Running ECCsplorer test-data and test-run

[Hessainekkeh]

Hello Dear

I am trying to use ECCsplorer pipeline, I tied all installation details, I also tried to follow all instructions as mini-workshop,

Finally when I ran it as test run, it did not work as the following command:

eccsplorer testdata/aDNA_R1.fastq testdata/aDNA_R2.fastq testdata/gDNA_R1.fastq testdata/gDNA_R2.fastq --reference_genome testdata/RefGenomeSeq.fa --database testdata/RefSeq_DB.fa --output_dir testrun --trim_reads tru3 --read_count 1000

It showed the following error:

Error: unable to open file or unable to determine types for file stdin

• Please ensure that your file is TAB delimited (e.g., cat -t FILE).
• Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED). eccCand_001 (TR_map-all): Bedtools error, trying again.

Please, could I know how to solve this problem.

Many thanks in advance.

[crimBubble]

Hello, can you try to re-run the test using the -cpu 2 option. Bedtools sometimes shows weird behavior when to many occurences are run at once.

[Hessainekkeh]

Hello,

Many thanks for your response,

I tried that, unfortunately, it did not work as well.

Kind regards. Hessain

On Tue, 14 Feb 2023 at 12:50, LMann @.***> wrote:

Hello, can you try to re-run the test using the -cpu 2 option. Bedtools sometimes shows weird behavior when to many occurences are run at once.

— Reply to this email directly, view it on GitHub https://github.com/crimBubble/ECCsplorer/issues/12#issuecomment-1429696630, or unsubscribe https://github.com/notifications/unsubscribe-auth/AX7VIELBSXXXZ6B5ZXZ3CD3WXN5QDANCNFSM6AAAAAAUWVO7PQ . You are receiving this because you authored the thread.Message ID: @.***>

-- Hess Tel: +447561109768.

[ShixiangWang]

Same issue on centos

[crimBubble]

Hi @Hessainekkeh and @ShixiangWang , I tried to recreate the error but I am missing out on some information. Could you both please send an email to ludwig.mann@tu-dresden.de containing the following files and information:

• OS (operating system), PC class (Personal computer, notebook, workstation, server)
• the output of the command: conda list -n eccsplorer
• the TR-CO_summary_region-coverages_normalized.csv file from the output in testrun/eccpipe_results/mapping_results
• Bonus: modify the eccMapper.py and add print(region_in) to line 162 (make sure it is indented equally to the lines arround) and rerun the pipeline and add the printed line (shortly before the error massage) to the email

With this info I hope we can solve the problem.

[Hessainekkeh]

Hi,

Many thanks again for your help,

I did that, gratefully, the problem was solved.

[jgoodson]

For the benefit of anyone else reading this with the same issue, especially if you happen to be on CentOS/RHEL: the echo command built-in to the default bash shell in these distros requires the -e flag for the tab escape sequence \t to actually print a tab instead of the literal characters \t. You may modify the lines in lib/eccMapper.py that use:

subprocess.check_output('echo \'{region_}\' | bedtools coverage

to read

subprocess.check_output('echo -e \'{region_}\' | bedtools coverage

In general, echo is unreliable as its behavior depends on whether you are calling the echo build in to a shell (where its behavior depends on what shell you are running) or a standalone echo binary like at /bin/echo or /usr/bin/echo (where its behavior depends on whether you are running GNU coreutils echo or another version). printf might be a more reliable option, although the most compatible option would be to modify these commands to directly pass data to stdin via the subprocess function arguments and not depend on any specific shell behavior.