pp QC~kmergenie -c 8 -m 32 input_1/DRR015801_2.fastq.gz Checking the realpath of input files. 0 input_1/DRR015801_2.fastq.gz /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie /suikou/files/m768-data2/ecoli /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie centos:centos6 quay.io/biocontainers/kmergenie:1.7051--py310r42h6cc9453_7 using docker ++ docker pull quay.io/biocontainers/kmergenie:1.7051--py310r42h6cc9453_7 1.7051--py310r42h6cc9453_7: Pulling from biocontainers/kmergenie c1a16a04cedd: Already exists 4ca545ee6d5d: Already exists 3c930ece773d: Pulling fs layer 3c930ece773d: Verifying Checksum 3c930ece773d: Download complete 3c930ece773d: Pull complete Digest: sha256:9debb7e26050bf0126f5d4c88036666c1b811dfe960e7b8e9101154dd96d9b61 Status: Downloaded newer image for quay.io/biocontainers/kmergenie:1.7051--py310r42h6cc9453_7 quay.io/biocontainers/kmergenie:1.7051--py310r42h6cc9453_7 ++ set +ex running histogram estimation Traceback (most recent call last): File "/usr/local/bin/kmergenie", line 303, in best_k = execute_once(arguments_passed_list, first_pass=first_pass) File "/usr/local/bin/kmergenie", line 279, in execute_once ntcard_wrapper(k_interval) File "/usr/local/bin/kmergenie", line 221, in ntcard_wrapper max_read_length = get_read_length(read_file_list) File "/usr/local/bin/kmergenie", line 147, in get_read_length from readfq import readfq ModuleNotFoundError: No module named 'readfq' PID: 2855280 pp runtime error. Checking the realpath of input files. 0 input_1/DRR015801_2.fastq.gz /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie /suikou/files/m768-data2/ecoli /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/QC~kmergenie centos:centos6 docker.io/c2997108/centos7:kmergenie1.7051 using docker ++ docker pull docker.io/c2997108/centos7:kmergenie1.7051 kmergenie1.7051: Pulling from c2997108/centos7 2d473b07cdd5: Pulling fs layer 9573143be6f5: Pulling fs layer 270d093aeb8c: Pulling fs layer 2d473b07cdd5: Verifying Checksum 2d473b07cdd5: Download complete 2d473b07cdd5: Pull complete 270d093aeb8c: Verifying Checksum 270d093aeb8c: Download complete 9573143be6f5: Verifying Checksum 9573143be6f5: Download complete 9573143be6f5: Pull complete 270d093aeb8c: Pull complete Digest: sha256:8af77c53150f601df27df3706a2e95587e97583f9e1c62c8e2c614adba73d1f8 Status: Downloaded newer image for c2997108/centos7:kmergenie1.7051 docker.io/c2997108/centos7:kmergenie1.7051 ++ set +ex running histogram estimation Setting maximum kmer length to: 100 bp computing histograms (from k=21 to k=91): 71 81 51 61 91 41 31 21 ntCard wall-clock time over all k values: 49 seconds fitting model to histograms to estimate best k could not fit histograms-k91.histo estimation of the best k so far: 51 refining estimation around [45; 57], with a step of 2 running histogram estimation Setting maximum kmer length to: 100 bp computing histograms (from k=47 to k=57): 57 51 53 55 47 49 ntCard wall-clock time over all k values: 42 seconds fitting model to histograms to estimate best k could not fit histograms-k91.histo table of predicted num. of genomic k-mers: histograms.dat recommended coverage cut-off for best k: 2 best k: 49 PID: 2888715