#63 sortbyname.sh not creating out2 even when specified

[Max Rozenblum]

Hi I am trying to sort paired FASTQs with reads out of order using sortbyname.sh so that reformat.sh with vpair will catch if reads are incorrectly paired instead of simply being out of order.

$ ./bbmap/sortbyname.sh in=unit_test_fq/randomly-shuffled_R1.fastq.gz in2=unit_test_fq/reads_R2.fastq.gz out=unit_test_fq/reordered_R1.fastq.gz out2=unit_test_fq/reordered_R2.fastq.gz ascending
java -ea -Xmx9792m -Xms9792m -cp /home/max/fastq_qc_redux/bbmap/current/ sort.SortByName in=unit_test_fq/randomly-shuffled_R1.fastq.gz in2=unit_test_fq/reads_R2.fastq.gz out=unit_test_fq/reordered_R1.fastq.gz out2=unit_test_fq/reordered_R2.fastq.gz ascending
Executing sort.SortByName [in=unit_test_fq/randomly-shuffled_R1.fastq.gz, in2=unit_test_fq/reads_R2.fastq.gz, out=unit_test_fq/reordered_R1.fastq.gz, out2=unit_test_fq/reordered_R2.fastq.gz, ascending]

Input is being processed as paired
Finished reading input.
Sorting.
Created a WriteThread for unit_test_fq/reordered_R1.fastq.gz
Time:                           0.104 seconds.
Reads Processed:         800    7.66k reads/sec
Bases Processed:        120k    1.15m bases/sec

I have tried using the overwrite flag as well, but only the R1 outfile gets written. Can't figured out what I am doing wrong. Any help would be greatly appreciated!

[Max Rozenblum]

Though the issue above still stands. I realize that running repair.sh on paired FASTQs will toss the singletons and reorder the reads into the same order (though it appears to be randomly ordered relative to the two input FASTQs) as out and out2.

[Brian Bushnell]

I was able to replicate this behavior and it is fixed for the next release (39.05, probably this week). Sometimes I don't notice this kind of issue because I always keep paired reads interleaved in a single file.