 tmp_nonduplicates.GWY7MD
-rw-rw-r-- 1 user1 user1 34917293 Nov 7 08:50 tmp_nonduplicates.XN8OXV
-rw-rw-r-- 1 user1 user1 12236675 Nov 7 09:51 tmp_normalcircs.GWY7MD
-rw-rw-r-- 1 user1 user1 8785263 Nov 7 08:50 tmp_normalcircs.XN8OXV
-rw-rw-r-- 1 user1 user1 54949462 Nov 7 07:48 tmp_printcirclines.GWY7MD
-rw-rw-r-- 1 user1 user1 38526594 Nov 7 07:48 tmp_printcirclines.XN8OXV
-rw-rw-r-- 1 user1 user1 803340 Nov 7 09:51 tmp_smallcircs.GWY7MD
-rw-rw-r-- 1 user1 user1 493444 Nov 7 08:50 tmp_smallcircs.XN8OXV
-rw-rw-r-- 1 user1 user1 8933322 Nov 7 07:47 tmp_twochimera

I don't see the LinearCount and CircSkipJunctions files in the folder. Please advise.

Anbupalam commented 4 years ago

Hi I am able to fix this issue.

tjakobi commented 4 years ago

Hi @Anbupalam,

just for clarification and for future reference, how did you solve the issue?

Cheers, Tobias

Anbupalam commented 4 years ago

Hi Tobias,

Sorry for the late reply.

I forgot to generate the .bai index files for the .bam files In my original submission. With the index files in the right folder the program produced all the relevant output files.

Thanks Anbu.

On Fri, Nov 15, 2019 at 12:35 AM Tobias Jakobi notifications@github.com wrote:

Hi @Anbupalam https://github.com/Anbupalam,

just for clarification and for future reference, how did you solve the issue?

Cheers, Tobias

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dieterich-lab/DCC/issues/71?email_source=notifications&email_token=AISHUCIHPE7YVPWWJ7YM7F3QTVH25A5CNFSM4JJ7DZWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEB3EMA#issuecomment-553890352, or unsubscribe https://github.com/notifications/unsubscribe-auth/AISHUCMQKVOQV4AJZIWIRRTQTVH25ANCNFSM4JJ7DZWA .

tjakobi commented 4 years ago

Hi @Anbupalam,

thank you for your feedback. I wonder why this even happens... there is a check to make sure all BAM files habe an index:

https://github.com/dieterich-lab/DCC/blame/68797f3e456d65cafd51ff20e93dd9ea0d45e765/DCC/main.py#L725

Would you have the complete log file of this run? Are you sure it terminated with status 0?

Cheers, Tobias

Anbupalam commented 4 years ago

Sorry, I don't have the log file now. I had to cleanup due to storage limitations. As it was run on cluster computer with job-submission, I only looked at the job exit status and I remember the exit status was OK but probably the log file would have reflected this issue.

Thanks Anbu.

On Mon, Nov 25, 2019 at 11:04 PM Tobias Jakobi notifications@github.com wrote:

Hi @Anbupalam https://github.com/Anbupalam,

thank you for your feedback. I wonder why this even happens... there is a check to make sure all BAM files habe an index:

https://github.com/dieterich-lab/DCC/blame/68797f3e456d65cafd51ff20e93dd9ea0d45e765/DCC/main.py#L725

Would you have the complete log file of this run? Are you sure it terminated with status 0?

Cheers, Tobias

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dieterich-lab/DCC/issues/71?email_source=notifications&email_token=AISHUCLMA6DHHIZW5BL3Q5DQVO5MJA5CNFSM4JJ7DZWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFCFF6Y#issuecomment-558125819, or unsubscribe https://github.com/notifications/unsubscribe-auth/AISHUCITN7Z2YT26MXEUAK3QVO5MJANCNFSM4JJ7DZWA .

tjakobi commented 4 years ago

Hi @Anbupalam,

okay, thank your for coming back to me.

I'll see if there might be any issue with the index detection.

Cheers, Tobias