Bismark-mapper error

[jeff-godwin]

Hi team,
I have set up methystar on my system. Thanks for the simple and seamless process. While running the pipeline, there's an issue in the Bismark mapping step. The trimmomatic and genome indexing is running fine. The output log is slightly similar to issue #1, but the solution is not applicable to my problem. I have attached the log file. Kindly let me know your thoughts.

Sample1.log
Thanks,
Jeff

[jeff-godwin]

There is some error in decompression of trimmomatic putput files through gzip.
Paired-end alignments will be performed

The provided filenames for paired-end alignments are /media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_1.fastq.gz and /media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_2.fastq.gz

gzip: stdout: Broken pipe
Finished subdividing /media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_1.fastq.gz for PID: 0 and offset 2 (sequences written out: 0)

Using the subset file >Sample1_paired_1.fastq.gz.temp.2< as new in-file 1 (instead of >/media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_1.fastq.gz<)

[rashmihazarika]

Hi Jeff,
I also see the following line in your log,

Core usage currently set to more than 20 threads. This might fail horribly but let's see how it goes... (set value: 50)

I am not very sure what might be happening but given the large number of contigs in your genome it may be helpful to lower the number of threads. Also, I guess you are using Samtools (Ver. > 1.9 ).

[jeff-godwin]

Hi Rashmi,

Thanks for getting back. I will try with fewer CPU threads.
Is there an issue with using samtools 1.12. The installation guide mentions samtools (Ver. > 1.9 ). Which would be an optimal version?