Hello,
I am running Scaff10x V.4.2 with the following command:
scaff10x -nodes 40 -longread 1 -plot 10x_coverage.png PacBioScaffolds.fasta 19-Bp_S1_L001_R1_001.fastq.gz 19-Bp_S1_L001_R2_001.fastq.gz Result_scaff10x.fasta
Scaff10x is running and also produces a couple of output files, of which align2.dat and try.out are empty:
0 Apr 30 17:40 align2.dat
28G Apr 29 22:56 align.dat
1.3G Apr 29 11:40 cleaN.fasta
2.9M Apr 29 22:56 core.61997
2.5G Apr 29 11:40 tarseq.fastq
19 Apr 29 11:58 tarseq.fastq.amb
1.6M Apr 29 11:58 tarseq.fastq.ann
1.3G Apr 29 11:58 tarseq.fastq.bwt
312M Apr 29 11:58 tarseq.fastq.pac
624M Apr 29 12:06 tarseq.fastq.sa
1.9M Apr 29 11:40 tarseq.tag
0 Apr 29 22:56 try.out
and I obtain the following error message:
...
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 545)
[M::mem_pestat] mean and std.dev: (192.88, 98.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 685)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 434416 reads in 662.155 CPU sec, 18.441 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/bwa mem -t 40 tarseq.fastq R1_001.fastq.gz 19-Bp_S1_L001_R2_001.fastq.gz
[main] Real time: 38988.280 sec; CPU: 1509159.415 sec
sh: line 1: 61997 Segmentation fault (core dumped) /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
Error running command: /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
Hello,
I am running Scaff10x V.4.2 with the following command:
scaff10x -nodes 40 -longread 1 -plot 10x_coverage.png PacBioScaffolds.fasta 19-Bp_S1_L001_R1_001.fastq.gz 19-Bp_S1_L001_R2_001.fastq.gz Result_scaff10x.fasta
Scaff10x is running and also produces a couple of output files, of which align2.dat and try.out are empty:
0 Apr 30 17:40 align2.dat
28G Apr 29 22:56 align.dat
1.3G Apr 29 11:40 cleaN.fasta
2.9M Apr 29 22:56 core.61997
2.5G Apr 29 11:40 tarseq.fastq
19 Apr 29 11:58 tarseq.fastq.amb
1.6M Apr 29 11:58 tarseq.fastq.ann
1.3G Apr 29 11:58 tarseq.fastq.bwt
312M Apr 29 11:58 tarseq.fastq.pac
624M Apr 29 12:06 tarseq.fastq.sa
1.9M Apr 29 11:40 tarseq.tag
0 Apr 29 22:56 try.out
and I obtain the following error message:
...
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 545)
[M::mem_pestat] mean and std.dev: (192.88, 98.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 685)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 434416 reads in 662.155 CPU sec, 18.441 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/bwa mem -t 40 tarseq.fastq R1_001.fastq.gz 19-Bp_S1_L001_R2_001.fastq.gz
[main] Real time: 38988.280 sec; CPU: 1509159.415 sec
sh: line 1: 61997 Segmentation fault (core dumped) /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
Error running command: /cluster/software/scaff10x/Scaff10X-4.2/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out