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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
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zcat: can't stat #85

Closed EwersAquaGenomics closed 7 months ago

EwersAquaGenomics commented 7 months ago

Dear Rosemeis, I installed pcangsd as described on your github page onto my Mac (os Ventura). I generated a beagle file like so in angsd: % angsd -GL 2 -out input -nThreads 4 -doGlf 2 -doMajorMinor 1 -doMaf 2 -SNP_pval 1e-6 -bam GER-BE-Asia.bamlist

But when I ran pcangsd as shown below, I got an error message... Some googling suggests this may be a mac issue. Do you have any ideas how I could solve this?

Thank you! Christine

% pcangsd -b input.beagle.gz -o output/trial

PCAngsd v1.21 Jonas Meisner and Anders Albrechtsen. Using 20 thread(s).

Parsing Beagle file. zcat: can't stat: input.beagle.gz (input.beagle.gz.Z): No such file or directory Traceback (most recent call last): File "/Users/ewers.christine/opt/anaconda3/bin/pcangsd", line 8, in sys.exit(main()) File "/Users/ewers.christine/opt/anaconda3/lib/python3.8/site-packages/pcangsd/pcangsd.py", line 158, in main L = reader_cy.readBeagle(args.beagle) File "pcangsd/reader_cy.pyx", line 14, in pcangsd.reader_cy.readBeagle File "pcangsd/reader_cy.pyx", line 52, in pcangsd.reader_cy.readBeagle ValueError: negative dimensions are not allowed

EwersAquaGenomics commented 7 months ago

I found a solution to my problem. I added ".Z" to the end of my beagle file and specified this file (with the .Z ending) in the pcangsd command like so:

% pcangsd -b input.beagle.gz.Z -o output/trial