There was an error while finishing writing a bigWig file! The output is likely truncated.

[lubitelpospat]

Dear @lubitelpospat,
I could reproduce the error. It happens when the alignment file does not contain any coverage for ERCCs or SIRVs. I have implemented a warning in commit #6.

Originally posted by @entzian in #6
Hello @entzian,
Sorry, I had to open a new issue because I don't have the right permissions to re-open my previous issue.
I checked both my alignment and quantification files - they both return many sequences mapping to SIRVs and many SIRV/ERCC features quantified. I used joined fasta and GTF files, according to the recently-updated README.
Can you please help me to further troubleshoot this?

[entzian]

Dear @lubitelpospat,
thanks for contacting our tech support and sharing the example data. I could not reproduce the error with the example data. I can confirm that the one sample contains ERCCs and SIRVs. When I execute the command I get the correct output:

SIRVsuite -i config.csv -o output_all -a
2025-02-05 13:12:55 INFO     helper: reading sample sheet
2025-02-05 13:12:57 INFO     SIRV_concentration: creating SIRV E0 concentration boxplot
2025-02-05 13:12:58 INFO     SIRV_concentration: creating SIRV E0 concentration heatmap
2025-02-05 13:13:02 INFO     ERCC_correlation: calculating correlation of ERCC spike-in ratios
2025-02-05 13:13:03 INFO     SIRVset_coverage: calculating spike-in gene coverage

The file config.csv contains:

sample_name;alignment_path;counting_path;read_orientation;counting_feature;replication_group
sample_1;./path-to-the-bam-file/bam-file.bam;./path-to-transcripts-summary-file/transcripts_summary_file.dat;FWD;transcript;none

Could you please make sure that you have installed the latest version. When you execute

SIRVsuite --version

you should see

SIRVsuite 0.1.3

I have installed in with:

python3.9 -m pip install SIRVsuite