Open neptuneyt opened 4 years ago
Honestly, no idea - i have never used kneaddata. If you absolutely cannot get it to work, another way to handle this is to assemble all the reads without filtering out the host, and then remove the host sequences from the assembly itself by using any alignment software (even just blastn should work). Or you could just leave the host sequences in the data and proceed all the way - the extra filtering rarely makes a huge difference on the quality besides it taking longer to process, since if the host is eukaryotic its sequences will be easily clustered into their own bin during the binning, or left in the "unbinned" pile. Good luck!
This problem seems to be due to the Bmfilter can not process unpaired and not sorted fastq file processed by kneaddata.
Info: no ./bmtagger.conf found Using following programs: /public1/home/mambaforge-pypy3/envs/metawrap-env/bin/bmfilter /public1/home/mambaforge-pypy3/envs/metawrap-env/bin/srprism /public1/home/mambaforge-pypy3/envs/metawrap-env/bin/blastn /public1/home/mambaforge-pypy3/envs/metawrap-env/bin/extract_fullseq MAIN SCRIPT IS /public1/home/mambaforge-pypy3/envs/metawrap-env/bin/bmtagger.sh (PID=453912) RUNNING bmfilter
real 1m18.859s user 0m0.526s sys 0m22.310s FAILED: bmfilter with rc=134
Something went wrong with running Bmtagger! Exiting.
What should I do next? thank you.
Hi, I trimmd host plant sequence via kneaddata, and then run below command to trim human sequence,
and return below error information:
It
DID WORK
when I try to useRAW fastq
which did not process by kneaddata, the problem seems to derive from this step, there are demo fastq file which processed by kneaddata: " STA-032A_1.fastq ""STA-032A_2.fastq"
Who anyone faces this problem, and how can I handle it? Thanks a lot.