Unfortunately, mapping using gi numbers are no longer supported.
Hello,
I have been following the generic pipeline for generateing .megan file. I have 2 samples and already generated .megan file for one of them. However, the next sample had been stuck on the step of .daa file generation for a while now.
The command used is :
~/Tools/diamond/bin/diamond blastx --query ../00fastq/sample.fq.gz --db nr --daa ./sample.daa
The sample file size is ~500 mb. The log file shows the following message:
Masking low complexity seeds… [0.305s]
Searching alignments… [75.809s]
Deallocating buffers… [0.564s]
Clearing query masking… [7.9s]
Opening temporary output file… [0s]
Computing alignments… [2472.54s]
Deallocating reference… [0.333s]
Loading reference sequences… [16.142s]
Masking reference…
I understand this means the process is going on but the slow progress concerns me as it has been more than 3 days were the other sample of same size took only a day. I don’t understand if it has stopped or not. There is .daa file created in the sample name but is empty. The nr database is the same as mentioned in the pipeline. Hope you would help me in this case.
Thank you.
Please address questions regarding the DIAMOND program to Benjamin Buckfink via the DIAMOND GitHub page.