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marcus1487 / nanoraw

Genome guided re-segmention and visualization for raw nanopore sequencing data.
https://pypi.python.org/pypi/nanoraw
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no data in corrected-group #36

Closed sathishkumarRamaswamy closed 7 years ago

sathishkumarRamaswamy commented 7 years ago

Dear Team, I am running following commands, I didnt get any error/warnning message, but i am not getting corrected group data.

nanoraw genome_resquiggle \$g1Dir $genomeFn --bwa-mem-executable ./bwa \ --normalization-type median \ --corrected-group RawGenomeCorrected_bwamem_000 --overwrite \ --failed-reads-filename testing.group1.bwamem.failed_read.txt \ --2d --processes 4

marcus1487 commented 7 years ago

Hi, Happy to help.

What was the output to stderr and/or the --failed-read-filename? As a first guess, have you double checked that $g1Dir contains the FAST5 files (e.g. ls $g1Dir | less should give you a long list of FAST5 files)?

If the FAST5 files are in a subdirectory (or group of subdirectory, using the newest version of Metrichor I believe does this), nanoraw cannot find them without specific instruction as to where to look. I have not had a chance to put up instructions for this, but you should be able to use the --fast5-pattern with a pattern in double quotes specifying the location of all FAST5 files. If this is the case then you should have output that indicates that very few files were to be processed (i.e. Correcting 0 files with 1 subgroup(s)/read(s) each (Will print a dot for each 100 files completed).).

Hopefully this might be helpful, but if there is another issue, maybe some more detail might help to identify the issue. Thanks!

marcus1487 commented 7 years ago

Without more information I am closing this issue. Provide more info if this issue persists.

smm19900210 commented 6 years ago

hi marcus1487, i met the same problem, but i got corrected group, but it empty. what should i do?