Segmentation fault: 11 during FragGeneScan
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#2 Segmentation fault: 11 during FragGeneScan
I'm trying to run MaxBin2 on my contigs produced by IDBA-UD, but I run into a segfault error during the FragGeneScan step. Here is the command used and output:
run_MaxBin.pl -contig /Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/cec_results/contig.cec.fa -out cec.contig.bin -reads /Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/data/cec_reads.fa -thread 24 -plotmarker
MaxBin 2.2.4
Input contig: /Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/cec_results/contig.cec.fa
out header: cec.contig.bin
Located reads file [/Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/data/cec_reads.fa]
Thread: 24
Running Bowtie2 on reads file [/Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/data/cec_reads.fa]...this may take a while...
Reading SAM file to estimate abundance values...
Searching against 107 marker genes to find starting seed contigs for [/Users/parfreylab/Desktop/lab_member_files/kevin/assembly/star/idba_ud_bb/cec_results/contig.cec.fa]...
Running FragGeneScan....
Error running FragGeneScan. Output recorded in cec.contig.bin.contig.tmp.frag.out and cec.contig.bin.contig.tmp.frag.err.
=== Please make sure that you are running FragGeneScan 1.18 or above. ===
=== There are known bugs in v1.17 and before that will crash FragGeneScan program. ===
I tried running FragGeneScan (version 1.30) using the same commands found in the cec.contig.bin.contig.tmp.frag.out file, but this resulted in a segmentation fault. Could you please help me with this problem?
This is a bit weird. May I ask if you have tried the simulated dataset like 20X, as posted on https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html ? Thanks.
Yu-Wei
Hi Yu-Wei, I was actually able to run MaxBin2 successfully on a Linux cluster (I was previously trying to run it locally on Mac OSX), so I will consider this issue closed. Thanks!