failure to align any reads on iteration 4

[r.mo...@gmail.com]

Dear Dr Miller (or any other helpful observers)

I am running emirge on 8 metagenomic samples, on a cluster. Seven of the samples are still running, one is up to it #26 and still going. One sample (sample104) fails at the 4th iteration seemingly because no reads align. I have re-run several times to fix various errors, in new folder each time, but this is the last error I can not figure out how to fix. 

The script is:

emirge.py /proj/b2016272/nobackup/Erken_metagenomes/emirge/104 --phred33 -j 0.99 -a 16 -i 210 -s 100 -l 126 \

-1 /proj/b2016272/nobackup/Erken_metagenomes/fastq/P4710_104_1P.fastq \

-2 /proj/b2016272/nobackup/Erken_metagenomes/fastq/P4710_104_2P.fastq \

-b /proj/b2016272/private/Erken_metagenomes/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed \

-f /proj/b2016272/private/Erken_metagenomes/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta

The final error message is:

ValueError: need at least one array to concatenate

I have attached the log file. Please note that the 'no EOF' error message for the BAM file exists in the log files of the other samples that are still running.

thank you for your time

rhi

[rlsim...@gmail.com]

I have the same error - did anyone ever solve this?

[Drishti Kaul]

Hi!

I got the same error for one out of my 27 samples, and it seems like the values for mean insert size and std dev have some effect here.

I tried re-running the sample with higher values of i and s, and that seemed to take care of the error. What values are you using for those parameters?

-Drishti