NxTrim-0.4.0 Segmentation fault (core dumped)

[wangyugui]

[root@T630 NxTrim-0.4.0]# ./nxtrim -1 /arch/fastq/juglans.DNA/Mate/SRR2057824_1.fastq.gz -2 /arch/fastq/juglans.DNA/Mate/SRR2057824_2.fastq.gz -O mate
Output: mate.*.fastq.gz
Trimming:
R1: /arch/fastq/juglans.DNA/Mate/SRR2057824_1.fastq.gz
R2: /arch/fastq/juglans.DNA/Mate/SRR2057824_2.fastq.gz
Segmentation fault (core dumped)
[root@T630 NxTrim-0.4.0]# gdb ./nxtrim ./core.76735

(gdb) where
#0 0x00007fb25dd99961 in __strlen_sse2_pminub () from /lib64/libc.so.6
#1 0x00000000004082cd in fastqReader::next(fqread&) ()
#2 0x0000000000408b04 in pairReader::next(readPair&) ()
#3 0x000000000040264d in main ()

(gdb) q
[root@T630 NxTrim-0.4.0]# zless /arch/fastq/juglans.DNA/Mate/SRR2057824_1.fastq.gz
[root@T630 NxTrim-0.4.0]# zless /arch/fastq/juglans.DNA/Mate/SRR2057824_1.fastq.gz|head
@DJB77P1:542:H881JADXX:1:1101:1162:2100
NTTTATTTTTTTTCTTTTTCCTCTCGGTTTCTCTCTGTCTCTCACCGTGTGCTTCTCTCGATCATCTCTCTCTCCCTCTCTATCATTTTTTCAACTGCCCAGGCACCTGTCTCTNATACACATCTAGATGTGTATAAGAGACAGGAGTGTG
+DJB77P1:542:H881JADXX:1:1101:1162:2100
#1=BDFDDHDFDHIIIIGHGFEE>FGDBDGH@F9B?DDFGIEGHHGGG;=CCDH>CHEHE?CDBCECCAECCCCCCCC9?C>CCCDDD@CBC@@>@ACAB488ABBA3+:@cc#+88?C@CCC:CAD:BCDDDC>@cc?<B?<9?>:

@DJB77P1:542:H881JADXX:1:1101:1155:2123
TGCGCGAGAAAACTATTGAGTAAAAGGCAAGAAAGTGTGAGACAATTATCTGGAAACTGTCTCTTATACACATCTAGATGTGTATAAGAGACAGGTTCTTGGNTAAATTTATGTNTTGGTTGATGTTTACCCATGTGATCTTGAGTTTGAA
+DJB77P1:542:H881JADXX:1:1101:1155:2123
?@@da@@@FFDHHDEHIHIFCFHI<CFGH@GIEGC9?09?FAGGHIIIIGG8;C=@FGGA=CEAEHEEAA>;;@cc3;3..>BCC@@;9=(58,55::@@#+8?B@@3>@::#+++(+289::4>>>AAC@CC(:(::4>C>C######
@DJB77P1:542:H881JADXX:1:1101:1180:2131
CATTAATTATTGCATACTGCTAGTATATCTAGAAGCATTGCATATTATTTGTCATGTACGAGGAGTATGTAGCCCTGTGTTGCATGTCCCGTCGTTTCAGTCACAATCCAATCCCAAGCGGGGGCTGGGAGCGCCACACAATGTATAGATT
[root@T630 NxTrim-0.4.0]#

[wangyugui]

Are there any other good tools that can remove adapter of mate pair lib?

The result of trimmomatic 0.35(simple mode) seems Not Good
(the k-mer result reported by fastQC is NOT good)

[wangyugui]

a dirty fix.

diff --git a/fastqlib.cpp b/fastqlib.cpp
index eff47d7..08a9af2 100755
--- a/fastqlib.cpp
+++ b/fastqlib.cpp
@@ -215,7 +215,12 @@ int fastqWriter::write(readPair & p) {

remove
r.set((string)seq->name.s+(string)+" "+seq->comment.s,(string)seq->seq.s,"+",(string)seq->qual.s);

add
if(seq->comment.s!=NULL){
r.set((string)seq->name.s+" "+seq->comment.s,(string)seq->seq.s,"+",(string)seq->qual.s);
}else{
r.set((string)seq->name.s,(string)seq->seq.s,"+",(string)seq->qual.s);
}

[jaredo]

Thanks for the bug report. I just pushed a fix (very similar to your own).

The bug was introduced in v0.4.0 when I swapped to kseq for file i/o.

[wangyugui]

The bug is fixed and please close the issue.

And the result of NxTrim is much better than trimmomatic (simple mode) when mate lib fastq file.
Thanks for your job.