User: yifan wang

gravatar for yifan wang
yifan wang20
Reputation:
20
Status:
New User
Location:
china
Last seen:
1 year, 1 month ago
Joined:
3 years, 9 months ago
Email:
j*********@gmail.com


<progress style="position: fixed; left: 0px; bottom: 0px; display: none; z-index: 99999;"></progress><progress style="position: fixed; left: 0px; bottom: 0px; display: none; z-index: 99999;"></progress>

Posts by yifan wang

<prev • 16 results • page 1 of 2 • next >
0
votes
1
answer
667
views
1
answers
Comment: C: Markduplicates did not find output file with glob pattern
... i think you are right, i used to set tmp as ./tmp run by individual step. i will have a try using $(runtime.tmpdir) and ./tmp ...
written 14 months ago by yifan wang20
0
votes
1
answer
667
views
1
answers
Comment: C: Markduplicates did not find output file with glob pattern
... 1. home/bpvast/anaconda3/bin/cwltool **1.0.20190228200117** 2. https://github.com/Johnnywang92/GATK-CWL-WorkFlow-201903/blob/master/GATK-v1.0-Workflow.cwl 3. yesterday i did as your suggestion, the markDuplicates-2019-03-21.bam did not show in **mycache** and i upload the error message at https: ...
written 14 months ago by yifan wang20
0
votes
1
answer
667
views
1
answers
Comment: C: Markduplicates did not find output file with glob pattern
... yes, it is. I have enough space in the tmp directory ...
written 14 months ago by yifan wang20
13
votes
1
answer
667
views
1
answer
Markduplicates did not find output file with glob pattern
... [workflow ] starting step markDuplicates [step markDuplicates] start [job markDuplicates] /tmp/28h_j0bq$ docker \ run \ -i \ --volume=/tmp/28h_j0bq:/pXbDAg:rw \ --volume=/tmp/q2gfy6t7:/tmp:rw \ --volume=/tmp/zzuqc4mx/samtools-sort-2019-03-21.bam:/v ...
cwl written 14 months ago by yifan wang20 • updated 14 months ago by Michael R. Crusoe1.8k
2
votes
2
answers
571
views
2
answers
Comment: C: CWL NO JSON object could be decoded
... Thanks for your answer, it worked ...
written 15 months ago by yifan wang20
0
votes
2
answers
571
views
2
answers
Answer: A: CWL NO JSON object could be decoded
... Script## bwa_index.cwl ## class: CommandLineTool cwlVersion: v1.0 $namespaces: sbg: 'https://www.sevenbridges.com/' baseCommand: - bwa - index inputs: - id: algorithm type: string? inputBinding: position: 0 prefi ...
written 15 months ago by yifan wang20
4
votes
2
answers
571
views
2
answers
CWL NO JSON object could be decoded
... I run CWL as cwl-runner bwa_index.cwl index.yml And get ERROR Message as following /Users/yifanwang/Test/CWL_work/venv_cwl/bin/cwl-runner 1.0.20181217162649 Resolved 'bwa_index.cwl' to 'file:///Users/yifanwang/Test/CWL_work/bwa_index.cwl' Workflow error, try again with --debug for more ...
json cwl written 15 months ago by yifan wang20 • updated 7 months ago by Biostar ♦♦ 20
0
votes
2
answers
1.8k
views
2
answers
Comment: C: genome assembly, larger genome size than expect
... I am still working on platanus scaffolding here is the stat info. Total sequences 569886 Total bases 755283165 Min sequence length 100 Max sequence length 412374 Average sequence length 1325.32 Median sequence length 200.00 N25 length 47550 N50 ...
written 2.9 years ago by yifan wang20
0
votes
2
answers
1.8k
views
2
answers
Comment: C: genome assembly, larger genome size than expect
... thanks for your suggestions, i tried Platanus for assembly and i got information, the contig.fa is 1013Mb and there is 370Mb contigBubble.fa ...
written 2.9 years ago by yifan wang20
0
votes
2
answers
1.8k
views
2
answers
Comment: C: genome assembly, larger genome size than expect
... here is the info : Total sequences 2402525 Total bases 1524700266 Min sequence length 100 Max sequence length 157402 Average sequence length 634.62 Median sequence length 201.00 N25 length 7101 N50 length 2063 N75 length 524 N90 length 199 N95 length 128 As 26.62 % Ts 26.16 % Gs 18.51 % Cs 18.77 % ( ...
written 2.9 years ago by yifan wang20

Latest awards to yifan wang

Popular Question 2.9 years ago, created a question with more than 1,000 views. For genome assembly, larger genome size than expect
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1325 users visited in the last hour