BWA error when aligning multiple files
2
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3.6 years ago
Clovering ▴ 20

I am using BWA to align reads which have been filtered through stacks to reference files using a script similar to that below:

set -ueo pipefail
FILES="M17
M526
M954
LG11
LG204
LG309
LG110
M224
M236
M527
M955
LG12
LG229
LG310
"
i=1

for FNAME in $FILES do time bwa mem -t 12 -M /Directory/Lisp_final /Directory/$FNAME\.1.fq.gz /Directory/$FNAME\.2.fq.gz > /Directory/$FNAME\.sam
let "i+=1";
done


When I run each sample individually it runs fine, but when I try to run all of the files in the directory as seen above (I have >300 samples with corresponding files), I receive the below error:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 857144 sequences (120000160 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 6876, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 134, 139)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (19, 219)
[M::mem_pestat] mean and std.dev: (117.13, 31.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 259)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[mem_sam_pe] [mem_sam_pe] paired reads have different names: "29_1_1101_2537_1125/1", "29_1_1101_2537_1125/2"
paired reads have different names: "29_1_1101_13702_1172/1", "29_1_1101_13702_1172/2"
[mem_sam_pe] paired reads have different names: "29_1_1101_4716_1172/1", "29_1_1101_4716_1172/2"

[mem_sam_pe] paired reads have different names: "29_1_1101_15139_1282/1", "29_1_1101_15139_1282/2"


Any help would be much appreciated.

software error alignment • 1.2k views
0
Entering edit mode
3.6 years ago

at least one of you fastq file pairs (among the many) uses an old school naming scheme where the read names are not identical across the pair.

29_1_1101_2537_1125/1 vs 29_1_1101_2537_1125/2

0
Entering edit mode

Thank you. Do you know why this might be? Or how to move forward with this being the case?

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Entering edit mode
3.6 years ago
h.mon 34k

The /1 and /2 appended to the read names causes trouble for BWA, see possible solutions at:

Is there a more elegant solution to the bwa-mem: paired reads have different names error?

paired reads have different names (bwa-mem)