[maker-devel] Issue with single contig
Carson Holt
carsonhh at gmail.com
Thu Oct 22 13:31:11 MDT 2020
Your datacenter may have implemented the temporary storage (“/tmp” by default) to be in memory storage. As a result, every file you store is really being stored in RAM behind the scenes. Or you have specified TMP= in the control files to point to in memory storage. The result is that, at some point there was not enough memory left. You may want to ask about this and ensure that you can point to a real node based disk storage like traditional /tmp space.
—Carson
> On Oct 9, 2020, at 5:39 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
>
> 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 <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201022/a58959aa/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201022/a58959aa/attachment-0003.p7s>
More information about the maker-devel
mailing list