VIRTUS

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create index failed

10

Hello, I tried to create index, however, the process has failed at the stage to get transcripts.fa. The command and log is as follows: :~$ createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml INFO /usr/bin/cwltool 2.0.20200224214940...

km-2021

salmon quant issues

1

Hi, I am trying virtus first time, got an error, could you help to figure it out? salmon quant -i /var/lib/cwl/stg6e961d4d-2bda-4856-afe4-02b076648d2c/salmon_index_human -l A -1 /var/lib/cwl/stg0 97f1658-65e2-4fec-87cd-aba471ac1e4e/SRR11858782.1_1.fastp.fastq -2 /var/lib/cwl/stg095da09f-34ee-441a-a49e-d3f8dab1e5 3b/SRR11858782.1_2.fastp.fastq -p...

sunnyyakima

Tool definition failed validation error when running createindex_singlevirus.cwl

7

ERROR Tool definition failed validation: The CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: v1.0 v1.1 v1.1.0-dev1 (with --enable-dev flag only) v1.2 v1.2.0-dev1 (with --enable-dev...

jlee110

When parsing a virus-less file, an error occurs in pd.read_csv. https://github.com/yyoshiaki/VIRTUS/blob/master/tool/mk_summary_virus_count/mk_summary_virus_count.py

yyoshiaki

Parallel processing

1

Hi, I have 800 samples to run. I have calculated that the processing may take 50 days on my system. Is there a way to break up the runs into...

gailrosen

Cluster methods used by VIRTUS and heatmap issue

1

### Dear [yyoshiaki](https://github.com/yyoshiaki), ### I`m having a issue during a VIRTUS run, I have two cases: 1° case: I have 14 samples divided in 3 groups, Group 01: 4 samples...

patrick-douglas

EXITING because of FATAL ERROR: could not create output file: ...virtus143/Log.out Check if the path ... exists and you have permissions to write there

1

Hi Yoshiaki, While I was trying to run the VIRTUS.PE.cwl, it throw an error "EXITING because of FATAL ERROR: could not create output file: /media/ozy/Seagate/virtus143/Log.out Check if the path /media/ozy/Seagate/virtus143/...

ozy913

Hello thank you for developing VIRTUS and VIRTUS2. great tools I would need to use them in singulality mode trying to run the following ``` cwltool --rm-tmpdir --singularity ./VIRTUS.PE.singlevirus.cwl VIRTUS.PE.singlevirus.SRR26589924_1.moderna.sg.yaml...

antoine4ucsd