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metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
MIT License
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Help: "the file did not appear to be a SAM or BAM format file" #18

Open Danrui-Wang opened 1 year ago

Danrui-Wang commented 1 year ago

Hi @metaGmetapop , thank you for developing MetaPop! At the very start, I encountered a problem, " the file did not appear to be a SAM or BAM format file". Then I downloaded the test files, but the same error occurred again. "MetaPop Started at: 18/10/2022 14:11:58 Checking: Kang_0011_ST001_A_only_virome_viruses for correctness... the file did not appear to be a SAM or BAM format file. Skipping this file." I'm pretty sure the files are in BAM format. Maybe something else went wrong. Do you have any advice?

marina-vn commented 1 year ago

Hi @Danrui-Wang , I have run into the same problem, did you get any solution?

yugen-miyahara commented 1 year ago

got the same issues, here is the error:

metapop --input_samples ~/for_metapop/bam --reference ~/for_metapop/reference --norm ~/formetapop/Kang test_dataset_bp_numbers.txt Using: 8 threads. Combining files: /home/miyyu932/for_metapop/reference/Reference_Viral_Populations.fasta samtools: /home/miyyu932/miniconda3/envs/metapop/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/miyyu932/miniconda3/envs/metapop/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/miyyu932/miniconda3/envs/metapop/bin/../lib/libncursesw.so.6: no version information available (required by samtools) Genes will be predicted with prodigal and placed in Genomes and Genes. MetaPop Started at: 11/01/2023 18:56:18

Checking: Kang_0011_ST001_A_only_virome_viruses for correctness... the file did not appear to be a SAM or BAM format file. Skipping this file. Checking: Kang_0011_ST003_A_only_virome_viruses for correctness... the file did not appear to be a SAM or BAM format file. Skipping this file. Checking: Kang_0037_ST001_A_only_virome_viruses for correctness... the file did not appear to be a SAM or BAM format file. Skipping this file. Traceback (most recent call last): File "/home/miyyu932/miniconda3/envs/metapop/bin/metapop", line 8, in sys.exit(main()) File "/home/miyyu932/miniconda3/envs/metapop/lib/python3.7/site-packages/metapop/metapop_main.py", line 297, in main metapop.metapop_filter.filt(original_bams, filter_command_base, bdb, threads, mag_contig_dict, mag_length_dict, joined_fastas) File "/home/miyyu932/miniconda3/envs/metapop/lib/python3.7/site-packages/metapop/metapop_filter.py", line 101, in filt pool = multiprocessing.Pool(min(threads, len(md_files))) File "/home/miyyu932/miniconda3/envs/metapop/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/home/miyyu932/miniconda3/envs/metapop/lib/python3.7/multiprocessing/pool.py", line 169, in init raise ValueError("Number of processes must be at least 1") ValueError: Number of processes must be at least 1

marina-vn commented 1 year ago

Did you made any progress with this?

arisandz commented 1 year ago

Hi! I had the same issue. It resolved when i updated the samtools.