report2.tsv file generated instead of a report.tsv file which caused an error

[Bondada20]

- Upload your log file
[62:12] Cross-run analysis
[62:12] Reading quantification information: 59 files
[62:19] Quantifying peptides
[86:08] Quantification parameters: 0.27949, 0.000571631, 0.000185364, 0.268875, 0.0125771, 0.272661, 0.0109451, 0.888314, 0.0532102, 0.834404, 0.0655802, 0.203289, 2.07869, 0.0160716, 0.106948, 0.452636
[91:33] Quantifying proteins
[91:35] Calculating q-values for protein and gene groups
[91:37] Calculating global q-values for protein and gene groups
[91:37] Protein groups with global q-value <= 0.01: 8306
[91:54] Compressed report saved to diann-output/report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[91:54] Saving precursor levels matrix
[91:56] Precursor levels matrix (1% precursor and protein group FDR) saved to diann-output/report.pr_matrix.tsv.
[91:56] Saving protein group levels matrix
[91:56] Protein groups matrix saved to diann-output/report.pg_matrix.tsv.
[91:56] Saving gene group levels matrix
[91:56] Gene groups matrix saved to diann-output/report.gg_matrix.tsv.
[91:56] Saving unique genes levels matrix
[91:56] Unique genes matrix saved to diann-output/report.unique_genes_matrix.tsv.
[91:56] Manifest saved to diann-output/report.manifest.txt
[91:56] Stats report saved to diann-output/report.stats.tsv

The following warnings or errors (in alphabetic order) were detected at least the indicated number of times:
WARNING: unrecognised option [--] : 1
Finished

How to cite:
using DIA-NN: Demichev et al, Nature Methods, 2020, https://www.nature.com/articles/s41592-019-0638-x
analysing Scanning SWATH: Messner et al, Nature Biotechnology, 2021, https://www.nature.com/articles/s41587-021-00860-4
analysing PTMs: Steger et al, Nature Communications, 2021, https://www.nature.com/articles/s41467-021-25454-1
analysing dia-PASEF: Demichev et al, Nature Communications, 2022, https://www.nature.com/articles/s41467-022-31492-0
analysing Slice-PASEF: Szyrwiel et al, biorxiv, 2022, https://doi.org/10.1101/2022.10.31.514544
plexDIA / multiplexed DIA: Derks et al, Nature Biotechnology, 2023, https://www.nature.com/articles/s41587-022-01389-w
CysQuant: Huang et al, Redox Biology, 2023, https://doi.org/10.1016/j.redox.2023.102908
using QuantUMS: Kistner at al, biorxiv, 2023, https://doi.org/10.1101/2023.06.20.545604
[91:57] Log saved to diann-output/report.log.txt
Process 'DIA-NN' finished, exit code: 0
DIA-NN: Propagate information [Work dir: /fp/path_to_working_directory/diann-output]
java -cp /fragpipe_bin/fragPipe-22.0/fragpipe/tools/batmass-io-1.33.4.jar:/fragpipe_bin/fragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/fragpipe_bin/fragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation /fp/path_to_working_directory
java.nio.file.NoSuchFileException: /fp/path_to_working_directory/diann-output/report.tsv
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
at java.base/java.nio.file.Files.newByteChannel(Files.java:432)
at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:422)
at java.base/java.nio.file.Files.newInputStream(Files.java:160)
at java.base/java.nio.file.Files.newBufferedReader(Files.java:2922)
at java.base/java.nio.file.Files.newBufferedReader(Files.java:2955)
at com.dmtavt.fragpipe.tools.diann.Propagation.editReport(Propagation.java:213)
at com.dmtavt.fragpipe.tools.diann.Propagation.propagate(Propagation.java:190)
at com.dmtavt.fragpipe.tools.diann.Propagation.main(Propagation.java:69)
Process 'DIA-NN: Propagate information' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 2 remaining tasks

**- Describe the issue or question:**
I am running FragPipe via the Linux command line, and it seems that DIA-NN 2.0 is generating a "report2.tsv" file instead of a "report.tsv" file, which caused my job to be canceled (see screenshot). Do you have any idea why this is happening?

When I ran another job and manually created the "report.tsv" file in the "diann-output" folder, the job completed without an error (see screenshot). However, both the report2.tsv file (which caused FragPipe to cancel) and the manually created report.tsv file in the diann-output folder are empty.

Also, can I use the main output "report.parquet" for downstream analysis in R regardless of the error?

Thanks!

[Bondada20]

I saw this reply from Diann issues: vdemichev/DiaNN#1407

Q: the document "Report saved to \results\report.tsv." disappeared

A: DIA-NN now writes reports in .parquet format, this is easily accessible from R or Python, please see https://github.com/vdemichev/DiaNN?tab=readme-ov-file#output

[Bondada20]

By the way, the above error also occured for diann-2.0.2. I tested diann-1.8.1.8 and it ran without any error (see screenshot).

I think I will stick to this version for now. But it would be nice to use the latest version of diann with fragpipe.

[fcyu]

Thanks for the feedback. DIA-N 2.0+ generates slightly different reports compared to the old version. The next release of FragPipe will have this issue addressed.

Similar to #1998

Best,

Fengchao

[Bondada20]

Thanks! What do you think of me using the "report.parquet" for downstream analysis in R regardless of the error?

[fcyu]

Yes, you can do that. That error won't affect the results, just some "auxiliary" columns are missing.

Best,

Fengchao