search

LANL-Bioinformatics / MeGAMerge

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
Other
14 stars 7 forks source link

run error #4

Open igsbma opened 8 years ago

igsbma commented 8 years ago

Hi there, I run into this error from minimus2 "Bad file descriptor". Could you advice? thanks!

Bing

$ cat nucmer.error 20160706|100857| 13213| ERROR: mummer and/or mgaps returned non-zero, please file a bug report

$ cat mmerge.o8916691 Running Newbler assembly with 966644 sequences runAssembly -force -large -rip -mi 98 -ml 80 -pairt -cpu 4 -a 200 -o megamerge//newbler megamerge//newblerIn.fasta 1>/dev/null 2>/dev/null Running Minimus2 with 420675 sequences minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 megamerge//minimus.fasta 1>/dev/null 2>/dev/null Bad file descriptor at /home/bma/bin/MeGAMerge-1.1.pl line 280. minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 megamerge//minimus.fasta 1>/dev/null 2>/dev/null failed: Bad file descriptor

in "minimus.fasta.runAmos.log", this is the part that runs error

,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "megamerge//minimus.fasta.ntref" of length 394792805

construct suffix tree for sequence of length 394792805

(maximum input length is 536870908)

process 3947928 characters per dot

...............................................................................................ERROR: mummer and/or mgaps returned non-zero, please file a bug report

!!! 2016-07-06 10:08:57 Command: /usr/local/packages/mummer/nucmer -maxmatch -c 80 megamerge//minimus.fasta.ref.seq megamerge//minimus.fasta.qry.seq -p megamerge//minimus.fasta exited with status: 1 !!! END - Elapsed time: 0d 0h 10m 31s

scholzmb commented 8 years ago

Sorry for the delay. If you can re-run using the --debug option, it will help.