Hello,
I have used deblur for filtering but after the completion of command there are no output files. I have attached the deblur log file with this question. Kindly help.deblur.log.txt (150.0 KB)
Hello!
If you look near the end of the log you will see:
INFO(140086093551360)2019-08-09 17:42:59,778:finished processing per sample fasta files
INFO(140086093551360)2019-08-09 17:43:00,660:create_otu_table for 100 samples, into output table /tmp/tmpefmj40f_/all.biom
INFO(140086093551360)2019-08-09 17:43:20,083:for output biom table loaded 100 samples, 30651 unique sequences
INFO(140086093551360)2019-08-09 17:43:20,498:keeping 2913 (out of 30651 sequences) with >=10 reads
Meaning you have 100 samples with a lot of reads which are small in number.
Then a few down lines you remove 1 remove 1 sequence as an artifact (this seems normal).
WARN(140086093551360)2019-08-09 17:44:16,954:removed 99 samples with reads per sample<1
You also haver this line meaning you only have 1 sample remaining, my guess is if you loosen the quality controls a bit you might have some useable data.
What command did you run?
1 Like