[maker-devel] Issue with single contig
Zoe Clarke
zoe.clarke at utoronto.ca
Fri Oct 9 05:39:57 MDT 2020
Hello!
Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.
I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:
ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.
I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:
0 run.log.child.112 WCK01_AAF20200214_F8-ctg57.118-119.raw.section WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1 run.log.child.113 WCK01_AAF20200214_F8-ctg57.118.pred.raw.section WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10 run.log.child.114 WCK01_AAF20200214_F8-ctg57.118.raw.section WCK01_AAF20200214_F8-ctg57.55.raw.section
11 run.log.child.115 WCK01_AAF20200214_F8-ctg57.119-120.raw.section WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12 run.log.child.116 WCK01_AAF20200214_F8-ctg57.119.pred.raw.section WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2 run.log.child.117 WCK01_AAF20200214_F8-ctg57.119.raw.section WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3 run.log.child.118 WCK01_AAF20200214_F8-ctg57.11.pred.raw.section WCK01_AAF20200214_F8-ctg57.56.raw.section
4 run.log.child.119 WCK01_AAF20200214_F8-ctg57.11.raw.section WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5 run.log.child.12 WCK01_AAF20200214_F8-ctg57.120-121.raw.section WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6 run.log.child.120 WCK01_AAF20200214_F8-ctg57.120.pred.raw.section WCK01_AAF20200214_F8-ctg57.57.raw.section
7 run.log.child.121 WCK01_AAF20200214_F8-ctg57.120.raw.section WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8 run.log.child.122 WCK01_AAF20200214_F8-ctg57.121-122.raw.section WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9 run.log.child.123 WCK01_AAF20200214_F8-ctg57.12-13.raw.section WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff run.log.child.124 WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff run.log.child.125 WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff run.log.child.13 WCK01_AAF20200214_F8-ctg57.121.pred.raw.section WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff run.log.child.14 WCK01_AAF20200214_F8-ctg57.121.raw.section WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff run.log.child.15 WCK01_AAF20200214_F8-ctg57.122-123.raw.section WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff run.log.child.16 WCK01_AAF20200214_F8-ctg57.122.pred.raw.section WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff run.log.child.17 WCK01_AAF20200214_F8-ctg57.122.raw.section WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff run.log.child.18 WCK01_AAF20200214_F8-ctg57.123-124.raw.section WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff run.log.child.19 WCK01_AAF20200214_F8-ctg57.123.pred.raw.section WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff run.log.child.2 WCK01_AAF20200214_F8-ctg57.123.raw.section WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff run.log.child.20 WCK01_AAF20200214_F8-ctg57.124-125.raw.section WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff run.log.child.21 WCK01_AAF20200214_F8-ctg57.124.pred.raw.section WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff run.log.child.22 WCK01_AAF20200214_F8-ctg57.124.raw.section WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff run.log.child.23 WCK01_AAF20200214_F8-ctg57.125.pred.raw.section WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff run.log.child.24 WCK01_AAF20200214_F8-ctg57.125.raw.section WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff run.log.child.25 WCK01_AAF20200214_F8-ctg57.12.pred.raw.section WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff run.log.child.26 WCK01_AAF20200214_F8-ctg57.1-2.raw.section WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff run.log.child.27 WCK01_AAF20200214_F8-ctg57.12.raw.section WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff run.log.child.28 WCK01_AAF20200214_F8-ctg57.13-14.raw.section WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann run.log.child.29 WCK01_AAF20200214_F8-ctg57.13.pred.raw.section WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def run.log.child.3 WCK01_AAF20200214_F8-ctg57.13.raw.section WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq run.log.child.30 WCK01_AAF20200214_F8-ctg57.14-15.raw.section WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff run.log.child.31 WCK01_AAF20200214_F8-ctg57.14.pred.raw.section WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff run.log.child.32 WCK01_AAF20200214_F8-ctg57.14.raw.section WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff run.log.child.33 WCK01_AAF20200214_F8-ctg57.15-16.raw.section WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff run.log.child.34 WCK01_AAF20200214_F8-ctg57.15.pred.raw.section WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff run.log.child.35 WCK01_AAF20200214_F8-ctg57.15.raw.section WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff run.log.child.36 WCK01_AAF20200214_F8-ctg57.16-17.raw.section WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff run.log.child.37 WCK01_AAF20200214_F8-ctg57.16.pred.raw.section WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff run.log.child.38 WCK01_AAF20200214_F8-ctg57.16.raw.section WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff run.log.child.39 WCK01_AAF20200214_F8-ctg57.17-18.raw.section WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff run.log.child.4 WCK01_AAF20200214_F8-ctg57.17.pred.raw.section WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff run.log.child.40 WCK01_AAF20200214_F8-ctg57.17.raw.section WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff run.log.child.41 WCK01_AAF20200214_F8-ctg57.18-19.raw.section WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff run.log.child.42 WCK01_AAF20200214_F8-ctg57.18.pred.raw.section WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff run.log.child.43 WCK01_AAF20200214_F8-ctg57.18.raw.section WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff run.log.child.44 WCK01_AAF20200214_F8-ctg57.19-20.raw.section WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff run.log.child.45 WCK01_AAF20200214_F8-ctg57.19.pred.raw.section WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff run.log.child.46 WCK01_AAF20200214_F8-ctg57.19.raw.section WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff run.log.child.47 WCK01_AAF20200214_F8-ctg57.1.pred.raw.section WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff run.log.child.48 WCK01_AAF20200214_F8-ctg57.1.raw.section WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff run.log.child.49 WCK01_AAF20200214_F8-ctg57.20-21.raw.section WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff run.log.child.5 WCK01_AAF20200214_F8-ctg57.20.pred.raw.section WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff run.log.child.50 WCK01_AAF20200214_F8-ctg57.20.raw.section WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff run.log.child.51 WCK01_AAF20200214_F8-ctg57.21-22.raw.section WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff run.log.child.52 WCK01_AAF20200214_F8-ctg57.21.pred.raw.section WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff run.log.child.53 WCK01_AAF20200214_F8-ctg57.21.raw.section WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann run.log.child.54 WCK01_AAF20200214_F8-ctg57.22-23.raw.section WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def run.log.child.55 WCK01_AAF20200214_F8-ctg57.22.pred.raw.section WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq run.log.child.56 WCK01_AAF20200214_F8-ctg57.22.raw.section WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff run.log.child.57 WCK01_AAF20200214_F8-ctg57.23-24.raw.section WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff run.log.child.58 WCK01_AAF20200214_F8-ctg57.23.pred.raw.section WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff run.log.child.59 WCK01_AAF20200214_F8-ctg57.2-3.raw.section WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff run.log.child.6 WCK01_AAF20200214_F8-ctg57.23.raw.section WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff run.log.child.60 WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff run.log.child.61 WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff run.log.child.62 WCK01_AAF20200214_F8-ctg57.24-25.raw.section WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff run.log.child.63 WCK01_AAF20200214_F8-ctg57.24.pred.raw.section WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff run.log.child.64 WCK01_AAF20200214_F8-ctg57.24.raw.section WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff run.log.child.65 WCK01_AAF20200214_F8-ctg57.25-26.raw.section WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff run.log.child.66 WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff run.log.child.67 WCK01_AAF20200214_F8-ctg57.25.pred.raw.section WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff run.log.child.68 WCK01_AAF20200214_F8-ctg57.25.raw.section WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff run.log.child.69 WCK01_AAF20200214_F8-ctg57.26-27.raw.section WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff run.log.child.7 WCK01_AAF20200214_F8-ctg57.26.pred.raw.section WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff run.log.child.70 WCK01_AAF20200214_F8-ctg57.26.raw.section WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff run.log.child.71 WCK01_AAF20200214_F8-ctg57.27-28.raw.section WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff run.log.child.72 WCK01_AAF20200214_F8-ctg57.27.pred.raw.section WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff run.log.child.73 WCK01_AAF20200214_F8-ctg57.27.raw.section WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff run.log.child.74 WCK01_AAF20200214_F8-ctg57.28-29.raw.section WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff run.log.child.75 WCK01_AAF20200214_F8-ctg57.28.pred.raw.section WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff run.log.child.76 WCK01_AAF20200214_F8-ctg57.28.raw.section WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff run.log.child.77 WCK01_AAF20200214_F8-ctg57.29-30.raw.section WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff run.log.child.78 WCK01_AAF20200214_F8-ctg57.29.pred.raw.section WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff run.log.child.79 WCK01_AAF20200214_F8-ctg57.29.raw.section WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff run.log.child.8 WCK01_AAF20200214_F8-ctg57.2.pred.raw.section WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff run.log.child.80 WCK01_AAF20200214_F8-ctg57.2.raw.section WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff run.log.child.81 WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff run.log.child.82 WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff run.log.child.83 WCK01_AAF20200214_F8-ctg57.30-31.raw.section WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff run.log.child.84 WCK01_AAF20200214_F8-ctg57.30.pred.raw.section WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff run.log.child.85 WCK01_AAF20200214_F8-ctg57.30.raw.section WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff run.log.child.86 WCK01_AAF20200214_F8-ctg57.31-32.raw.section WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff run.log.child.87 WCK01_AAF20200214_F8-ctg57.31.pred.raw.section WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff run.log.child.88 WCK01_AAF20200214_F8-ctg57.31.raw.section WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff run.log.child.89 WCK01_AAF20200214_F8-ctg57.32-33.raw.section WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff run.log.child.9 WCK01_AAF20200214_F8-ctg57.32.pred.raw.section WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff run.log.child.90 WCK01_AAF20200214_F8-ctg57.32.raw.section WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff run.log.child.91 WCK01_AAF20200214_F8-ctg57.33-34.raw.section WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff run.log.child.92 WCK01_AAF20200214_F8-ctg57.33.pred.raw.section WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff run.log.child.93 WCK01_AAF20200214_F8-ctg57.33.raw.section WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff run.log.child.94 WCK01_AAF20200214_F8-ctg57.34-35.raw.section WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff run.log.child.95 WCK01_AAF20200214_F8-ctg57.34.pred.raw.section WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff run.log.child.96 WCK01_AAF20200214_F8-ctg57.3-4.raw.section WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff run.log.child.97 WCK01_AAF20200214_F8-ctg57.34.raw.section WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff run.log.child.98 WCK01_AAF20200214_F8-ctg57.35-36.raw.section WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff run.log.child.99 WCK01_AAF20200214_F8-ctg57.35.pred.raw.section WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff WCK01_AAF20200214_F8-ctg57.0-1.raw.section WCK01_AAF20200214_F8-ctg57.35.raw.section WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff WCK01_AAF20200214_F8-ctg57.0.pred.raw.section WCK01_AAF20200214_F8-ctg57.36-37.raw.section WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff WCK01_AAF20200214_F8-ctg57.0.raw.section WCK01_AAF20200214_F8-ctg57.36.pred.raw.section WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann WCK01_AAF20200214_F8-ctg57.100-101.raw.section WCK01_AAF20200214_F8-ctg57.36.raw.section WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def WCK01_AAF20200214_F8-ctg57.100.pred.raw.section WCK01_AAF20200214_F8-ctg57.37-38.raw.section WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq WCK01_AAF20200214_F8-ctg57.100.raw.section WCK01_AAF20200214_F8-ctg57.37.pred.raw.section WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff WCK01_AAF20200214_F8-ctg57.101-102.raw.section WCK01_AAF20200214_F8-ctg57.37.raw.section WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff WCK01_AAF20200214_F8-ctg57.10-11.raw.section WCK01_AAF20200214_F8-ctg57.38-39.raw.section WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff WCK01_AAF20200214_F8-ctg57.101.pred.raw.section WCK01_AAF20200214_F8-ctg57.38.pred.raw.section WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff WCK01_AAF20200214_F8-ctg57.101.raw.section WCK01_AAF20200214_F8-ctg57.38.raw.section WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff WCK01_AAF20200214_F8-ctg57.102-103.raw.section WCK01_AAF20200214_F8-ctg57.39-40.raw.section WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover WCK01_AAF20200214_F8-ctg57.39.pred.raw.section WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover WCK01_AAF20200214_F8-ctg57.39.raw.section WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff WCK01_AAF20200214_F8-ctg57.102.pred.raw.section WCK01_AAF20200214_F8-ctg57.3.pred.raw.section WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff WCK01_AAF20200214_F8-ctg57.102.raw.section WCK01_AAF20200214_F8-ctg57.3.raw.section WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff WCK01_AAF20200214_F8-ctg57.103-104.raw.section WCK01_AAF20200214_F8-ctg57.40-41.raw.section WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff WCK01_AAF20200214_F8-ctg57.103.pred.raw.section WCK01_AAF20200214_F8-ctg57.40.pred.raw.section WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff WCK01_AAF20200214_F8-ctg57.103.raw.section WCK01_AAF20200214_F8-ctg57.40.raw.section WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff WCK01_AAF20200214_F8-ctg57.104-105.raw.section WCK01_AAF20200214_F8-ctg57.41-42.raw.section WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff WCK01_AAF20200214_F8-ctg57.104.pred.raw.section WCK01_AAF20200214_F8-ctg57.41.pred.raw.section WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff WCK01_AAF20200214_F8-ctg57.104.raw.section WCK01_AAF20200214_F8-ctg57.41.raw.section WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff WCK01_AAF20200214_F8-ctg57.105-106.raw.section WCK01_AAF20200214_F8-ctg57.42-43.raw.section WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff WCK01_AAF20200214_F8-ctg57.105.pred.raw.section WCK01_AAF20200214_F8-ctg57.42.pred.raw.section WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff WCK01_AAF20200214_F8-ctg57.105.raw.section WCK01_AAF20200214_F8-ctg57.42.raw.section WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff WCK01_AAF20200214_F8-ctg57.106-107.raw.section WCK01_AAF20200214_F8-ctg57.43-44.raw.section WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff WCK01_AAF20200214_F8-ctg57.106.pred.raw.section WCK01_AAF20200214_F8-ctg57.43.pred.raw.section WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff WCK01_AAF20200214_F8-ctg57.106.raw.section WCK01_AAF20200214_F8-ctg57.43.raw.section WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff WCK01_AAF20200214_F8-ctg57.107-108.raw.section WCK01_AAF20200214_F8-ctg57.44-45.raw.section WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff WCK01_AAF20200214_F8-ctg57.107.pred.raw.section WCK01_AAF20200214_F8-ctg57.44.pred.raw.section WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff WCK01_AAF20200214_F8-ctg57.107.raw.section WCK01_AAF20200214_F8-ctg57.44.raw.section WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff WCK01_AAF20200214_F8-ctg57.108-109.raw.section WCK01_AAF20200214_F8-ctg57.45-46.raw.section WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff WCK01_AAF20200214_F8-ctg57.108.pred.raw.section WCK01_AAF20200214_F8-ctg57.45.pred.raw.section WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff WCK01_AAF20200214_F8-ctg57.108.raw.section WCK01_AAF20200214_F8-ctg57.4-5.raw.section WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff WCK01_AAF20200214_F8-ctg57.109-110.raw.section WCK01_AAF20200214_F8-ctg57.45.raw.section WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann WCK01_AAF20200214_F8-ctg57.109.pred.raw.section WCK01_AAF20200214_F8-ctg57.46-47.raw.section WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def WCK01_AAF20200214_F8-ctg57.109.raw.section WCK01_AAF20200214_F8-ctg57.46.pred.raw.section WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq WCK01_AAF20200214_F8-ctg57.10.pred.raw.section WCK01_AAF20200214_F8-ctg57.46.raw.section WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann WCK01_AAF20200214_F8-ctg57.10.raw.section WCK01_AAF20200214_F8-ctg57.47-48.raw.section WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def WCK01_AAF20200214_F8-ctg57.110-111.raw.section WCK01_AAF20200214_F8-ctg57.47.pred.raw.section WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq WCK01_AAF20200214_F8-ctg57.110.pred.raw.section WCK01_AAF20200214_F8-ctg57.47.raw.section WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann WCK01_AAF20200214_F8-ctg57.110.raw.section WCK01_AAF20200214_F8-ctg57.48-49.raw.section WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def WCK01_AAF20200214_F8-ctg57.111-112.raw.section WCK01_AAF20200214_F8-ctg57.48.pred.raw.section WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq WCK01_AAF20200214_F8-ctg57.11-12.raw.section WCK01_AAF20200214_F8-ctg57.48.raw.section WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff WCK01_AAF20200214_F8-ctg57.111.pred.raw.section WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann WCK01_AAF20200214_F8-ctg57.111.raw.section WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def WCK01_AAF20200214_F8-ctg57.112-113.raw.section WCK01_AAF20200214_F8-ctg57.49-50.raw.section WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq WCK01_AAF20200214_F8-ctg57.112.pred.raw.section WCK01_AAF20200214_F8-ctg57.49.pred.raw.section WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff WCK01_AAF20200214_F8-ctg57.112.raw.section WCK01_AAF20200214_F8-ctg57.49.raw.section WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta WCK01_AAF20200214_F8-ctg57.113-114.raw.section WCK01_AAF20200214_F8-ctg57.4.pred.raw.section WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta WCK01_AAF20200214_F8-ctg57.113.pred.raw.section WCK01_AAF20200214_F8-ctg57.4.raw.section WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index WCK01_AAF20200214_F8-ctg57.113.raw.section WCK01_AAF20200214_F8-ctg57.50-51.raw.section WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff WCK01_AAF20200214_F8-ctg57.114-115.raw.section WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0 WCK01_AAF20200214_F8-ctg57.114.pred.raw.section WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1 WCK01_AAF20200214_F8-ctg57.114.raw.section WCK01_AAF20200214_F8-ctg57.50.pred.raw.section WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10 WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover WCK01_AAF20200214_F8-ctg57.50.raw.section WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100 WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101 WCK01_AAF20200214_F8-ctg57.115-116.raw.section WCK01_AAF20200214_F8-ctg57.51-52.raw.section WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102 WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover WCK01_AAF20200214_F8-ctg57.51.pred.raw.section WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103 WCK01_AAF20200214_F8-ctg57.115.pred.raw.section WCK01_AAF20200214_F8-ctg57.51.raw.section WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104 WCK01_AAF20200214_F8-ctg57.115.raw.section WCK01_AAF20200214_F8-ctg57.52-53.raw.section WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105 WCK01_AAF20200214_F8-ctg57.116-117.raw.section WCK01_AAF20200214_F8-ctg57.52.pred.raw.section WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106 WCK01_AAF20200214_F8-ctg57.116.pred.raw.section WCK01_AAF20200214_F8-ctg57.52.raw.section WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107 WCK01_AAF20200214_F8-ctg57.116.raw.section WCK01_AAF20200214_F8-ctg57.53-54.raw.section WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108 WCK01_AAF20200214_F8-ctg57.117-118.raw.section WCK01_AAF20200214_F8-ctg57.53.pred.raw.section WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109 WCK01_AAF20200214_F8-ctg57.117.pred.raw.section WCK01_AAF20200214_F8-ctg57.53.raw.section WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11 WCK01_AAF20200214_F8-ctg57.117.raw.section WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110 WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111 WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover WCK01_AAF20200214_F8-ctg57.54.raw.section
I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:
Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089
I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?
Thanks so much!
Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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