Hi, I am trying to use hiclib for analysis of Hi-C data. I have successfully used it in the past, but now I have a problem with mapping reads to a genome. After the first iteration and creation of fastq.gz file with reads for the second iteration (it's size stops rising) the programme gets stuck. You can see three terminal windows here, with the running programme, top and iotop. Python uses a lot of memory, but there is no processor usage. And it doesn't write anything to disk, though reads something. And this lasts for over 1hr. I tried with both gzip and pigz, looks the same. I believe this is not normal behaviour? Log of what you see in the first terminal is attached.
And this is how I run mapping:
mapping.iterative_mapping( bowtie_path='/usr/bin/bowtie2', bowtie_index_path='/media/ilya/SSD/genomes/Dd/index/Dd', fastq_path='../fastq/repA/read1.fastq.bz2', out_sam_path='../bams/repA/forw.bam', min_seq_len=20, len_step=5, nthreads=8, #max_reads_per_chunk = 10000000, #optional, on low-memory machines temp_dir='tmp', # optional, keep temporary files here bowtie_flags='--very-sensitive', bash_reader='bzcat')
I am running Ubuntu 14.04 on a computer with 8Gb RAM, i7-4702MQ processor and use the latest mirnylib/hiclib (installed both with
pip install bitbucket... yesterday).