QC~kmergenie

input_1:FASTQ(.gz)

input_1/DRR015801_2.fastq.gz

Command

Output

histograms_report.html

Log

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