{"action":"closed","issue":{"url":"https://api.github.com/repos/meren/anvio/issues/383","repository_url":"https://api.github.com/repos/meren/anvio","labels_url":"https://api.github.com/repos/meren/anvio/issues/383/labels{/name}","comments_url":"https://api.github.com/repos/meren/anvio/issues/383/comments","events_url":"https://api.github.com/repos/meren/anvio/issues/383/events","html_url":"https://github.com/meren/anvio/issues/383","id":167067578,"number":383,"title":"anvi-self-test fails: input_file_path issue/bam files not found","user":{"login":"jwippler","id":20599545,"avatar_url":"https://avatars.githubusercontent.com/u/20599545?v=3","gravatar_id":"","url":"https://api.github.com/users/jwippler","html_url":"https://github.com/jwippler","followers_url":"https://api.github.com/users/jwippler/followers","following_url":"https://api.github.com/users/jwippler/following{/other_user}","gists_url":"https://api.github.com/users/jwippler/gists{/gist_id}","starred_url":"https://api.github.com/users/jwippler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jwippler/subscriptions","organizations_url":"https://api.github.com/users/jwippler/orgs","repos_url":"https://api.github.com/users/jwippler/repos","events_url":"https://api.github.com/users/jwippler/events{/privacy}","received_events_url":"https://api.github.com/users/jwippler/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2016-07-22T15:13:09Z","updated_at":"2016-07-28T09:08:22Z","closed_at":"2016-07-28T09:08:22Z","body":"Dear developers,\r\n\r\nI've installed anvio and all required dependencies (at least they work when called individually and they are all in $PATH), but when I run anvi-self-test, I get the following error:\r\n\r\n```\r\n[Fri Jul 22][16:46:10][jwippler@sunray-1][~]\r\n$ anvi-self-test --debug\r\n\r\n\r\n:: Output directory ...\r\n\r\n/tmp/tmpXL1NU6/test-output\r\n\r\n\r\n\r\n:: Anvo'o version ...\r\n\r\nAnvi'o version ...............................: 2.0.2\r\nProfile DB version ...........................: 16\r\nContigs DB version ...........................: 6\r\nSamples information DB version ...............: 2\r\nAuxiliary HDF5 DB version ....................: 1\r\nUsers DB version (for anvi-server) ...........: 1\r\n\r\n\r\n:: Initializing raw BAM files ...\r\n\r\n[22 Jul 16 16:47:35 SORT] Sorting BAM File... May take a while depending on the size.                                                                                open: No such file or directory\r\nSorted BAM File ..............................: /tmp/tmpXL1NU6/test-output/SAMPLE-01.bam                                                                              \r\n\r\n\r\nConfig Error: Sorry. Something went wrong. Samtools thinks it generated the sorted output, yet\r\n              it is not there :(                                                              \r\n\r\n\r\n\r\nAnvi'o's self-test is done, and the temporary output files are still here: /tmp/tmpXL1NU6\r\n```\r\n\r\nSeems that pysam can't find the bam files, because input_file_path isn't set properly:\r\n\r\n```\r\n[Fri Jul 22][17:00:19][jwippler@sunray-1][~/tools/anvio/bin]\r\n$ cat anvi-init-bam \r\n\r\n[part not shown]\r\n\r\nfilesnpaths.is_file_exists(input_file_path)\r\n    filesnpaths.is_output_file_writable(output_file_path)\r\n\r\n    progress.new('SORT')\r\n    progress.update('Sorting BAM File... May take a while depending on the size.')\r\n\r\n    pysam.sort(\"-o\", output_file_path, input_file_path)\r\n    progress.end()\r\n\r\n    run.info('Sorted BAM File', output_file_path)\r\n    if not os.path.exists(output_file_path):\r\n        raise ConfigError, \"Sorry. Something went wrong. Samtools thinks it generated the sorted output, yet it is not there :(\"\r\n\r\n[part not shown]\r\n```\r\n\r\nIn any case, the bam files are present in the test directory of anvi'o:\r\n\r\n```\r\n[Fri Jul 22][16:58:54][jwippler@sunray-1][~/tools/anvio/tests/sandbox]\r\n$ l\r\ntotal 1.5M\r\ndrwxr-xr-x 2 jwippler symbiosis    7 2016-07-22 16:14 anvi_pangenome_files\r\ndrwxr-xr-x 3 jwippler symbiosis    3 2016-07-22 16:14 anvi_server_files\r\ndrwxr-xr-x 2 jwippler symbiosis    6 2016-07-22 16:14 BAMs_SF\r\ndrwxr-xr-x 2 jwippler symbiosis    4 2016-07-22 16:14 example_external_collections\r\ndrwxr-xr-x 2 jwippler symbiosis    4 2016-07-22 16:14 example_files_for_centrifuge_taxonomy\r\ndrwxr-xr-x 2 jwippler symbiosis    5 2016-07-22 16:14 example_files_for_external_binning_results\r\ndrwxr-xr-x 2 jwippler symbiosis    6 2016-07-22 16:14 external_hmm_profile\r\ndrwxr-xr-x 2 jwippler symbiosis   10 2016-07-22 16:14 files_for_manual_interactive\r\ndrwxr-xr-x 2 jwippler symbiosis    6 2016-07-22 16:14 myrast_cmdline\r\ndrwxr-xr-x 2 jwippler symbiosis    5 2016-07-22 16:14 myrast_gui\r\ndrwxr-xr-x 2 jwippler symbiosis    2 2016-07-22 16:40 test-output\r\n-rw-r--r-- 1 jwippler symbiosis 1.7K 2016-07-22 16:14 additional_view_data.txt\r\n-rw-r--r-- 1 jwippler symbiosis 3.6K 2016-07-22 16:14 additional_view.txt\r\n-rw-r--r-- 1 jwippler symbiosis   58 2016-07-22 16:14 adjacent_positions_for_linkmers.txt\r\n-rw-r--r-- 1 jwippler symbiosis 226K 2016-07-22 16:14 Brown_et_al-CPR-Campbell_et_al_BSCG.txt\r\n-rw-r--r-- 1 jwippler symbiosis 3.2K 2016-07-22 16:14 concoct.txt\r\n-rw-r--r-- 1 jwippler symbiosis  56K 2016-07-22 16:14 contigs.fa\r\n-rw-r--r-- 1 jwippler symbiosis   61 2016-07-22 16:14 distant_positions_for_linkmers.txt\r\n-rw-r--r-- 1 jwippler symbiosis  337 2016-07-22 16:14 example_clustering_configuration.ini\r\n-rw-r--r-- 1 jwippler symbiosis 4.1K 2016-07-22 16:14 example_external_gene_calls.txt\r\n-rw-r--r-- 1 jwippler symbiosis 5.4K 2016-07-22 16:14 example_gene_functions_input_matrix.txt\r\n-rw-r--r-- 1 jwippler symbiosis   59 2016-07-22 16:14 example_genes_of_interest.txt\r\n-rw-r--r-- 1 jwippler symbiosis  36K 2016-07-22 16:14 example_interpro_output.tsv\r\n-rw-r--r-- 1 jwippler symbiosis  481 2016-07-22 16:14 example_interpro_output.tsv.README\r\n-rw-r--r-- 1 jwippler symbiosis    6 2016-07-22 16:14 sample_CONCOCT_bin_id.txt\r\n-rw-r--r-- 1 jwippler symbiosis   85 2016-07-22 16:14 sample_contig_ids.txt\r\n-rw-r--r-- 1 jwippler symbiosis   12 2016-07-22 16:14 sample_gene_call_ids.txt\r\n-rwxr-xr-x 1 jwippler symbiosis 536K 2016-07-22 16:14 SAMPLE-RAW-01.bam\r\n-rwxr-xr-x 1 jwippler symbiosis 159K 2016-07-22 16:14 SAMPLE-RAW-02.bam\r\n-rwxr-xr-x 1 jwippler symbiosis 614K 2016-07-22 16:14 SAMPLE-RAW-03.bam\r\n-rw-r--r-- 1 jwippler symbiosis  152 2016-07-22 16:14 samples-information.txt\r\n-rw-r--r-- 1 jwippler symbiosis  163 2016-07-22 16:14 samples-order.txt\r\n-rw-r--r-- 1 jwippler symbiosis 1.7K 2016-07-22 16:14 short_reads_for_SNV_testing.ini\r\n-rw-r--r-- 1 jwippler symbiosis 1.3K 2016-07-22 16:14 single_contig.fa\r\n-rw-r--r-- 1 jwippler symbiosis  168 2016-07-22 16:14 smtp_config_sample.ini\r\n```\r\nI'm not good enough at reading python code to understand where the issue is coming from. \r\nTherefore any help from you wizards would be much appreciated (expecto patronum!)\r\nMany thanks in advance!\r\n\r\nJuliane\r\n"}}
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