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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies
MIT License
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I/O error Raised from: std.internal.file.File.__init__.3 [e] /home/vagrant/.seq/lib/seq/stdlib/internal/file.seq:14:13 #4

Closed jmkidd closed 2 years ago

jmkidd commented 2 years ago

Hi, I've installed biser using pip install biser in a conda environment running python 3.7. When running biser i get a file I/O error an a reference to /home/vagrant/.seq/lib/seq/stdlib/internal/file.seq.

Could you help troubleshoot? Is there something wrong with the prebuilt pip package?

Here is the info printed. Thanks Jeff

Running BISER on 1 genome(s): mCanLor1.2.masked

  1. Hard-masking genomes 100%|████████████████████████████████████████| 1/1 Hard-masking: 01:05s (single: 01:00s)

  2. Putative SD detection 100%|████████████████████████████████████████| 40/40 Search: 03:40s (single: 28:46s)

  3. Putative SD alignment 100%|████████████████████████████████████████| 50/50 Align: 11:13s (single: 58:13s)

  4. SD decomposition 100%|████████████████████████████████████████| 2621/2621 Decomposition: 03:22s (single: 04:25s) ERROR: BISER failed: [p] /home/jmkidd/links/kidd-lab-scratch/jmkidd-projects/miniconda3/envs/biserENV/lib/python3.9/site-packages/biser/exe/biser.exe translate -o mCanLor1.2-BISER.out.bed /nfs/turbo/jmkidddata/jmkidd-projects/people-projects/anthony-projects/test-BISER/biser-temp/biser7htlmq2n/final.bed /nfs/turbo/jmkidddata/jmkidd-projects/people-projects/anthony-projects/test-BISER/mCanLor1.2.masked.fasta [o] [e] Loading took 10.8591s [e] Translating took 0.00149958s [e] Translate took 10.8607s [e] IOError: file /nfs/turbo/jmkidddata/jmkidd-projects/people-projects/anthony-projects/test-BISER/biser-temp/biser7htlmq2n/final.bed could not be opened [e] [e] Raised from: std.internal.file.File.init.3 [e] /home/vagrant/.seq/lib/seq/stdlib/internal/file.seq:14:13

jmkidd commented 2 years ago

Update: if I use the --keep-temp option it seems to run fine.

inumanag commented 2 years ago

Let me take a look. Thanks for the report.

inumanag commented 2 years ago

Fixed. Please try v1.1 (should be available through pip).

saraebell commented 2 years ago

updating to v1.1 solved this issue for me, thank you.