log file from Kallisto

[ale07alvarez]

Hi, I have three output files from Kallisto:

1. abundance.h5
2. abundance.txt
3. run_info.json

MultiQC is supposed to be able to read a log file from Kallisto but when I run: multiqc . in the directory containing these three files I get the following:

[INFO   ]         multiqc : This is MultiQC v1.0.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '.'
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

[ewels]

Hi @ale07alvarez,

I just had a look at how the Kallisto module works for you. The search pattern shows that it looks for any file that contains the string [quant] finding pseudoalignments for the reads. The example test data that I built the module around shows the files that it's looking for.

So, MultiQC works with Kallisto logs, not output files. To get MultiQC to work with Kallisto, you need to capture the Kallisto log output (eg. kallisto command &> samplename_kallisto.log). MultiQC will ignore the three files that you listed (unfortunately, run_info.json doesn't contain much in the way of interesting information, such as pseudo-alignment rate).

I hope this helps!

Phil

[ewels]

ps. Let me know how you get on! Feel free to re-open this issue if you're still running into trouble.

Phil

[kascchmc]

I also had this problem, but &>file.log gives a syntax error. I don't know how else to create the log file.

[ShwetaCh]

Hello @ewels

I have got the log files ready in the same directory however multiqc still did not recognize the files. Am I missing something?

Thanks!
Shweta

(base) schavan@gvl-hpc-cluster:$ multiqc .
[WARNING]         multiqc : MultiQC Version v1.11 now available!
[INFO   ]         multiqc : This is MultiQC v1.8
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /mnt/galaxy/home/schavan/projects/bulk_rna_seq/RUN1/RPTR147_PT12.4_S2.Post.QUANT
Searching 7 files..  [####################################]  100%
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

Files in the dir:

total 20G
-rw-rw-r-- 1 schavan schavan 2.1K Jan 27 20:31 RPTR147_PT12.4_S2.Post.kallisto.log
-rw-rw-r-- 1 schavan schavan 530M Jan 27 21:23 fusion.txt
-rw-rw-r-- 1 schavan schavan 7.2G Jan 27 21:23 pseudoaln.bin
-rw-rw-r-- 1 schavan schavan  592 Jan 27 21:27 run_info.json
-rw-rw-r-- 1 schavan schavan 7.6M Jan 27 21:27 abundance.tsv
-rw-rw-r-- 1 schavan schavan  92M Jan 27 22:16 abundance.h5
-rw-rw-r-- 1 schavan schavan  12G Jan 27 22:30 pseudoalignments.bam

[ewels]

Hi @kascchmc and @ShwetaCh,

Please make a new issue next time - spotting new messages on old closed issues is tough.

Please see the docs for the files that Kallisto uses: https://multiqc.info/docs/#kallisto

Note - MultiQC parses the standard out from Kallisto, not any of its output files (abundance.h5, abundance.tsv, and run_info.json). As such, you must capture the Kallisto stdout to a file when running to use the MultiQC module.

Capturing standard out and standard error to files is standard bash, it's nothing fancy or specific to either Kallisto or MultiQC. You should be able to find plenty of help online about it. For example: https://linuxize.com/post/bash-redirect-stderr-stdout/

Let me know if anything is unclear 🙂

Phil

[ShwetaCh]

@ewels My bad, you may close this, this issue is now resolved for me!
(Kallisto log files even if existing did not have the relevant info, once I fixed this, I could get MutliQC to produce appropriate reports.)