Milraa string index out of range

[mohamma1]

I tried using Milraa (both released version and development version) on Nanopore reads and the Oxytricha Mac genome from https://knot.math.usf.edu/mds_ies_db/downloads.html. I used the --secondary=no and --MD options as instructed when first aligning using minimap2. However, I get a "String index out of range error" as follows:

Traceback (most recent call last): File ".../.conda/envs/bleties/bin/bleties", line 386, in args.func(args) File ".../.conda/envs/bleties/lib/python3.7/site-packages/bleties/main.py", line 152, in milraa args.subreads_cons_len_threshold) File ".../.conda/envs/bleties/lib/python3.7/site-packages/bleties/Milraa.py", line 1486, in reportPutativeIesInsertSubreads rname, gffpos, gffpos, consseq, breakpointid) File ".../.conda/envs/bleties/lib/python3.7/site-packages/bleties/Milraa.py", line 917, in reportAdjustPointers self._refgenome[ctg], ins_start, ins_end, consseq, breakpointid) File ".../.conda/envs/bleties/lib/python3.7/site-packages/bleties/Milraa.py", line 263, in getPointers while iesseq[i] == seq[end+i]: File ".../.conda/envs/bleties/lib/python3.7/site-packages/Bio/SeqRecord.py", line 455, in getitem return self.seq[index] File ".../.conda/envs/bleties/lib/python3.7/site-packages/Bio/Seq.py", line 323, in getitem return self._data[index] IndexError: string index out of range.

[kbseah]

Thanks for reporting this. Could you please attach the full MILRAA log output and the command that you used?

To confirm, is this is the MAC reference genome file? https://knot.math.usf.edu/mds_ies_db/data/fasta/oxytri_mac.fna

[mohamma1]

The genome file was a previous version of the one that was downloadable from mds_ies_db. I checked and the new version is in fact different. I think the inputs, especially the nanopore library, are too large to attach here. Maybe we can find another channel to transfer my input files.

I used the commands:

minimap2 -a -x map-ont -t 8 --secondary=no --MD ~/Public/mds_ies_db/mds_ies_db_oxytri_mac_200608.mmi -o mac_310_0_long_no_sec_md.sam 0_long.fq.gz &

samtools view -b -o mac_310_0_long_no_sec_md.bam mac_310_0_long_no_sec_md.sam &

bleties milraa --bam mac_310_0_long_no_sec_md_srt.bam --ref ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna --type subreads --out mac_310_0_long_no_sec_md_srt_miltraa &

The bleties milraa output log, apart from the stderr, is:

[2021-06-23 14:17:29,370] main.milraa INFO BleTIES v0.1.9 [2021-06-23 14:17:29,370] main.milraa INFO Dependencies: [2021-06-23 14:17:29,444] main.milraa INFO - pysam: 0.15.4 [2021-06-23 14:17:29,444] main.milraa INFO - biopython: 1.76 [2021-06-23 14:17:29,444] main.milraa INFO - htslib: 1.9 [2021-06-23 14:17:29,444] main.milraa INFO - spoa: v4.0.3 at .../.conda/envs/bleties_dev/bin/spoa [2021-06-23 14:17:29,444] main.milraa INFO - NCRF: 1.01.02 at .../.conda/envs/bleties_dev/bin/NCRF [2021-06-23 14:17:29,444] main.milraa INFO - muscle: v3.8.1551 at .../.conda/envs/bleties_dev/bin/muscle [2021-06-23 14:17:29,444] main.milraa INFO Command line: [2021-06-23 14:17:29,444] main.milraa INFO /home/mohammed/.conda/envs/bleties_dev/bin/bleties milraa --bam mac_310_0_long_no_sec_md_srt.bam --ref ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna --type subreads --out mac_310_0_long_no_sec_md_srt_miltraa [2021-06-23 14:17:29,444] main.milraa INFO Started BleTIES MILRAA [2021-06-23 14:17:29,445] main.read_bam_ref INFO Opening alignment file mac_310_0_long_no_sec_md_srt.bam [2021-06-23 14:17:29,541] main.read_bam_ref INFO Alignment file contains 1171693 reads mapped to 22460 reference sequences [2021-06-23 14:17:29,541] main.read_bam_ref INFO Reading mapping sequence file to memory ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna [2021-06-23 14:18:48,704] main.milraa INFO Processing alignment to find putative IESs [2021-06-23 14:25:16,378] main.milraa INFO Finding coordinates and consensus sequences of IESs from subread mappings [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_5: 0 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_5: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_7: 36 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_7: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_11: 5 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_11: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_12: 7 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_12: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_14: 8 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_14: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_16: 1 [2021-06-23 14:25:16,379] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_16: 0 [2021-06-23 14:25:16,379] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_17: 119 [2021-06-23 14:25:16,379] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_17: 2 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_18: 3 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_18: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_19: 1 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_19: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_20: 1 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_20: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_23: 17 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_23: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_24: 13 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_24: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_26: 11 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_26: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_28: 5 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_28: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_29: 0 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_29: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_30: 7 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_30: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_32: 26 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_32: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_34: 1 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_34: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_36: 1 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_36: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_40: 34 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_40: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_41: 2 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_41: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_42: 6 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_42: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_43: 16 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_43: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_48: 0 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_48: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_49: 5 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_49: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_54: 2 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_54: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_55: 3 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_55: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_56: 2 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_56: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_57: 1 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_57: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_60: 16 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_60: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_61: 46 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_61: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_64: 1 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_64: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_65: 2 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_65: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_66: 15 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_66: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_68: 5 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_68: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_73: 3 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_73: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_74: 8 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_74: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_76: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_76: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_77: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_77: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_81: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_81: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_85: 172 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_85: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_86: 29 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_86: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_87: 8 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_87: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_89: 43 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_89: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_92: 4 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_92: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_93: 3 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_93: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_94: 1 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_94: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_98: 10 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_98: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_99: 23 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_99: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_101: 25 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_101: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_103: 6 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_103: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_104: 2 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_104: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_105: 31 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_105: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_106: 12 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_106: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_107: 5 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_107: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_108: 33 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_108: 1 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_112: 3 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_112: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_113: 1 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_113: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_115: 0 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_115: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_116: 6 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_116: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_117: 0 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_117: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_121: 5 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_121: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_126: 5 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_126: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_127: 0 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_127: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_130: 6 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_130: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_131: 3 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_131: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_132: 7 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_132: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_133: 2 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_133: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_135: 1 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_135: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_136: 2 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_136: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_139: 14 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_139: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_141: 2 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_141: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_142: 1 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_142: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_143: 1 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_143: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_144: 6 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_144: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_145: 116 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_145: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_146: 29 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_146: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_150: 0 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_150: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_151: 0 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_151: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_154: 34 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_154: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_156: 40 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_156: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_158: 7 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_158: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_162: 0 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_162: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_163: 0 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_163: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_166: 1 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_166: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_167: 19 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_167: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_169: 90 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_169: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_171: 3 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_171: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_172: 1 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_172: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_173: 7 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_173: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_175: 11 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_175: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_176: 1 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_176: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_177: 2 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_177: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_178: 6 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_178: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_179: 3 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_179: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_180: 2 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_180: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_184: 10 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_184: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_185: 7 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_185: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_186: 1 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_186: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_187: 77 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_187: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_188: 3 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_188: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_189: 1 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_189: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_190: 3 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_190: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_192: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_192: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_196: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_196: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_197: 8 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_197: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_198: 28 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_198: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_199: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_199: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_200: 26 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_200: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_201: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_201: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_203: 13 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_203: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_207: 3 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_207: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_208: 1 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_208: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_209: 4 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_209: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_210: 6 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_210: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_212: 7 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_212: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_213: 26 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_213: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_214: 5 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_214: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_215: 1 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_215: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_217: 9 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_217: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_220: 2 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_220: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_223: 0 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_223: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_224: 6 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_224: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_226: 7 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_226: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_227: 4 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_227: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_228: 2 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_228: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_230: 1 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_230: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_231: 6 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_231: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_232: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_232: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_236: 8 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_236: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_238: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_238: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_239: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_239: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_240: 4 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_240: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_241: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_241: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_242: 5 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_242: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_243: 1 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_243: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_244: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_244: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_245: 5 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_245: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_246: 2 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_246: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_247: 16 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_247: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_249: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_249: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_250: 7 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_250: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_252: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_252: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_256: 9 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_256: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_258: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_258: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_260: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_260: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_261: 3 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_261: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_263: 9 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_263: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_264: 23 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_264: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_265: 18 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_265: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_270: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_270: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_271: 3 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_271: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_273: 57 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_273: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_274: 3 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_274: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_276: 2 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_276: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_277: 1 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_277: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_278: 10 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_278: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_280: 4 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_280: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_282: 4 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_282: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_283: 1 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_283: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_284: 3 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_284: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_286: 5 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_286: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_288: 0 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_288: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_290: 118 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_290: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_291: 0 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_291: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_292: 1 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_292: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_294: 4 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_294: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_295: 3 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_295: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_298: 7 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_298: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_300: 6 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_300: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_301: 3 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_301: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_305: 1 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_305: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_309: 0 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_309: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_310: 3 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_310: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_316: 1 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_316: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_317: 1 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_317: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_318: 13 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_318: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_319: 0 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_319: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_322: 5 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_322: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_323: 11 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_323: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_324: 2 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_324: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_327: 6 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_327: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_330: 1 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_330: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_331: 2 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_331: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_338: 20 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_338: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_341: 1 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_341: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_342: 9 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_342: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_343: 8 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_343: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_345: 5 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_345: 0 [2021-06-23 14:25:17,278] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_346: 62 [2021-06-23 14:25:17,278] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_346: 3 [2021-06-23 14:25:20,362] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_347: 0 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_347: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_348: 8 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_348: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_351: 16 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_351: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_353: 1 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_353: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_354: 5 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_354: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_355: 8 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_355: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_362: 4 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_362: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_363: 0 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_363: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_366: 8 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_366: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_367: 22 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_367: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_368: 5 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_368: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_369: 0 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_369: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_370: 165 [2021-06-23 14:25:20,365] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_370: 0 [2021-06-23 14:25:20,365] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_371: 5 [2021-06-23 14:25:20,365] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_371: 1 [2021-06-23 14:25:20,420] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_372: 2 [2021-06-23 14:25:20,420] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_372: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_374: 15 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_374: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_378: 8 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_378: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_379: 5 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_379: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_381: 0 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_381: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_382: 2 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_382: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_385: 4 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_385: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_387: 5 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_387: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_388: 26 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_388: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_391: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_391: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_393: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_393: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_395: 3 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_395: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_397: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_397: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_401: 7 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_401: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_404: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_404: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_410: 0 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_410: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_411: 0 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_411: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_412: 16 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_412: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_413: 5 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_413: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_417: 0 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_417: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_418: 1 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_418: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_425: 16 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_425: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_426: 12 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_426: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_429: 1 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_429: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_430: 32 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_430: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_433: 1 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_433: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_434: 2 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_434: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_437: 13 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_437: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_439: 5 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_439: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_441: 4 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_441: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_444: 3 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_444: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_445: 3 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_445: 0 [2021-06-23 14:25:20,425] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_446: 65 [2021-06-23 14:25:20,425] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_446: 4 [2021-06-23 14:25:20,846] Milraa INFO Predicted insert further than 5 bp from preliminary position for OXYTRI_MAC_446, 9567 [2021-06-23 14:25:21,322] Milraa INFO Predicted insert further than 5 bp from preliminary position for OXYTRI_MAC_446, 9638

[kbseah]

Hm ok so it looks like it does find potential inserts but fails when reporting.

For the sake of troubleshooting, could you subset the bam file to only alignments for one representative contig in the reference, and run Milraa with the --contig option to process only that contig?

If you get a similar error as before, we can then work with the smaller dataset to try and reproduce the error and troubleshoot.

On Thu, Jun 24, 2021, 19:40 mohamma1 @.***> wrote:

The genome file was a previous version of the one that was downloadable from mds_ies_db. I checked and the new version is in fact different. I think the inputs, especially the nanopore library, are too large to attach here. Maybe we can find another channel to transfer my input files.

I used the commands:

minimap2 -a -x map-ont -t 8 --secondary=no --MD ~/Public/mds_ies_db/mds_ies_db_oxytri_mac_200608.mmi -o mac_310_0_long_no_sec_md.sam 0_long.fq.gz &

samtools view -b -o mac_310_0_long_no_sec_md.bam mac_310_0_long_no_sec_md.sam &

bleties milraa --bam mac_310_0_long_no_sec_md_srt.bam --ref ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna --type subreads --out mac_310_0_long_no_sec_md_srt_miltraa &

The bleties milraa output log, apart from the stderr, is:

[2021-06-23 14:17:29,370] main.milraa INFO BleTIES v0.1.9 [2021-06-23 14:17:29,370] main.milraa INFO Dependencies: [2021-06-23 14:17:29,444] main.milraa INFO - pysam: 0.15.4 [2021-06-23 14:17:29,444] main.milraa INFO - biopython: 1.76 [2021-06-23 14:17:29,444] main.milraa INFO - htslib: 1.9 [2021-06-23 14:17:29,444] main.milraa INFO - spoa: v4.0.3 at .../.conda/envs/bleties_dev/bin/spoa [2021-06-23 14:17:29,444] main.milraa INFO - NCRF: 1.01.02 at .../.conda/envs/bleties_dev/bin/NCRF [2021-06-23 14:17:29,444] main.milraa INFO - muscle: v3.8.1551 at .../.conda/envs/bleties_dev/bin/muscle [2021-06-23 14:17:29,444] main.milraa INFO Command line: [2021-06-23 14:17:29,444] main.milraa INFO /home/mohammed/.conda/envs/bleties_dev/bin/bleties milraa --bam mac_310_0_long_no_sec_md_srt.bam --ref ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna --type subreads --out mac_310_0_long_no_sec_md_srt_miltraa [2021-06-23 14:17:29,444] main.milraa INFO Started BleTIES MILRAA [2021-06-23 14:17:29,445] main.read_bam_ref INFO Opening alignment file mac_310_0_long_no_sec_md_srt.bam [2021-06-23 14:17:29,541] main.read_bam_ref INFO Alignment file contains 1171693 reads mapped to 22460 reference sequences [2021-06-23 14:17:29,541] main.read_bam_ref INFO Reading mapping sequence file to memory ../mds_ies_db/mds_ies_db_oxytri_mac_200608.fna [2021-06-23 14:18:48,704] main.milraa INFO Processing alignment to find putative IESs [2021-06-23 14:25:16,378] main.milraa INFO Finding coordinates and consensus sequences of IESs from subread mappings [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_5: 0 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_5: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_7: 36 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_7: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_11: 5 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_11: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_12: 7 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_12: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_14: 8 [2021-06-23 14:25:16,378] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_14: 0 [2021-06-23 14:25:16,378] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_16: 1 [2021-06-23 14:25:16,379] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_16: 0 [2021-06-23 14:25:16,379] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_17: 119 [2021-06-23 14:25:16,379] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_17: 2 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_18: 3 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_18: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_19: 1 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_19: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_20: 1 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_20: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_23: 17 [2021-06-23 14:25:17,113] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_23: 0 [2021-06-23 14:25:17,113] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_24: 13 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_24: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_26: 11 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_26: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_28: 5 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_28: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_29: 0 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_29: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_30: 7 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_30: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_32: 26 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_32: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_34: 1 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_34: 0 [2021-06-23 14:25:17,114] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_36: 1 [2021-06-23 14:25:17,114] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_36: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_40: 34 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_40: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_41: 2 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_41: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_42: 6 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_42: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_43: 16 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_43: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_48: 0 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_48: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_49: 5 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_49: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_54: 2 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_54: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_55: 3 [2021-06-23 14:25:17,115] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_55: 0 [2021-06-23 14:25:17,115] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_56: 2 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_56: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_57: 1 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_57: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_60: 16 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_60: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_61: 46 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_61: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_64: 1 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_64: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_65: 2 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_65: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_66: 15 [2021-06-23 14:25:17,116] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_66: 0 [2021-06-23 14:25:17,116] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_68: 5 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_68: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_73: 3 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_73: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_74: 8 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_74: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_76: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_76: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_77: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_77: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_81: 7 [2021-06-23 14:25:17,117] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_81: 0 [2021-06-23 14:25:17,117] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_85: 172 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_85: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_86: 29 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_86: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_87: 8 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_87: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_89: 43 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_89: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_92: 4 [2021-06-23 14:25:17,118] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_92: 0 [2021-06-23 14:25:17,118] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_93: 3 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_93: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_94: 1 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_94: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_98: 10 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_98: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_99: 23 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_99: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_101: 25 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_101: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_103: 6 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_103: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_104: 2 [2021-06-23 14:25:17,119] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_104: 0 [2021-06-23 14:25:17,119] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_105: 31 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_105: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_106: 12 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_106: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_107: 5 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_107: 0 [2021-06-23 14:25:17,120] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_108: 33 [2021-06-23 14:25:17,120] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_108: 1 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_112: 3 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_112: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_113: 1 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_113: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_115: 0 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_115: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_116: 6 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_116: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_117: 0 [2021-06-23 14:25:17,260] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_117: 0 [2021-06-23 14:25:17,260] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_121: 5 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_121: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_126: 5 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_126: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_127: 0 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_127: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_130: 6 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_130: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_131: 3 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_131: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_132: 7 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_132: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_133: 2 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_133: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_135: 1 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_135: 0 [2021-06-23 14:25:17,261] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_136: 2 [2021-06-23 14:25:17,261] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_136: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_139: 14 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_139: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_141: 2 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_141: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_142: 1 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_142: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_143: 1 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_143: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_144: 6 [2021-06-23 14:25:17,262] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_144: 0 [2021-06-23 14:25:17,262] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_145: 116 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_145: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_146: 29 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_146: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_150: 0 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_150: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_151: 0 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_151: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_154: 34 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_154: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_156: 40 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_156: 0 [2021-06-23 14:25:17,263] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_158: 7 [2021-06-23 14:25:17,263] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_158: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_162: 0 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_162: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_163: 0 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_163: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_166: 1 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_166: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_167: 19 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_167: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_169: 90 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_169: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_171: 3 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_171: 0 [2021-06-23 14:25:17,264] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_172: 1 [2021-06-23 14:25:17,264] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_172: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_173: 7 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_173: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_175: 11 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_175: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_176: 1 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_176: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_177: 2 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_177: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_178: 6 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_178: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_179: 3 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_179: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_180: 2 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_180: 0 [2021-06-23 14:25:17,265] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_184: 10 [2021-06-23 14:25:17,265] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_184: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_185: 7 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_185: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_186: 1 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_186: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_187: 77 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_187: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_188: 3 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_188: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_189: 1 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_189: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_190: 3 [2021-06-23 14:25:17,266] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_190: 0 [2021-06-23 14:25:17,266] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_192: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_192: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_196: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_196: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_197: 8 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_197: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_198: 28 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_198: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_199: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_199: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_200: 26 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_200: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_201: 1 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_201: 0 [2021-06-23 14:25:17,267] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_203: 13 [2021-06-23 14:25:17,267] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_203: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_207: 3 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_207: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_208: 1 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_208: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_209: 4 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_209: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_210: 6 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_210: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_212: 7 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_212: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_213: 26 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_213: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_214: 5 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_214: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_215: 1 [2021-06-23 14:25:17,268] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_215: 0 [2021-06-23 14:25:17,268] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_217: 9 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_217: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_220: 2 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_220: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_223: 0 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_223: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_224: 6 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_224: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_226: 7 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_226: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_227: 4 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_227: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_228: 2 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_228: 0 [2021-06-23 14:25:17,269] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_230: 1 [2021-06-23 14:25:17,269] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_230: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_231: 6 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_231: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_232: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_232: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_236: 8 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_236: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_238: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_238: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_239: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_239: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_240: 4 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_240: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_241: 3 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_241: 0 [2021-06-23 14:25:17,270] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_242: 5 [2021-06-23 14:25:17,270] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_242: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_243: 1 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_243: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_244: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_244: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_245: 5 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_245: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_246: 2 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_246: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_247: 16 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_247: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_249: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_249: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_250: 7 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_250: 0 [2021-06-23 14:25:17,271] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_252: 0 [2021-06-23 14:25:17,271] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_252: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_256: 9 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_256: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_258: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_258: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_260: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_260: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_261: 3 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_261: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_263: 9 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_263: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_264: 23 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_264: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_265: 18 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_265: 0 [2021-06-23 14:25:17,272] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_270: 1 [2021-06-23 14:25:17,272] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_270: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_271: 3 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_271: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_273: 57 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_273: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_274: 3 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_274: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_276: 2 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_276: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_277: 1 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_277: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_278: 10 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_278: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_280: 4 [2021-06-23 14:25:17,273] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_280: 0 [2021-06-23 14:25:17,273] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_282: 4 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_282: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_283: 1 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_283: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_284: 3 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_284: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_286: 5 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_286: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_288: 0 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_288: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_290: 118 [2021-06-23 14:25:17,274] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_290: 0 [2021-06-23 14:25:17,274] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_291: 0 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_291: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_292: 1 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_292: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_294: 4 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_294: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_295: 3 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_295: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_298: 7 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_298: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_300: 6 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_300: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_301: 3 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_301: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_305: 1 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_305: 0 [2021-06-23 14:25:17,275] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_309: 0 [2021-06-23 14:25:17,275] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_309: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_310: 3 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_310: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_316: 1 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_316: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_317: 1 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_317: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_318: 13 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_318: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_319: 0 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_319: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_322: 5 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_322: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_323: 11 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_323: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_324: 2 [2021-06-23 14:25:17,276] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_324: 0 [2021-06-23 14:25:17,276] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_327: 6 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_327: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_330: 1 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_330: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_331: 2 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_331: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_338: 20 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_338: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_341: 1 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_341: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_342: 9 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_342: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_343: 8 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_343: 0 [2021-06-23 14:25:17,277] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_345: 5 [2021-06-23 14:25:17,277] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_345: 0 [2021-06-23 14:25:17,278] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_346: 62 [2021-06-23 14:25:17,278] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_346: 3 [2021-06-23 14:25:20,362] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_347: 0 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_347: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_348: 8 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_348: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_351: 16 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_351: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_353: 1 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_353: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_354: 5 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_354: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_355: 8 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_355: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_362: 4 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_362: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_363: 0 [2021-06-23 14:25:20,363] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_363: 0 [2021-06-23 14:25:20,363] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_366: 8 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_366: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_367: 22 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_367: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_368: 5 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_368: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_369: 0 [2021-06-23 14:25:20,364] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_369: 0 [2021-06-23 14:25:20,364] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_370: 165 [2021-06-23 14:25:20,365] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_370: 0 [2021-06-23 14:25:20,365] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_371: 5 [2021-06-23 14:25:20,365] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_371: 1 [2021-06-23 14:25:20,420] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_372: 2 [2021-06-23 14:25:20,420] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_372: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_374: 15 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_374: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_378: 8 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_378: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_379: 5 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_379: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_381: 0 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_381: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_382: 2 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_382: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_385: 4 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_385: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_387: 5 [2021-06-23 14:25:20,421] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_387: 0 [2021-06-23 14:25:20,421] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_388: 26 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_388: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_391: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_391: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_393: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_393: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_395: 3 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_395: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_397: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_397: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_401: 7 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_401: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_404: 1 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_404: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_410: 0 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_410: 0 [2021-06-23 14:25:20,422] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_411: 0 [2021-06-23 14:25:20,422] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_411: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_412: 16 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_412: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_413: 5 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_413: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_417: 0 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_417: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_418: 1 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_418: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_425: 16 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_425: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_426: 12 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_426: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_429: 1 [2021-06-23 14:25:20,423] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_429: 0 [2021-06-23 14:25:20,423] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_430: 32 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_430: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_433: 1 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_433: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_434: 2 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_434: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_437: 13 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_437: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_439: 5 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_439: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_441: 4 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_441: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_444: 3 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_444: 0 [2021-06-23 14:25:20,424] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_445: 3 [2021-06-23 14:25:20,424] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_445: 0 [2021-06-23 14:25:20,425] Milraa INFO Unfiltered insert clusters in contig OXYTRI_MAC_446: 65 [2021-06-23 14:25:20,425] Milraa INFO Insert clusters with cov > 10 in contig OXYTRI_MAC_446: 4 [2021-06-23 14:25:20,846] Milraa INFO Predicted insert further than 5 bp from preliminary position for OXYTRI_MAC_446, 9567 [2021-06-23 14:25:21,322] Milraa INFO Predicted insert further than 5 bp from preliminary position for OXYTRI_MAC_446, 9638

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[mohamma1]

Sorry, closed the issue when I was trying to close my comment.

Attached are files for OXYTRI_MAC_446 that was sufficient to reproduce the error.

The command I used is: bleties milraa --bam mac_310_0_long_no_sec_md_srt_mac_446.bam --ref mds_ies_db_oxytri_mac_200608.fna --type subreads --contig OXYTRI_MAC_446 --out mac_310_0_long_no_sec_md_srt_mac_446_miltraa

mac_310_0_long_no_sec_md_srt_mac_446.zip

mds_ies_db_oxytri_mac_200608.zip

[kbseah]

Thanks for sending this data to help us troubleshoot!

I've created a new branch issue_26 to patch this issue, which works with the test data for contig OXYTRI_MAC_446. Could you try installing this development version of bleties to a separate conda environment and seeing if it also works on the rest of your dataset? To install the development version:

git clone git@github.com:Swart-lab/bleties.git
cd bleties
git checkout issue_26
conda env create -f ./env.yaml -p ../bleties_test_env # make new conda env one folder up
conda activate ../bleties_test_env
pip install .
bleties --version # should say 0.1.10-alpha

The command that I ran:

bleties --log test_issue_26.log --log_level DEBUG \
    milraa --bam mac_310_0_long_no_sec_md_srt_mac_446.bam \
    --ref mds_ies_db_oxytri_mac_200608.fna \
    --contig OXYTRI_MAC_446 --out test_issue_26

One thing I noticed is that the Oxytricha MAC contigs are very short, as expected for the hypotrich ciliates. The realignment of assembled IES inserts was also tricky because the IESs were also short and there was some repetitive sequence content. The coverage of insert-bearing reads was also low.

Some practical suggestions that you might consider:

• Annotate telomeres and other tandem repeats on the contigs, and either mask them before mapping or filter out any spurious IESs that are predicted in those sequence regions.
• Use parameter --subreads_flank_len 50 (default is 100). This sets the flanking sequence length around inserts in a read that is also extracted for the insert reassembly step.
• Set --min_ies_length to the shortest IES you expect to find (default is 15), and --min_break_coverage to the expected coverage (default 10), although if the coverage is lower than 10 the assembled sequence may not be reliable and you will get more spurious IES predictions.
• bleties doesn't have a built-in parallelization option, but you can parallelize Milraa commands per contig with ParaFly (http://parafly.sourceforge.net) or HpcGridRunner, by making a list of bleties milraa commands, one per contig with the --contig option, and a per-contig output prefix. At the end you can combine the GFF and Fasta output files. This should help things go faster.

Hope that this helps. Please let me know if the patch works for the rest of the data. If they do, I can merge this into master and release.

[mohamma1]

Ok, it seems to be working so far. I will reopen it if I encounter it again. Thanks for the quick fix!