Data missing when transfroming FASTQ to Adam #1393

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A-Tsai opened this Issue Feb 17, 2017 · 0 comments

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A-Tsai commented Feb 17, 2017

I found some reads are lost when transforming FASTQ to Adam format. There are 500 reads in a FASTQ file, but only 435 reads are available in adam. I use adam flagstat to check the read count and get the following reads. After comparing the result, the last 65 reads are missing. I did use different input file to double check this issue and it happens for all of my testing data.

commands:
adam-submit -- transform -force_load_fastq -print_metrics /test.500.fastq /output
adam-submit -- flagstat /output

Results:
435 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 primary duplicates
0 + 0 primary duplicates - both read and mate mapped
0 + 0 primary duplicates - only read mapped
0 + 0 primary duplicates - cross chromosome
0 + 0 secondary duplicates
0 + 0 secondary duplicates - both read and mate mapped
0 + 0 secondary duplicates - only read mapped
0 + 0 secondary duplicates - cross chromosome
0 + 0 mapped (0.00%:0.00%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (0.00%:0.00%)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:0.00%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

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