BWA error when aligning multiple files

Question

[Whirlingdaf]

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.

Answer 1

[Istvan Albert]

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

[Whirlingdaf]

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

Answer 2

[h.mon]

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)