ERROR Found in .tabixToTmp

[hcph]

Hello, When I using ArchR to analysis the scATAC-seq, the error comes, the genomeAnnotation is self-built using BSgenome package, and the chromosome name is chr1A_part1 chr1A_part2 chr1B_part1 chr1B_part2..... I wondering whether it is the chromosome causes this error. Hope you help, thanks. ArrowFiles <- createArrowFiles(

• inputFiles = "/public/workspace/xuyongyue/ZLH/scATAC-seq/R1/fragments.tsv.gz",
• sampleNames ="huada",
• geneAnnotation = geneAnnotation,
• genomeAnnotation = genomeAnnotation,
• minTSS = 4,
• minFrags = 1000,
• addTileMat = TRUE,
• addGeneScoreMat = TRUE
• ) ArchR logging to : ArchRLogs/ArchR-createArrows-7ba8299e96ac-Date-2021-07-30_Time-20-32-13.log If there is an issue, please report to github with logFile! 2021-07-30 20:32:13 : Batch Execution w/ safelapply!, 0 mins elapsed. 2021-07-30 20:32:13 : (huada : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0.001 mins elapsed. 2021-07-30 20:32:13 : (huada : 1 of 1) Tabix Bed To Temporary File, 0.002 mins elapsed. 2021-07-30 20:32:20 : (huada : 1 of 1) Reading TabixFile 8 Percent, 0.121 mins elapsed. 2021-07-30 20:32:34 : (huada : 1 of 1) Reading TabixFile 16 Percent, 0.355 mins elapsed. 2021-07-30 20:32:47 : (huada : 1 of 1) Reading TabixFile 24 Percent, 0.564 mins elapsed. 2021-07-30 20:33:00 : (huada : 1 of 1) Reading TabixFile 32 Percent, 0.787 mins elapsed. 2021-07-30 20:33:12 : (huada : 1 of 1) Reading TabixFile 40 Percent, 0.985 mins elapsed. 2021-07-30 20:33:26 : (huada : 1 of 1) Reading TabixFile 47 Percent, 1.211 mins elapsed. 2021-07-30 20:33:39 : (huada : 1 of 1) Reading TabixFile 55 Percent, 1.434 mins elapsed. 2021-07-30 20:33:51 : (huada : 1 of 1) Reading TabixFile 63 Percent, 1.624 mins elapsed. 2021-07-30 20:34:04 : (huada : 1 of 1) Reading TabixFile 71 Percent, 1.854 mins elapsed. 2021-07-30 20:34:15 : (huada : 1 of 1) Reading TabixFile 79 Percent, 2.038 mins elapsed. 2021-07-30 20:34:27 : (huada : 1 of 1) Reading TabixFile 87 Percent, 2.224 mins elapsed. 2021-07-30 20:34:39 : (huada : 1 of 1) Reading TabixFile 95 Percent, 2.424 mins elapsed.

---

2021-07-30 20:34:50 : ERROR Found in .tabixToTmp for (huada : 1 of 1) LogFile = ArchRLogs/ArchR-createArrows-7ba8299e96ac-Date-2021-07-30_Time-20-32-13.log

<simpleError in H5Lcreate_external(target_file_name = tmpChrFilei, target_obj_name = h5ls(tmpChrFilei)$name[2], link_loc = fid, link_name = paste0("Fragments/", chunkName[1], "/", group[2])): HDF5. Links. Unable to initialize object.>

[hcph]

when set thread=1, then fix it

[YaoyJiang]

when set thread=1, then fix it

why should thread be set to 1?