Question: Hi, I am running BWA mem for aligning my PE reads against Human reference genome (GRCh38) although it is running but I am encountering with an error message. Please have a look on the command and the resulting message:

```
/usr/local/bwa-0.7.12/bwa mem -t 14 \
-M /san/illumina_two/rsindhu_sge/Human_ref_genomes/GRCh38/FINAL/GRCh38.fa \
Read1.fastq.gz Read2.fastq.gz > Read12.bwa.sam
```

A part of message:

```
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1429588 sequences (140000077 bp)...
[M::process] read 1431216 sequences (140000054 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (19, 558476, 545, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (126, 180, 401)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 951)
[M::mem_pestat] mean and std.dev: (243.78, 179.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1226)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (334, 387, 448)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (106, 676)
[M::mem_pestat] mean and std.dev: (391.91, 87.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 790)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (24, 49, 80)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 192)
[M::mem_pestat] mean and std.dev: (54.23, 40.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 248)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 1429588 reads in 1170.454 CPU sec, 83.775 real sec
[M::process] read 1429172 sequences (140000054 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (15, 558767, 537, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 207, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 670)
[M::mem_pestat] mean and std.dev: (212.33, 136.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 860)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (332, 385, 446)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (104, 674)
[M::mem_pestat] mean and std.dev: (390.32, 87.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 788)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (24, 46, 86)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 210)
[M::mem_pestat] mean and std.dev: (56.51, 44.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 272)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (379, 1210, 2961)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8125)
[M::mem_pestat] mean and std.dev: (1898.40, 2191.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10707)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
..........
```

Also, The size of the .sam file was found to be small as compared to the file when there was no such error message (Earlier it was 34G and now 14G). Please provide your suggestions

Many Thanks
Ravi

Answer: These are just log messages, not errors.