iqbal-lab-org / mykrobe_tb_workflow Goto Github PK

Dear Michael,

im getting error of YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated
MissingInputException in line 15 of /home/fmr/Mykrobe_tb_workflow-master/rules/porechop.smk:
Missing input files for rule porechop:
data/basecalled/Test_15.fastq.gz
if you can please help me to resolve this issue asap.

thank you

Combine the nanoporeqc and mykrobe containers so there is only one required.

I think this is in here by accident

I have added the paths to the appropriate Singularity containers on yoda

hi i tried to reinstall it and run but the pipeline shows below error
TypeError in line 11 of /media/fmr/9af4a3cb-07fd-489a-85f8-9e2253be3d37/Mykrobe_tb_workflow-master/rules/reports.smk:
must be str, not int

File "/media/fmr/9af4a3cb-07fd-489a-85f8-9e2253be3d37/Mykrobe_tb_workflow-master/Snakefile", line 62, in

File "/media/fmr/9af4a3cb-07fd-489a-85f8-9e2253be3d37/Mykrobe_tb_workflow-master/rules/reports.smk", line 11, in
thanks

Originally posted by @shashibioinfo143 in #5 (comment)

Dear Micheal,

porechop step gets killed after 2 hrs start of analysis. I have tried to do Analysis for 28 Gb fastq.gz of M.Tb reads data on PC with 16 Gb RAM, 1Tb storage. I have tried to reinstall the pipeline and do analysis 5 times but still it shows the same error(PF below error). can you please help me to resolve the issue.

Thank you

bash:** line 1: 3889 Killed porechop --input data/basecalled/Test_15_pass.fastq.gz --output data/porechopped/Test_15_pass.fastq.gz --threads 1 --check_reads 25000 --extra_end_trim 10 --discard_middle --format fastq.gz > logs/porechop.log
[Mon Oct 21 16:52:12 2019]
Error in rule porechop:
jobid: 7
output: data/porechopped/Test_15_pass.fastq.gz
log: logs/porechop.log (check log file(s) for error message)
shell:
porechop --input data/basecalled/Test_15_pass.fastq.gz --output data/porechopped/Test_15_pass.fastq.gz --threads 1 --check_reads 25000 --extra_end_trim 10 --discard_middle --format fastq.gz > logs/porechop.log
(exited with non-zero exit code)

Looking very nice @mbhall88 - could you maybe add a screenshot of some standard output? or add some demo output in a demo directory, and link to it from the front page, somewhere high enough they dont need to scroll through it all to find it?