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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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bowtie_global Error 1 #326

Closed Ferossitiziano closed 4 years ago

Ferossitiziano commented 4 years ago

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 commented 4 years ago

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

Ferossitiziano commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

Ferossitiziano commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

Ferossitiziano commented 4 years ago

Yes, I have used the command

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

nservant commented 4 years ago

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 commented 4 years ago

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

nservant commented 4 years ago

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 commented 4 years ago

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

nservant commented 4 years ago

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

Ferossitiziano commented 4 years ago

Hi,

I have downloaded all the files on the level branch on the Github page and installed HiC-Pro again. Unfortunately, as already occurred, HiC-Pro works fine in the interactive mode but fail when it is launched with the -p option.

The error I get is still the same:

HiC-Pro mapping

stat: Bad file descriptor Warning: Could not open read file "rawdata/dixon_2M/SRR400264_00_R2.fq" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1

It cannot find the file rawdata/dixon_2M/SRR400264_00_R2.fq, but I don't really know why it is not looking for rawdata/dixon_2M/SRR400264_00_R2.fastq.gz, which exist.

Best, Federico

Ferossitiziano commented 4 years ago

Sorry, it looks like I still got version 2.11.3, I'll try to download 2.11.4.

Federico

Ferossitiziano commented 4 years ago

The pipeline in parallel mode worked fine with test_data using version 2.11.4. Thank you very much!

nservant commented 4 years ago

great !

Mlad22 commented 4 years ago

Hi! I have the same problem with the Bowtie_global error 1. How do I get the 2.11.4 version? I somehow always end up installing version 2.11.3.

Thanks, Best, Mlad

nservant commented 4 years ago

https://github.com/nservant/HiC-Pro/releases

Mlad22 commented 4 years ago

thank you!

nservant commented 4 years ago

Hi, Would you have more info ? logs please ? Look at the bowtie logs please. Nicolas

Le 15/05/2020 à 15:20, baishengjun a écrit :

Hi， I have the same problem with the Bowtie_global error 1. and I use hic-pro version 2.11.4 . my genome size 530M , I get errors. when I run genome size 430M , no errors. I use the same operation with hicpro. that is strange . how can I fix it ?

thanks

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Oksanak22 commented 11 months ago

Hi. I am suing HiC-Pro 3.1.0 When I run ./bin/HiC-Pro -i rawdata -o hic_results -c config-hicpro.txt

Run HiC-Pro 3.1.0

Fri Oct 27 10:33:53 PDT 2023 Bowtie2 alignment step1 ... Logs: logs/Sample1/mapping_step1.log [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit make: *** [/home/HiC-Pro_3.1.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

BERICP01 commented 8 months ago

Hi. I am suing HiC-Pro 3.1.0 When I run ./bin/HiC-Pro -i rawdata -o hic_results -c config-hicpro.txt

Run HiC-Pro 3.1.0

Fri Oct 27 10:33:53 PDT 2023 Bowtie2 alignment step1 ... Logs: logs/Sample1/mapping_step1.log [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit make: *** [/home/HiC-Pro_3.1.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

I have the same issue! Some samples are working, others I get this error, here is the log which seems related to the file descriptor:

HiC-Pro mapping

stat: Bad file descriptor Warning: Could not open read file "rawdata/501mel_sgCHD7-2/501mel-sgCHD7-2_S15_L004_R1_001.fastq.gz.fastq" for reading; skipping... Error: No input read files were valid

@nservant any help would be extremely grateful, I am using the last release of HiC-Pro 3.1.0 like @Oksanak22

Best Pietro