bowtie_global Error 1

[Ferossitiziano]

Dear Nicolas,

I made a test run in interactive mode with both test_data and my own data, using the following command, and it worked.

HiC-Pro -c config-hicpro.txt -i test_data/ -o Results

When I tried to repeat the analysis by adding "-p" to the previous command line to the submit the job with qsub, I had the following error message:

Exit: Error in reads alignment - Exit
make: *** [HiC-Pro_2.11.3/scripts/Makefile:88: bowtie_global] Error 1

I checked the logs and they reported the following:

##HiC-Pro mapping
stat: Bad file descriptor
Warning: Could not open read file "rawdata/dixon_2M/SRR400264_00_R1.fq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1

The test fastq files are dixon_2M/SRR400264_00_R1.fastq.gz and dixon_2M/SRR400264_00_R2.fastq.gz

Could you help me with this issue?

Federico

[nservant]

Hi,
Please which HiC-Pro version are you using ? Could you try to install the latest version ? 2.11.3
Thanks

[Ferossitiziano]

Hi,

I am already using version 2.11.3

It looks to me the pipeline is expecting the read file to be named with "fq" instead of "fastq.gz", but the "fq" file has not been created.

Thanks,
Federico

[nservant]

H,
Strange, we did a lot of test on this version.
Could you check that you have rights on the test_data ? it seems that the file are not readable ?
What about the bowte log ? could you check in the log what is the bowtie command ?

[Ferossitiziano]

Hi,

I think I have permission to access the test_data folder as it comes with "drwxr-xr-x".

This is the bowtie command:

bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/WT/WTRing1bFP75m_00_R1_mm10.bwt2glob.unmap.fastq --rg-id BMG --rg SM:WTRing1bFP75m_00_R1 -p 3 -x bowtie2_index/mm10 -U rawdata/WT/WTRing1bFP75m_00_R1.fastq.gz 2>> logs/WT/WTRing1bFP75m_00_R1_bowtie2.log| /hpcnfs/home/ieo5073/miniconda3/envs/HiCpro/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/WT/WTRing1bFP75m_00_R1_mm10.bwt2glob.bam

[nservant]

I'm not able to reproduce the issue :(
Where is the error ? because your bowtie command looks good with .fastq file (not .fq)
Is it in the bowtie2 log file ?

[nservant]

or could you check the rawdata folder please ? it should contain links to the rawdata file.
Are they correct ?

[Ferossitiziano]

Yes, the bowtie2 command works fine, I tried it myself as well straight from the command line.
I am running a generic bowtie2 alignment in local mode as this should be the following step in the pipeline, if I'm not wrong. It is working fine.

The link to rawdata looks fine, it points to my raw data. The "inputfiles_test.txt" looks wired to me as in only include the R1 file and not the corresponding R2 file. Is that fine?

[Ferossitiziano]

I added the R2 file to the "inputfiles_test.txt" and it gave me the same issue: bowtie_global Error 1.
So that was not the problem.

[nservant]

Yes, it's normal. You are using the '-p' option ?

[Ferossitiziano]

Yes, I have used the command

HiC-Pro -c config-hicpro.txt -i test_data/ -o Results -p

[nservant]

indeed ! I do have an error on my side too ... let me check that and I come back to you ...
Does it work without -p option ?

[Ferossitiziano]

Using the interactive mode without "-p" all the jobs work fine.
Thanks

[nservant]

Hi Frederico,
I just make a fix on the devel branch. Many thanks for reporting this issue.
I removed the 2.11.3 tag, and will release the 2.11.4 as soon as I will be sure that this version is ok.
Thanks again !

[Ferossitiziano]

Thank you for your help!! I will try to download the files you modified on the devel branch and I will test them.

[nservant]

Hi,
I just made a pre-relase 2.11.4 if you want to test.
I hope this one is fine ! thanks