amnona
commented
6 years ago Hi Bishnu, deblur_working_dir is a temporary directory produced by deblur during the processing. If you see this directory but not the reference-hit.biom etc. it means one of the two:
- deblur is still running
- deblur failed during the processing. Did deblur output some error message? Also, you can look at the deblur.log file to see exactly where the problem occurs. I would recommend deleting deblur.log (since new output is appended to the log file rather than rewriting it) and then rerunning deblur with more verbose log reporting. i.e. deblur (ALL YOUR PARAMETERS) --log-level 1 Can you copy the exact command you used for running deblur, and attach the deblur.log file after rerunning?
Cheers Amnon
On Wed, Jul 11, 2018 at 6:42 PM Bishnu Adhikari notifications@github.com wrote:
I was running deblur workflow using seqs.fna, output from split_libraries_fastq.py as demonstrated in the example, however, I was getting different outputs than those mentioned in the example. I am getting deblur_working_dir, deblur.log and split as outputs instead of getting reference-hit.seqs.fa, reference-non-hit.biom, reference-non-hit.biom, reference-non-hit.seqs.fa, all.biom, and all.seqs.fa as mentioned in the example. I used the deblur workflow previously once but was getting the exact outputs. I am wondering whether, the workflow has changed or something wrong, and I didn't see any changes in the github example usage. I didn't have any ideas how to use the information in current directories for futher downstream analysis if the output is correct. I would really appreciate your suggestions and feebacks on this issue.
Thank you
Best Regards Bishnu Adhikari
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bishnuadhikari
wasade
I was running deblur workflow using seqs.fna, output from split_libraries_fastq.py as demonstrated in the example, however, I was getting different outputs than those mentioned in the example. I am getting deblur_working_dir, deblur.log and split as outputs instead of getting reference-hit.seqs.fa, reference-non-hit.biom, reference-non-hit.biom, reference-non-hit.seqs.fa, all.biom, and all.seqs.fa as mentioned in the example. I used the deblur workflow previously once but was getting the exact outputs. I am wondering whether, the workflow has changed or something wrong, and I didn't see any changes in the github example usage. I didn't have any ideas how to use the information in current directories for futher downstream analysis if the output is correct. I would really appreciate your suggestions and feebacks on this issue.
Thank you
Best Regards Bishnu Adhikari