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Error: Network unreachable #57

Open tfaitova1 opened 7 months ago

tfaitova1 commented 7 months ago

Hi Oskar

I am facing an issue with running binny at PBS like server. After it finishes 8/8 jobs, it's complaining about establishing connestion to network: "Failed to establish a new connection: [Errno 101] Network is unreachable"

Full error file: runbinny.pbs.errors.txt

Header of assembly fasta by megahit:

k141_88732 flag=1 multi=3.0000 len=1671 CCTGTACGCAGTGGCGAGGCAGTGGGAAGCATTAAAGATTTTAAATCCATCCGCTTCATGCGTATGTTCCTGACCGGATTTGAGAAACCCGTTGTACTACGTTTCGCCACACTCGAATTAGTACGTGGTGAATGGCGTACCTATACCGATGCCTTGAACAACACACAGCAAGGTGCTTCTACCACCAGTTCCGCTACATTGGATGTATCTGCCGTCAACATCGAAGAAAACGGTGATCGCACCCCGGTAAACTATGTGATGCCTCCTGGAATTTCCCGCGTCATCGATCCCGGACAACCGCAACTCCGTCAACAGAATGAACAAGCCATGAGCTTGAAGCTGGAAAAGTTGGCTCCCGGTGATGCCCGTGCCGTCTACAAAAATACCGGTATGGACATGAGGCAGTACAAACGCCTGCAAATGTTTGCCCATGCCGAAGCCTTACCCGATCTCAGTACTGACCCACAAGACGGTGAGCTCTCCGTATTTATCCGCCTCGGTTCAGACTATCGTAGCAATTATTATGAATACGAAATTCCACTCACACTCACTCCCCACGGAGAGTATAATGGAAGCACTGCTGCCGGTTGCCTTGCCGTCTGGCCTAAGTCAAATAATCTGGATATCGACCTCAGTGTGCTGACCAATGCAAAAAAAGCACGCAATCGCCTGAAGAATATTTCAAATAGTGGTGTAACCTATGCCAAAGTCTATTCTGAATACGATCCGGATAAGCCTGCTAACAAAATAAGTGTAATTGGTAATCCTTCGTTGGCAGAAGTAAAGACCTTAATGATCGGAGTTCGCAATAATTCTCGTACTGTCAAGTCGGCAGAAGTCTGGGTAAACGAACTGCGTCTCACCGAATTCAATGAAGAAGGAGGTTGGGCTGCACAGGGCAATCTCAATGTGCAACTCTCTGATATAGGTAGCATCAATCTGGCCGGACACATGGAAACAGCCGGTTTCGGCGGATTGGAACAAAGTGTCAGTGAACGCCGTCTGGATGACTACTATCAATACAGCTTCACTACTACATTCGACCTTGGACGCTTCTTTCCCAAGAAAGCCAAACTGACTGCACCCATTTATTTCTCCTACTCCAAAGAAGCCACTACGCCCAAGTATAATCCGCTGGACAAAGATATGTTGCTGGATGATGCGCTTGATGCCTGCACTACCGATTGGGAACGCGACTCACTGATGAATATAGCCCGCGAAATTACTACTTACCGTAATTTCAGCCTCAGCAATGCACGGCTGGGTATCACCAGTAAGAATCCCATGCCATACGATCCGGGAAACTTTACTTTCAGCTACTCCCGTTCCCTACGTCATAATCAAGGCAGTACTACCGCCTATGAAAATGAAACAGACTGGCGTGCTGCTATGACTTATAACTACGCTCCCATATACCGTCCATGGGAACCTTTCAAAAGCATGGAGAACAAGTCTCCCTGGATGCGTTTTATTAAGGAATTCAACCTGAACTGGCTACCTCAAAGTATATCATTCAATACCGATATGACGCGCCATTACTACGAACTGCAACTTCGTGACCTGGAAGCATTGACCTCCGGAGCATCTGTGGGCAATGGAGATATCAGTATCGAAAGTATTCCAATCTCTGTAGCCAAAGAATTTCTCTGGAACCGTGACTTTGCCCTACGC

My config .yaml file:

mem: big_mem_avail: 6 big_mem_per_core_gb: 192 normal_mem_per_core_gb: 8 tmp_dir: tmp raws: assembly: "/g/data1b/oo46/Tereza/miniconda_binning/megahit_output/HOAM22040_PSP_HIC12252A30_S109/S109_final.contigs.fa" metagenomics_alignment: "/g/data1b/oo46/Tereza/miniconda_binning/bamsam_output/HOAM22040_PSP_HIC12252A30_S109.mapped.sorted.bam" contig_depth: "" sample: S109" outputdir: "S109_output" db_path: "" snakemake_env: "" prokka_env: "" mantis_env: "" conda_source: "" kmers: '2,3,4' mask_disruptive_sequences: 'True' extract_scmags: 'True' coassembly_mode: 'auto' NX_value: 90 min_cont_length_cutoff: 2250 # 500 max_cont_length_cutoff: 2250 # 1000 min_cont_length_cutoff_marker: 2250 # 250 max_cont_length_cutoff_marker: 2250 # 400 max_n_contigs: 5.0e5
max_marker_lineage_depth_lvl: 2 distance_metric: 'manhattan' embedding: max_iterations: 50 clustering: hdbscan_epsilon_range: '0.250,0.000' hdbscan_min_samples_range: '1,5,10' include_depth_initial: 'False' include_depth_main: 'False' bin_quality: min_completeness: 72.5 start_completeness: 92.5 purity: 90 write_contig_data: 'True'

Do you have a clue how to fix this?

Thanks Tereza

ohickl commented 7 months ago

Hi, sorry for the late reply. Maybe there is a network issues with your server? Did it work out in the end? I never encountered this particular error. Are all the expected output files there, e.g. bin fastas? Also does it work out fine with your megahit headers? We had problems in the past with the spaces.

Best Oskar