{"action":"opened","issue":{"url":"https://api.github.com/repos/chrisquince/DESMAN/issues/30","repository_url":"https://api.github.com/repos/chrisquince/DESMAN","labels_url":"https://api.github.com/repos/chrisquince/DESMAN/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/chrisquince/DESMAN/issues/30/comments","events_url":"https://api.github.com/repos/chrisquince/DESMAN/issues/30/events","html_url":"https://github.com/chrisquince/DESMAN/issues/30","id":359361927,"node_id":"MDU6SXNzdWUzNTkzNjE5Mjc=","number":30,"title":"ERROR estimateStrainCountDesman (3) with desmanflow","user":{"login":"xvazquezc","id":14157565,"node_id":"MDQ6VXNlcjE0MTU3NTY1","avatar_url":"https://avatars3.githubusercontent.com/u/14157565?v=4","gravatar_id":"","url":"https://api.github.com/users/xvazquezc","html_url":"https://github.com/xvazquezc","followers_url":"https://api.github.com/users/xvazquezc/followers","following_url":"https://api.github.com/users/xvazquezc/following{/other_user}","gists_url":"https://api.github.com/users/xvazquezc/gists{/gist_id}","starred_url":"https://api.github.com/users/xvazquezc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xvazquezc/subscriptions","organizations_url":"https://api.github.com/users/xvazquezc/orgs","repos_url":"https://api.github.com/users/xvazquezc/repos","events_url":"https://api.github.com/users/xvazquezc/events{/privacy}","received_events_url":"https://api.github.com/users/xvazquezc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-12T08:07:39Z","updated_at":"2018-09-12T08:07:39Z","closed_at":null,"author_association":"NONE","body":"Hi there,\r\n\r\nafter dealing with the Phylosift issue (#28), I was able to run the test data to completion without problem. Now I'm getting an error when DESMAN tries to estimate the strain count, not sure if could be due to the limited number of samples. Any idea?\r\n\r\nThank you in advance,\r\nXabi\r\n\r\n```\r\n$ ~/DESMAN/scripts/desmanflow.nf --speciescontigs=contig_list.txt --assembly=../../final.contigs.1000.fa --inputreads=../../../../fastq/\r\nN E X T F L O W  ~  version 0.31.1\r\nLaunching `/home/xabi/DESMAN/scripts/desmanflow.nf` [cranky_varahamihira] - revision: 46958c6af8\r\n[h2hco3, [/home/xabi/Desktop/SBI_projects/miriam/clive/fastq/h2hco3.r1.fq.gz, /home/xabi/Desktop/SBI_projects/miriam/clive/fastq/h2hco3.r2.fq.gz]]\r\n[isoprene, [/home/xabi/Desktop/SBI_projects/miriam/clive/fastq/isoprene.r1.fq.gz, /home/xabi/Desktop/SBI_projects/miriam/clive/fastq/isoprene.r2.fq.gz]]\r\n[warm up] executor > local\r\n[6b/70844a] Submitted process > mapReads (1)\r\n[02/5f5bb8] Submitted process > mapReads (2)\r\n[86/6f4b77] Submitted process > findEliteGenes\r\n[01/5a43f8] Submitted process > elitePileups (1)\r\n[4e/32277b] Submitted process > elitePileups (2)\r\n[66/107860] Submitted process > callEliteVariants\r\n[b0/7ae068] Submitted process > estimateStrainCountDesman (1)\r\n[53/028d56] Submitted process > estimateStrainCountDesman (2)\r\n[5e/a2e284] Submitted process > estimateStrainCountDesman (4)\r\n[06/a14411] Submitted process > estimateStrainCountDesman (3)\r\n[a4/00e91f] Submitted process > estimateStrainCountDesman (5)\r\n[14/6a2e2a] Submitted process > estimateStrainCountDesman (7)\r\n[24/60858b] Submitted process > estimateStrainCountDesman (8)\r\n[18/09f61f] Submitted process > estimateStrainCountDesman (6)\r\n[a7/5977de] Submitted process > estimateStrainCountDesman (13)\r\nERROR ~ Error executing process > 'estimateStrainCountDesman (3)'\r\n\r\nCaused by:\r\n  Process `estimateStrainCountDesman (3)` terminated with an error exit status (1)\r\n\r\nCommand executed:\r\n\r\n  /home/xabi/DESMAN/bin/desman outputsel_var.csv -e outputtran_df.csv -o cluster_4_1 -r 1000 -i 100 -g 4 -s 1 > cluster_4_1.out\r\n  cp */fit.txt fit_4_1.txt\r\n\r\nCommand exit status:\r\n  1\r\n\r\nCommand output:\r\n  (empty)\r\n\r\nCommand error:\r\n  Up and running. Check cluster_4_1/log_file.txt for progress\r\n  /home/xabi/.local/lib/python3.5/site-packages/numpy/core/fromnumeric.py:2957: RuntimeWarning: Mean of empty slice.\r\n    out=out, **kwargs)\r\n  /home/xabi/.local/lib/python3.5/site-packages/numpy/core/_methods.py:73: RuntimeWarning: invalid value encountered in true_divide\r\n    ret, rcount, out=ret, casting='unsafe', subok=False)\r\n  cp: cannot stat '*/fit.txt': No such file or directory\r\n\r\nWork dir:\r\n  /home/xabi/Desktop/SBI_projects/miriam/clive/megahit_coassembly/anvio/MAGs/Bin_1/work/06/a14411cfc1fc6ce73eaf28658394b9\r\n\r\nTip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`\r\n\r\n -- Check '.nextflow.log' file for details\r\nWARN: Killing pending tasks (4)\r\n```"}}
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