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
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