Example of multiple paired-end fastq samples in config_job file
vmkalbskopf opened this issue · 4 comments
Hi!
This looks like it will greatly simplify my workflows. But could you give an example how I would specify multiple paired-end fastq files? For instance I have the following files I'd like to analyse:
AA3.r1.fq.gz
AA3.r2.fq.gz
CVS.r1.fq.gz
CVS.r2.fq.gz
TRR.r1.fq.gz
TRR.r2.fq.gz
Hi, thanks for interest in VAP. This is a great question that wasn't explicitly pointed out.
VAP is able to process multiple single/paired-end fastq files using the same configuration file specification:
FASTQ = /path/to/all_fastq_files/*gz
The wildcard (*) specifies all the files in the folder (/path/to/all_fastq_files) are input files and they will be sorted and grouped based on their samplename and read (r1 and r2). The additional (gz) specifies only files ending with gz should be processed.
example of the config-specifications:
- /path/to/all_fastq_files/gz = all files in all_fastq_files folder that end with gz.
- /path/to/all_fastq_files/AAgz = all files in all_fastq_files folder that start with 'AA' and end with 'gz'
Your example files uses the proper fastqfile naming scheme for paired-end reads, so it should run as expected if all the files are in the same folder.
Hope this helps.
OK! Good to know!
My real sample names are more complex, but still have regular patterns, though usually without the r to indicated read direction for the pair. I'll let you know how it goes when I start the analysis.
@modupeore could you have a look at the attached error log file and let me know if my analysis is progressing accordingly? The analysis is running on the server but I think something is not right.
VAP-01-26-22_082815.txt
It looks like your STAR package is not properly configured. A lot of required packages are missing and because of this the STAR alignment (.sam) was not generated. This is a snippet from the first few lines:
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
/opt/exp_soft/STAR-2.7.9a/STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /opt/exp_soft/STAR-2.7.9a/STAR)
cp: cannot stat '2PASS/SRX10603401_SRR14240732.2nd.Aligned.out.sam': No such file or directory
[E::hts_open_format] Failed to open file SRX10603401_SRR14240732.2nd.Aligned.out.sam
samtools view: failed to open "SRX10603401_SRR14240732.2nd.Aligned.out.sam" for reading: No such file or directory