Error in fastqc

[antoniaprn]

Hello,

I keeping get this error with the name of the files(???). I file names are like this: 1_R1.fastq.gz 1_R2.fastq.gz 2_R1.fastq.gz 2_R2.fastq.gz and in metadata file I wrote like this:: sample group subject 1 C 2 T

(rasflow)[xxxxxxx RASflow-master]$ python main.py
main.py:8: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml.load(yamlfile)
Is quality control required?
 True
Is trimming required?
 False
Which mapping reference will be used?
 genome
Is DEA required?
 True
Is visualization required?
 True
Please double check the information above
Do you want to continue? (y/n)
y
Start RASflow on project: augusto
Are you sure that you want to do Quality Control?
 If yes, type 'y'; if not, type 'n' and set 'QC' to 'no' in the config file
y
Start Quality Control!
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       end
        2       getReads
        2       qualityControl
        1       summaryReport
        6

[Tue Mar 28 12:55:39 2023]
rule getReads:
    output: output/augusto/augusto/reads/1_forward.fastq.gz, output/augusto/augusto/reads/1_reverse.fastq.gz
    jobid: 5
    wildcards: sample=1

Job counts:
        count   jobs
        1       getReads
        1
cp: cannot stat 'home/xxxxxx/teste/1_*R1*.f*q.gz': No such file or directory
[Tue Mar 28 12:55:39 2023]
Error in rule getReads:
    jobid: 0
    output: output/augusto/augusto/reads/1_forward.fastq.gz, output/augusto/augusto/reads/1_reverse.fastq.gz

RuleException:
CalledProcessError in line 24 of /home/xxxxxx/RASflow-master/workflow/quality_control.rules:
Command ' set -euo pipefail;  scp -i None home/xxxxx/teste/1_*R1*.f*q.gz output/augusto/augusto/reads/1_forward.fastq.gz ' returned non-zero exit status 1.
  File "/home/xxxxxxx/RASflow-master/workflow/quality_control.rules", line 24, in __rule_getReads
  File "/home/xxxxxx/.conda/envs/rasflow/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/xxxxxxxx/RASflow-master/.snakemake/log/2023-03-28T125538.626392.snakemake.log
Quality control is done!
 Please check the report and decide whether trimming is needed
 Please remember to turn off the QC in the config file!

What I can be doing wrong? Thankyou in advance!!!

[zhxiaokang]

Hi, according to the error 'home/xxxxxx/teste/1_*R1*.f*q.gz': No such file or directory, it seems that your FASTQ files are not at home/xxxxxx/teste/. Please double check.

Btw, this line output: output/augusto/augusto/reads/1_forward.fastq.gz, output/augusto/augusto/reads/1_reverse.fastq.gz also looks suspicious. It seems that there's something wrong with your file paths' settings.