This is a re-posting of an older topic that I have still not resolved. This was covered in Error Running Breakdancer-Max: Max Kahan Error: 0 Breakdancer Installation/Running Problems: Error/Suspicious Messages During Installation prior threads. In the two prior threads it was suggested that I try updating to breakdancer version 1.4.4. I did this, and it did not resolve the issue. I'm still getting the same error.
Old post, updated for latest version follows:
I'm attempting to run breakdancer-max, and am running into an error that I can not find documentation on. My script looks like this:
#breakdancer directory BD="/share/apps/ngs-ccts/breakdancer-1.4.4" #File name FILE="CNTL3487.sort.bam" #Output directory DIR="breakdancer_test" #Create config file perl $BD/perl/bam2cfg.pl $FILE > $DIR/CNTL3487.cfg $BD/bin/breakdancer-max -d CNTL3487 $DIR/CNTL3487.cfg > $DIR/CNTL3487.ctx
And the output that I get looks like this:
[Tue Dec 10 13:32:15 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] Processing bam: CNTL3487.sort.bam [Tue Dec 10 13:32:18 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] selected_libs is : 1 [Tue Dec 10 13:32:18 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] Closing BAM file [Tue Dec 10 13:32:18 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] Send TERM signal for 3124 [Tue Dec 10 13:32:20 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] samtools pid process 3124 is still there... [Tue Dec 10 13:32:20 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] invoking kill -9 on 3124 ... [Tue Dec 10 13:32:20 2013 /share/apps/ngs-ccts/breakdancer-1.4.4/perl/bam2cfg.pl] Closing samtools process : 3124 Max Kahan error: 0
All of the output except for the Max Kahan error : 0 line is generated by bam2cfg.pl, and the Kahan line is generated by breakdancer-max. This also generates two files in the home directory (same directory I'm running in, and the one containing CNTL3487.sort.bam) with a size of 0 called CNTL3487.NA.2.fastq and CNTL3487.NA.2.fastq. It also creates a CNTL3487.ctx file in the breakdancer_test/ folder that looks like this:
#Software: 1.4.4 (commit ad4dca4) #Command: /share/apps/ngs-ccts/breakdancer-1.4.4/bin/breakdancer-max -d CNTL3487 breakdancer_test/CNTL3487.cfg #Library Statistics: #CNTL3487.sort.bam mean:605.16 std:159.56 uppercutoff:1222.92 lowercutoff:0 readlen:144 library:NA reflen:3005868224 seqcov:0.238852 phycov:0.501888 1:100 2:650 4:636 8:50 32:2722 #Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib CNTL3487.sort.bam
Note that the .bam file used here contains sequence reads from genomic material that first went through a capture step to isolate a region from Chr1.