PE library number of reads is odd - Exit Code 1

[jronwalker]

Hello,

I am currently trying to assemble contigs using megahit with the -r and --12 options. The log file appears to be showing me that the number of reads are not the same in one of my interleaved files. I ran a grep command to confirm the number of reads in the file and found that it was an even amount. Could you please assist in determining why I am getting the following error from the log file:

020-03-03 12:58:47 - MEGAHIT v1.2.8
2020-03-03 12:58:48 - Using megahit_core with POPCNT support
2020-03-03 12:58:49 - Convert reads to binary library
2020-03-03 12:58:49 - command /general/software/x86_64/easybuild/software/MEGAHIT/1.2.8-GCCcore-8.2.0/bin/megahit_core_popcnt buildlib /scratch/user/jronwalker/megahit_out_all_harvey/tmp/reads.lib /scratch/user/jronwalker/megahit_out_all_harvey/tmp/reads.lib
2020-03-03 12:59:05 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S1S10_S22_L005.unmerged.bbmasked.fastq.gz): interleaved, 6989828 reads, 150 max length'
2020-03-03 12:59:25 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 1 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S5S1_S31_L005.unmerged.bbmasked.fastq.gz): interleaved, 8659372 reads, 150 max length'
2020-03-03 12:59:38 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 2 (/scratch/user/jronwalker/megahit/raw_reads/GF-S1S10_S4_L005.unmerged.bbmasked.fastq.gz): interleaved, 5765382 reads, 150 max length'
2020-03-03 12:59:58 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 3 (/scratch/user/jronwalker/megahit/raw_reads/GF-S4S1_S9_L005.unmerged.bbmasked.fastq.gz): interleaved, 8543464 reads, 150 max length'
2020-03-03 13:00:14 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 4 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S1S10_S22_L006.unmerged.bbmasked.fastq.gz): interleaved, 7044966 reads, 150 max length'
2020-03-03 13:00:34 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 5 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S5S1_S31_L006.unmerged.bbmasked.fastq.gz): interleaved, 8679288 reads, 150 max length'
2020-03-03 13:00:48 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 6 (/scratch/user/jronwalker/megahit/raw_reads/GF-S1S10_S4_L006.unmerged.bbmasked.fastq.gz): interleaved, 5794176 reads, 150 max length'
2020-03-03 13:01:07 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 7 (/scratch/user/jronwalker/megahit/raw_reads/GF-S4S1_S9_L006.unmerged.bbmasked.fastq.gz): interleaved, 8610980 reads, 150 max length'
2020-03-03 13:01:24 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 8 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S1S10_S22_L007.unmerged.bbmasked.fastq.gz): interleaved, 7040622 reads, 150 max length'
2020-03-03 13:01:44 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 9 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S5S1_S31_L007.unmerged.bbmasked.fastq.gz): interleaved, 8701610 reads, 150 max length'
2020-03-03 13:01:58 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 10 (/scratch/user/jronwalker/megahit/raw_reads/GF-S1S10_S4_L007.unmerged.bbmasked.fastq.gz): interleaved, 5789520 reads, 150 max length'
2020-03-03 13:02:18 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 11 (/scratch/user/jronwalker/megahit/raw_reads/GF-S4S1_S9_L007.unmerged.bbmasked.fastq.gz): interleaved, 8650974 reads, 150 max length'
2020-03-03 13:02:34 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 12 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S1S10_S22_L008.unmerged.bbmasked.fastq.gz): interleaved, 6971732 reads, 150 max length'
2020-03-03 13:02:54 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 13 (/scratch/user/jronwalker/megahit/raw_reads/0_22-S5S1_S31_L008.unmerged.bbmasked.fastq.gz): interleaved, 8602666 reads, 150 max length'
2020-03-03 13:03:08 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 14 (/scratch/user/jronwalker/megahit/raw_reads/GF-S1S10_S4_L008.unmerged.bbmasked.fastq.gz): interleaved, 5722644 reads, 150 max length'
2020-03-03 13:03:27 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 15 (/scratch/user/jronwalker/megahit/raw_reads/GF-S4S1_S9_L008.unmerged.bbmasked.fastq.gz): interleaved, 8608920 reads, 150 max length'
2020-03-03 13:03:28 - b'ERROR sequence/io/sequence_lib.cpp : 71 - PE library number of reads is odd: 5!'
2020-03-03 13:03:28 - b'FATAL sequence/io/sequence_lib.cpp : 72 - File(s): /scratch/user/jronwalker/megahit/raw_reads/0_22-S1S1_S19_L005.unmerged.bbmasked.fastq.zip.gz'
2020-03-03 13:03:28 - Error occurs, please refer to /scratch/user/jronwalker/megahit_out_all_harvey/log for detail
2020-03-03 13:03:28 - Command: /general/software/x86_64/easybuild/software/MEGAHIT/1.2.8-GCCcore-8.2.0/bin/megahit_core_popcnt buildlib /scratch/user/jronwalker/megahit_out_all_harvey/tmp/reads.lib /scratch/user/jronwalker/megahit_out_all_harvey/tmp/reads.lib; Exit code 1

Attached is the command I am running on our server.
megahit_all_hprc.txt

Thank you!

[dombraccia]

I have had a similar issue arise when running megahit - specifically the line:

2020-03-03 13:03:28 - b'ERROR sequence/io/sequence_lib.cpp : 71 - PE library number of reads is odd: 5!'

any help on this would be great!

[AndreaQ7]

Actually I am obtaining the same error message too

[jeffkimbrel]

I am now receiving this error with v1.2.9... did anyone get any information about working around this error?