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zlib.error

See original GitHub issue

Greeting Hadrien, i have been trying to install with pip and pip3, although it says install is complete when i try to run it iss command not found. I have installed it with conda and im running this command iss generate --ncbi bacteria --n_genomes_ncbi 10 --model hiseq --output miseq_ncbi and it gives me the below output, the command works just fine on my other computer which i have ubuntu 14.04 while this one has ubuntu 18.04 INFO:iss.app:Starting iss generate INFO:iss.app:Using kde ErrorModel INFO:iss.download:Searching for bacteria to download INFO:iss.download:Downloading GCF_000204155.1 INFO:iss.download:Downloading GCF_008247605.1 INFO:iss.download:Downloading GCF_002591135.1 INFO:iss.download:Downloading GCF_008245065.1 INFO:iss.download:Downloading GCF_001735765.2 INFO:iss.download:Downloading GCF_002447735.1 INFO:iss.download:Downloading GCF_005221965.1 INFO:iss.download:Downloading GCF_900638625.1 INFO:iss.download:Downloading GCF_900322585.1 Traceback (most recent call last): File “/home/celik/anaconda3/envs/my_env/bin/iss”, line 10, in <module> sys.exit(main()) File “/home/celik/anaconda3/envs/my_env/lib/python3.7/site-packages/iss/app.py”, line 542, in main args.func(args) File “/home/celik/anaconda3/envs/my_env/lib/python3.7/site-packages/iss/app.py”, line 111, in generate_reads g, n, args.output + ‘_ncbi_genomes.fasta’) File “/home/celik/anaconda3/envs/my_env/lib/python3.7/site-packages/iss/download.py”, line 51, in ncbi assembly_to_fasta(url, output) File “/home/celik/anaconda3/envs/my_env/lib/python3.7/site-packages/iss/download.py”, line 75, in assembly_to_fasta request.content, zlib.MAX_WBITS | 32).decode() zlib.error: Error -3 while decompressing data: incorrect header check

Can you help me out with this?

Issue Analytics

State:
Created 4 years ago
Comments:12 (7 by maintainers)

Top GitHub Comments

1reaction

arthurvinxcommented, Jan 28, 2021

Thanks @HadrienG.

I intended to download random sequences and I noticed that the abundance file, automatically created, keeps only unique IDs.

Thus, even not setting a seed and merging files with duplicated genomes, this file helped me to keep track of the correct number of different genomes.

Also, thanks to the use of the sequence ID as header, it was easy to get the number of reads for each sequence.

The iss is indeed a great and well implemented software.

0reactions

HadrienGcommented, May 12, 2020

Should be fixed (finally!) in 1.4.6

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