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jkimlab / msPIPE

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issue with target directory after Mapping usind docker #2

Open criphg opened 1 year ago

criphg commented 1 year ago

Dear,

I am facing a problem using the docker image. Can you help me?

I use this command: docker run -v $(pwd)/Samples:/msPIPE/data:ro -v $(pwd)/ReUsableDatabase:/msPIPE/reference -v $(pwd)/WorkDir:/work_dir/ jkimlab/mspipe:latest msPIPE.py -p params_docker.conf -o Results -c 22

I have this error after Mapping:

  1. Mapping (bismark) .. start mv: target '/work_dir/Results/methylCALL/Sample1_rep1/data/Sample1_rep1_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Sample1_rep1/data/Sample1_rep1_bismark_mapping_report.txt' is not a directory mv: target '/work_dir/Results/methylCALL/Sample1_rep2/data/Sample1_rep2_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Sample1_rep2/data/Sample1_rep2_bismark_mapping_report.txt' is not a directory mv: target '/work_dir/Results/methylCALL/Sample1_rep3/data/Sample1_rep3_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Sample1_rep3/data/Sample1_rep3_bismark_mapping_report.txt' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep1/data/Ctl_rep1_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep1/data/Ctl_rep1_bismark_mapping_report.txt' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep2/data/Ctl_rep2_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep2/data/Ctl_rep2_bismark_mapping_report.txt' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep3/data/Ctl_rep3_bismark.bam' is not a directory mv: target '/work_dir/Results/methylCALL/Ctl_rep3/data/Ctl_rep3_bismark_mapping_report.txt' is not a directory

    /// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Sample1_rep1/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Sample1_rep1/multiqc_report.html | multiqc | Data : Results/methylCALL/Sample1_rep1/multiqc_data | multiqc | MultiQC complete

/// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Sample1_rep2/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.11_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.4_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.5_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Sample1_rep2/multiqc_report.html | multiqc | Data : Results/methylCALL/Sample1_rep2/multiqc_data | multiqc | MultiQC complete

/// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Sample1_rep3/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Sample1_rep3/multiqc_report.html | multiqc | Data : Results/methylCALL/Sample1_rep3/multiqc_data | multiqc | MultiQC complete

/// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Ctl_rep1/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Ctl_rep1/multiqc_report.html | multiqc | Data : Results/methylCALL/Ctl_rep1/multiqc_data | multiqc | MultiQC complete

/// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Ctl_rep2/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.11_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.4_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.14_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Error calculating percentage for Ctl10_R1_val_1.fq.gz.temp.16_bismark_bt2_PE_report.txt - ignoring sample. | bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Ctl_rep2/multiqc_report.html | multiqc | Data : Results/methylCALL/Ctl_rep2/multiqc_data | multiqc | MultiQC complete /// MultiQC 🔍 | v1.12

| multiqc | MultiQC Version v1.14 now available! | multiqc | Search path : /work_dir/Results/methylCALL/Ctl_rep3/data | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 100/100
| bismark | Found 1 alignment reports | cutadapt | Found 2 reports | fastqc | Found 2 reports | multiqc | Compressing plot data | multiqc | Report : Results/methylCALL/Ctl_rep3/multiqc_report.html | multiqc | Data : Results/methylCALL/Ctl_rep3/multiqc_data | multiqc | MultiQC complete

.. done

$ multiqc /work_dir/Results/methylCALL/Sample1_rep1/data -o /work_dir/Results/methylCALL/Sample1_rep1 $ multiqc /work_dir/Results/methylCALL/Sample1_rep2/data -o /work_dir/Results/methylCALL/Sample1_rep2 $ multiqc /work_dir/Results/methylCALL/Sample1_rep3/data -o /work_dir/Results/methylCALL/Sample1_rep3 $ multiqc /work_dir/Results/methylCALL/Ctl_rep1/data -o /work_dir/Results/methylCALL/Ctl_rep1 $ multiqc /work_dir/Results/methylCALL/Ctl_rep2/data -o /work_dir/Results/methylCALL/Ctl_rep2 $ multiqc /work_dir/Results/methylCALL/Ctl_rep3/data -o /work_dir/Results/methylCALL/Ctl_rep3

  1. Calling (bismark) .. start $ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/Results/methylCALL/Sample1_rep2/methylcontext /work_dir/Results/methylCALL/Sample1_rep2/data/Sample1_rep2_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/Results/methylCALL/Sample1_rep2/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/Results/methylCALL/Sample1_rep3/methylcontext /work_dir/Results/methylCALL/Sample1_rep3/data/Sample1_rep3_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/Results/methylCALL/Sample1_rep3/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/Results/methylCALL/Sample1_rep1/methylcontext /work_dir/Results/methylCALL/Sample1_rep1/data/Sample1_rep1_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/Results/methylCALL/Sample1_rep1/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/Results/methylCALL/Ctl_rep2/methylcontext /work_dir/Results/methylCALL/Ctl_rep2/data/Ctl_rep2_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/Results/methylCALL/Ctl_rep2/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/Results/methylCALL/Ctl_rep3/methylcontext /work_dir/Results/methylCALL/Ctl_rep3/data/Ctl_rep3_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/Results/methylCALL/Ctl_rep3/logs/log.Bismark_call.txt

METHYLATION CALLING IS NOT COMPLETED. ERR: problem in methylation calling step

criphg commented 1 year ago

I figure out what I made wrong, I use Resuts in the place of result for docker directory, but now I have a new error, some help about?

$ multiqc /work_dir/result/methylCALL/HFD_rep1/data -o /work_dir/result/methylCALL/HFD_rep1 $ multiqc /work_dir/result/methylCALL/HFD_rep2/data -o /work_dir/result/methylCALL/HFD_rep2 $ multiqc /work_dir/result/methylCALL/HFD_rep3/data -o /work_dir/result/methylCALL/HFD_rep3 $ multiqc /work_dir/result/methylCALL/ICD_rep1/data -o /work_dir/result/methylCALL/ICD_rep1 $ multiqc /work_dir/result/methylCALL/ICD_rep2/data -o /work_dir/result/methylCALL/ICD_rep2 $ multiqc /work_dir/result/methylCALL/ICD_rep3/data -o /work_dir/result/methylCALL/ICD_rep3

  1. Calling (bismark) .. start

Now testing Bismark result file >/work_dir/result/methylCALL/HFD_rep2/data/HFD_rep2_bismark.sorted.bam< for positional sorting (which would be bad...)
Now testing Bismark result file >/work_dir/result/methylCALL/ICD_rep1/data/ICD_rep1_bismark.sorted.bam< for positional sorting (which would be bad...)
Now testing Bismark result file >/work_dir/result/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam< for positional sorting (which would be bad...)
Now testing Bismark result file >/work_dir/result/methylCALL/ICD_rep2/data/ICD_rep2_bismark.sorted.bam< for positional sorting (which would be bad...)
Now testing Bismark result file >/work_dir/result/methylCALL/HFD_rep1/data/HFD_rep1_bismark.sorted.bam< for positional sorting (which would be bad...)
Now testing Bismark result file >/work_dir/result/methylCALL/ICD_rep3/data/ICD_rep3_bismark.sorted.bam< for positional sorting (which would be bad...) $ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/HFD_rep3/methylcontext /work_dir/result/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/HFD_rep3/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/ICD_rep2/methylcontext /work_dir/result/methylCALL/ICD_rep2/data/ICD_rep2_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/ICD_rep2/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/ICD_rep1/methylcontext /work_dir/result/methylCALL/ICD_rep1/data/ICD_rep1_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/ICD_rep1/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/HFD_rep2/methylcontext /work_dir/result/methylCALL/HFD_rep2/data/HFD_rep2_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/HFD_rep2/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/HFD_rep1/methylcontext /work_dir/result/methylCALL/HFD_rep1/data/HFD_rep1_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/HFD_rep1/logs/log.Bismark_call.txt

$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/mm10/ -o /work_dir/result/methylCALL/ICD_rep3/methylcontext /work_dir/result/methylCALL/ICD_rep3/data/ICD_rep3_bismark.sorted.bam

There's a problem executing the upper command. check logfile > /work_dir/result/methylCALL/ICD_rep3/logs/log.Bismark_call.txt

METHYLATION CALLING IS NOT COMPLETED. ERR: problem in methylation calling step

####################Content of log.bismark_call.txt

Bismark methylation extractor version v0.23.1dev

Output will be written into the directory: /work_dir/result/methylCALL/HFD_rep3/methylcontext/ Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data

Setting the option '--bedGraph' since this is required for the genome-wide cytosine report

Setting core usage to single-threaded (default). Consider using --multicore to speed up the extraction process.

Summarising Bismark methylation extractor parameters:

Bismark paired-end SAM format specified (default) Number of cores to be used: 1 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Output path specified as: /work_dir/result/methylCALL/HFD_rep3/methylcontext/

Summarising bedGraph parameters:

Generating additional output in bedGraph and coverage format bedGraph format: coverage format:

Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting methylation information for all cytosine context (sorting may take a long time, you have been warned ...) The bedGraph UNIX sort command will use the following memory setting: '2G'. Temporary directory used for sorting is the output directory

Summarising genome-wide cytosine methylation report parameters:

Generating comprehensive genome-wide cytosine report (output format: ) Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files Using 1-based genomic coordinates (default) Genome folder was specified as /msPIPE/reference/mm10/

Checking file >>/work_dir/result/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam<< for signs of file truncation...

The IDs of Read 1 (A00801:306:H7JKWDSX5:1:1654:6298:24455_1:N:0:AGCGAGAT+GATACTGG) and Read 2 (A00801:306:H7JKWDSX5:1:1654:6352:24486_1:N:0:AGCGAGAT+GATACTGG) are not the same. This might be the result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead or sort the file using 'samtools sort -n' (by read name). This may also occur using samtools merge as it does not guarantee the read order. To properly merge files please use 'samtools merge -n' or 'samtools cat'.

rockman507 commented 1 year ago

Have you tried calling samtools sort -n? I am currently having this problem and that seems to have allowed it to keep going.

rockman507 commented 1 year ago

@criphg the commit last week fixes the second issue you brought up.

criphg commented 1 year ago

Thank you @rockman507 for the help, but I not sure about how to solve the sort problem.

I pull docker image again and use as specified above and have same error that before.

I install the dependencies and I cloned the last commit and try to run mspipe in local machine and have error in methylation calling step associated with sort:

  1. Calling (bismark) .. start $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/data/HFD_rep1_bismark.sorted.bam $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep2/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep2/data/HFD_rep2_bismark.sorted.bam $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep1/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep1/data/ICD_rep1_bismark.sorted.bam $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep2/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep2/data/ICD_rep2_bismark.sorted.bam $ /home/yanlab/Tools/msPIPE/bin/Bismark/bismark_methylation_extractor -p --multicore 8 --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /home/yanlab/Tools/msPIPE/reference/mm10/ -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep3/methylcontext /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep3/data/ICD_rep3_bismark.sorted.bam

Now testing Bismark result file >/media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam< for positional sorting (which would be bad...) Now testing Bismark result file >/media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep1/data/ICD_rep1_bismark.sorted.bam< for positional sorting (which would be bad...) Now testing Bismark result file >/media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep2/data/ICD_rep2_bismark.sorted.bam< for positional sorting (which would be bad...) There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep2/logs/log.Bismark_call.txt

Now testing Bismark result file >/media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep3/data/ICD_rep3_bismark.sorted.bam< for positional sorting (which would be bad...) There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/logs/log.Bismark_call.txt

There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep1/logs/log.Bismark_call.txt

There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/logs/log.Bismark_call.txt

There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep2/logs/log.Bismark_call.txt

There's a problem executing the upper command. check logfile > /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/ICD_rep3/logs/log.Bismark_call.txt

METHYLATION CALLING IS NOT COMPLETED. ERR: problem in methylation calling step

log.Basmark_call.txt for sample HFD_rep1:

Bismark methylation extractor version v0.23.1dev

Output will be written into the directory: /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/methylcontext/ Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data

Setting the option '--bedGraph' since this is required for the genome-wide cytosine report

Summarising Bismark methylation extractor parameters:

Bismark paired-end SAM format specified (default) Number of cores to be used: 8 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Output path specified as: /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/methylcontext/

Summarising bedGraph parameters:

Generating additional output in bedGraph and coverage format bedGraph format: coverage format:

Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting methylation information for all cytosine context (sorting may take a long time, you have been warned ...) The bedGraph UNIX sort command will use the following memory setting: '2G'. Temporary directory used for sorting is the output directory

Summarising genome-wide cytosine methylation report parameters:

Generating comprehensive genome-wide cytosine report (output format: ) Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files Using 1-based genomic coordinates (default) Genome folder was specified as /home/yanlab/Tools/msPIPE/reference/mm10/

Checking file >>/media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/data/HFD_rep1_bismark.sorted.bam<< for signs of file truncation... Captured error message: '[E::hts_open_format] Failed to open file /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep1/data/HFD_rep1_bismark.sorted.bam'

[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...

heesun9 commented 1 year ago

Hi I am one of the msPIPE team members.

Please try running the pipeline with the --skip_mapping option after manually re-sorting all bam files as shown below.

samtools sort -n -@ 8 -o /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/data/HFD_rep3_bismark.sorted.bam /media/yanlab/HDD/Rubens/msPIPE/msPIPE_native/results/methylCALL/HFD_rep3/data/HFD_rep3_bismark.bam

Alternatively, build a new image and run the updated pipeline. Using the same reference directory and running it with --skip_trimming will restart from the mapping step.

We updated the sorting-related problem in the mapping step. But we're having trouble uploading an updated image to the docker hub. please build the image directly via dockerfile as below rather than docker pull.

git clone https://github.com/jkimlab/msPIPE.git
cd msPIPE
docker build -t jkimlab/mspipe:latest .
criphg commented 1 year ago

I discovered that using more than 8 cores caused bam file truncation, using different samples and despite sufficient memory (it don't exhaust the maximum memory capacity at any point). Limiting the core count resolved alignment and sorting issues. However, I faced another obstacle processing bedGraph files (step 4.2), resulting in 8TB of large temporary ".methXtractor.temp" files per sample that filled my 20Tb storage. Deleting them, I attempted to skip trimming, alignment and calling steps but encountered an error due to the missing "doParallel" package in docker image.

criphg commented 12 months ago

Are these 8TB temp large files expected? I'm not certain if I made a mistake. Would you help me?

Below, I'll provide you with the Docker command and some additional details you might need. Let me know if you need more information. Docker was installed from github file following the instructions above.

Docker command line (first try): docker run -v $(pwd)/Samples:/msPIPE/data -v $(pwd)/reference:/msPIPE/reference -v $(pwd)/Results:/work_dir/ jkimlab/mspipe:latest msPIPE.py -p params_format.conf -c 8 -o HFDvsICD_result

Delleting huge temp files (*.methXtractor.temp, located in "Results/methylCall//methylcontext" directories) and try to skip initial steps: docker run -v $(pwd)/Samples:/msPIPE/data -v $(pwd)/reference:/msPIPE/reference -v $(pwd)/Results:/work_dir/ jkimlab/mspipe:latest msPIPE.py -p params_format.conf -c 8 -o HFDvsICD_result --skip_trimming --skip_mapping --skip_calling

Here my configuration file for the samples (Paired-end fastq files are in Samples direrectory): [DMR] ANALYSIS1 = HFD, ICD

[REFERENCE] UCSC_NAME = mm10

[LIB1] SAMPLE_NAME = HFD LIB_NAME = HFD_rep1 LIB_TYPE = P FILE_1 = /msPIPE/data/HFD7_R1.fq.gz FILE_2 = /msPIPE/data/HFD7_R2.fq.gz

[LIB2] SAMPLE_NAME = HFD LIB_NAME = HFD_rep2 LIB_TYPE = P FILE_1 = /msPIPE/data/HFD8_R1.fq.gz FILE_2 = /msPIPE/data/HFD8_R2.fq.gz

[LIB3] SAMPLE_NAME = HFD LIB_NAME = HFD_rep3 LIB_TYPE = P FILE_1 = /msPIPE/data/HFD9_R1.fq.gz FILE_2 = /msPIPE/data/HFD9_R2.fq.gz

[LIB4] SAMPLE_NAME = ICD LIB_NAME = ICD_rep1 LIB_TYPE = P FILE_1 = /msPIPE/data/ICD7_R1.fq.gz FILE_2 = /msPIPE/data/ICD7_R2.fq.gz

[LIB5] SAMPLE_NAME = ICD LIB_NAME = ICD_rep2 LIB_TYPE = P FILE_1 = /msPIPE/data/ICD8_R1.fq.gz FILE_2 = /msPIPE/data/ICD8_R2.fq.gz

[LIB6] SAMPLE_NAME = ICD LIB_NAME = ICD_rep3 LIB_TYPE = P FILE_1 = /msPIPE/data/ICD10_R1.fq.gz FILE_2 = /msPIPE/data/ICD10_R2.fq.gz

######################################################## Configuration of system: Gigabyte: M292-K92 AMD EPYC™ 7702 processors Dual processor, 64-core, 128 threads 500 Gb, ddr4 20Tb internal storage NAS HD.

Ubuntu 22.04.2 LTS

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/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn800801:30878_5008017JKWDSX5:1:1420:32+G7556.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_J06:H7JKWDSX5_1:N:r15.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH22:N:0:GTAAGGTG+GC:306AATTCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH5843032253:26470_1:N:0:GTAA420:32099:16470_1:N:0:GT.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH584304:G+GCA32.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH58438.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH5843:1420:32099:16470_1:N:0:GTAAGGTG+GCKWDSX5:1:1420:32036:28166_1:N:0:GTAAGGTG+GCAATTCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH5845:1:JH584304.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH5845:1:JTCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH584h.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH58:H7JKWDSX5:1:1420:30364:1783_1:G+GCA32.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH58GGTG+GT20:324.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH58H7JKWDSX5:1CAATTCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH:6:553:4178_1:N:0:0hXTG1+GCGGTG+GT2JKWDSX5_1:N:r15.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrUn_JH:6:553:4178_1:N:0:GTAAGGT232.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrchrchrUn_JH584304.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh0504470:80080_1:N:T42A2.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh09.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh0910r823536hr11A2008:9_07:5602X2A142353C+-8G70:5h040:03052030:5GT597.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh0910r823536hr11A2008:907:5602X801Gchr1:C14745610142816599:3711:50r11102A0:5GT:354364+4G2874hr111115r23H3550G208G11G354.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh09449:3228822691324062H30607.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh0:1441:326DJH5H.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh53AA142A106Tn_JH58400801:9G0121:1.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh53AAGGTG+C:306::H7.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh54:0:GTAAGGT99:16470_1:N:0:GTAAN:04-.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh5CAAT5_1:14TCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh778.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrh9:10430410X51654:1.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrhATTCG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrhT1::1:2.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrhr11.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrn_J.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0154:2008087409:16404.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr038:3G0240:5:ch:N2926771GAA06:HT8:9AG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr082::32+GT597.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0954:20080T.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0:HTG72+GTG_0147-.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0:HTG72+GTG_014TA1:4232.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W042X6571h43165840354:5083.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W43C1Gch4:20N9_08430.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W43C1Gchr1:C14745610142816599:313510240:170NH7.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W43_1517D31035r.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W442816599:31351024.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0W47T617W7168A1:410:604T525:92X6571h43165840354:5083.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0WT_1224055:ch434.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2bismark.sorted.txt.gz.chrr0.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1267:38G_7_401:5:ch091:2008:5:c66081:N:C4:Gr.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1292240r8238:3.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_12TA1:9:10401h49K58661G71h4r842801Gchr161G71h45661G71h45660:5:ch230240:5:ch230240:5:ch230240:5:ch-:9JH5H.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_12TA1:9:1040::08T.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_12TA1:9:51:c:39:9JH5H.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_161G1Gchr:N:chr560:2WDSX3G.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_161_28747521CAA062030925:T11:AA041:.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_161_28747521CAA064JH58+9149_3.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_161_287475DSX7823:G1:N:C147T2801Gchr11035821:92:3120:2+G71:GTA0:GTA14N:A.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_16G71:G7309_1:61G71h661G71h45662.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_16G71:GTA0:GTA142816599:32792:16:H769680616_2K0560:1G71h4562:T8941:1024XGG2N:1h4280H58430454:20080T.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_172DSXA.methXtractor.temp/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1G.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH4:561G40:5:926834302161G71h4r86h3-8G.methXtractor.temp/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH58430454:20:ch:N:06G:084ch:171311315GG28747580X040:5hr:4:G03021::1GCKWD0:3A29:32_58021327130G232.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843154:r788AG3:H784:30GH9H9.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843154GC24.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843154GC292:5chr161G40:5:922_12130:5G60:1G0:1H7.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH58435H1GH8226434.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843C+-8G.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843C62AG.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843C6961:5:9267:38G_585320AW3.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5843CW7168A9_2W40:1G0:N080590164:3ch664:G4G7364:8264:G704141.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5:::4c8708AG3:H784540913T.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH5:::92240r8238:3G034.methXtractor.temp/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr0_1GH82270020306N:8.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr11.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr16_0.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr16_1Un_JH26:H74716:01.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrr87:G02030:5hr149_3.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG200:3U8720T:G3220:c143.methXtractor.temp/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG200:3U8720T:G3264:G7041471h4r840282423r55H.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG20:-6.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG20:-8G.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG20:5081011:92:3120:0:G41711:81314C70_12TA1:913508386N:A01:78264:G7041G75AG75Ac:30364:G4N:A01661G71h3U8720T:G35:ch:N068.methXtractor.temp /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrAG20:5081012n_JHKWDS203C028801GTA-7:5AG75AG75An_J000326H.methXtractor.temp/work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHH_context_HFD_rep2_bismark.sorted.txt.gz.chrrUn_JH58:1:1DSX5:1AGGTG+GC:306:H7JKWDSX5:1:1420N:04-.methXtractor.temp

/work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext/CHG_context_HFD_rep1_bismark.sorted.txt.gz /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext/CHG_context_HFD_rep1_bismark.txt.gz

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CpG.cov --dir /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/methylcontext /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/methylcontext/CpGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/logs/log.CpG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/methylcontext/CHGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/logs/log.CHG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHH.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHHcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/logs/log.CHH_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/methylcontext/CHGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/ICD_rep3/logs/log.CHG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/ICD_rep1/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/ICD_rep1/methylcontext/CHGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/ICD_rep1/logs/log.CHG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/methylcontext/CHGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/logs/log.CHG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep2/methylcontext/CHGcontext $ /msPIPE/bin/Bismark/bismark2bedGraph -o CpG.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext/CpGcontext

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/logs/log.CpG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHH.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext/CHHcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/logs/log.CHH_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHG.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/methylcontext/CHGcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep1/logs/log.CHG_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHH.cov --dir /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/methylcontext/CHHcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/HFD_rep3/logs/log.CHH_bismark2bedGraph.txt

$ /msPIPE/bin/Bismark/bismark2bedGraph -o CHH.cov --dir /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/methylcontext --CX /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/methylcontext/CHHcontext*

There's a problem executing the upper command. check logfile > /work_dir/HFDvsICD_result/methylCALL/ICD_rep2/logs/log.CHH_bismark2bedGraph.txt

multiprocessing.pool.RemoteTraceback: """ OSError: [Errno 28] No space left on device

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/msPIPE/lib/func.py", line 19, in multi_run_wrapper return subproc(*args) File "/msPIPE/lib/func.py", line 35, in subproc printlog(log_proc, f"*** check logfile > {logF}\n") File "/msPIPE/lib/func.py", line 15, in printlog O.close() OSError: [Errno 28] No space left on device """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/msPIPE/msPIPE.py", line 1001, in completed = Methylation_calling(callD) File "/msPIPE/msPIPE.py", line 682, in Methylation_calling value = Bismark_calling(callD) File "/msPIPE/msPIPE.py", line 553, in Bismark_calling multi_returns = pool.map(multi_run_wrapper, bedgraphCMD_list) File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value OSError: [Errno 28] No space left on device

jkimlab commented 11 months ago

When the bismark bedgraph is running, too big temp files are created and insufficient disk space appears to be the cause of the error.

issue link: bismark2bedGraph Error

We are planning a mspipe update to set an option to specify the buffer size on the bismark bedgraph step. When running after updating the program, specifying the maximum RAM memory in the -b option is expected to no longer create large temporary files.