./runglnexus.sh: line 2: 20506 Terminated

[gotouerina]

I used parabricks to combine GVCF

WARNING: destination /home/u220220932211/data/yxj_g_vcf already in mount list: destination is already in the mount point list WARNING: destination /home/u220220932211/pika already in mount list: destination is already in the mount point list WARNING: destination /home/u220220932211/pika/pika3 already in mount list: destination is already in the mount point list WARNING: destination /home/u220220932211/pika/pika2 already in mount list: destination is already in the mount point list WARNING: destination /home/u220220932211/pika/pika5 already in mount list: destination is already in the mount point list WARNING: destination /home/u220220932211/pika/pika4 already in mount list: destination is already in the mount point list [20506] [2023-10-25 10:59:17.005] [GLnexus] [info] glnexus_cli release v1.2.7-0-g0e74fc4 Aug 13 2020 [20506] [2023-10-25 10:59:17.005] [GLnexus] [warning] jemalloc absent, which will impede performance with high thread counts. See https://github.com/dnanexus-rnd/GLnexus/wiki/Performance [20506] [2023-10-25 10:59:17.005] [GLnexus] [info] Loading config preset gatk [20506] [2023-10-25 10:59:17.013] [GLnexus] [info] config: unifier_config: drop_filtered: false min_allele_copy_number: 1 min_AQ1: 70 min_AQ2: 40 min_GQ: 40 max_alleles_per_site: 32 monoallelic_sites_for_lost_alleles: true preference: common genotyper_config: revise_genotypes: true min_assumed_allele_frequency: 9.99999975e-05 required_dp: 1 allow_partial_data: false allele_dp_format: AD ref_dp_format: MIN_DP output_residuals: false more_PL: false squeeze: false trim_uncalled_alleles: false output_format: BCF liftover_fields:

• {orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
• {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}
• {orig_names: [SB], name: SB, description: "##FORMAT=<ID=SB,Number=4,Type=Integer,Description=\"Per-sample component statistics which comprise the Fishers Exact Test to detect strand bias.\">", type: int, number: basic, default_type: missing, count: 4, combi_method: missing, ignore_non_variants: false}
• {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
• {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true} [20506] [2023-10-25 10:59:17.014] [GLnexus] [info] config CRC32C = 268790301 [20506] [2023-10-25 10:59:17.014] [GLnexus] [info] init database, exemplar_vcf=/home/u220220932211/data/yxj_g_vcf/BBZ.g.vcf.gz [20506] [2023-10-25 10:59:17.961] [GLnexus] [info] Initialized GLnexus database in GLnexus.DB [20506] [2023-10-25 10:59:17.962] [GLnexus] [info] bucket size: 30000 [20506] [2023-10-25 10:59:17.962] [GLnexus] [info] contigs: Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr20 Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 scaffold1 scaffold2 scaffold3 scaffold4 scaffold5 scaffold6 scaffold7 scaffold8 scaffold9 scaffold10 scaffold11 scaffold12 scaffold13 scaffold14 scaffold15 scaffold16 scaffold17 scaffold18 scaffold19 scaffold20 scaffold21 scaffold22 scaffold23 scaffold24 scaffold25 scaffold26 scaffold27 scaffold28 scaffold29 scaffold30 scaffold31 scaffold32 scaffold33 scaffold34 scaffold35 scaffold36 scaffold37 scaffold38 scaffold39 scaffold40 scaffold41 scaffold42 scaffold43 scaffold44 scaffold45 scaffold46 scaffold47 scaffold48 scaffold49 scaffold50 scaffold51 scaffold52 scaffold53 scaffold54 scaffold55 scaffold56 scaffold57 scaffold58 scaffold59 scaffold60 scaffold61 scaffold62 scaffold63 scaffold64 scaffold65 scaffold66 scaffold67 scaffold68 scaffold69 scaffold70 scaffold71 scaffold72 scaffold73 scaffold74 scaffold75 scaffold76 scaffold77 scaffold78 scaffold79 scaffold80 scaffold81 scaffold82 scaffold83 scaffold84 scaffold85 scaffold86 scaffold87 scaffold88 scaffold89 scaffold90 scaffold91 scaffold92 scaffold93 scaffold94 scaffold95 scaffold96 scaffold97 scaffold98 scaffold99 scaffold100 scaffold101 scaffold102 scaffold103 scaffold104 scaffold105 scaffold106 scaffold107 scaffold108 scaffold109 scaffold110 scaffold111 scaffold112 scaffold113 scaffold114 scaffold115 scaffold116 scaffold117 scaffold118 scaffold119 scaffold120 scaffold121 scaffold122 scaffold123 scaffold124 scaffold125 scaffold126 scaffold127 scaffold128 scaffold129 scaffold130 scaffold131 scaffold132 scaffold133 scaffold134 scaffold135 scaffold136 scaffold137 scaffold138 scaffold139 scaffold140 scaffold141 scaffold142 scaffold143 scaffold144 scaffold145 scaffold146 scaffold147 scaffold148 scaffold149 scaffold150 scaffold151 scaffold152 scaffold153 scaffold154 scaffold155 scaffold156 scaffold157 scaffold158 scaffold159 scaffold160 scaffold161 scaffold162 scaffold163 scaffold164 scaffold165 scaffold166 scaffold167 scaffold168 scaffold169 scaffold170 scaffold171 scaffold172 scaffold173 scaffold174 scaffold175 scaffold176 scaffold177 scaffold178 scaffold179 scaffold180 scaffold181 scaffold182 scaffold183 scaffold184 scaffold185 scaffold186 scaffold187 scaffold188 scaffold189 scaffold190 scaffold191 scaffold192 scaffold193 scaffold194 scaffold195 scaffold196 scaffold197 scaffold198 scaffold199 scaffold200 scaffold201 scaffold202 scaffold203 scaffold204 scaffold205 scaffold206 scaffold207 scaffold208 scaffold209 scaffold210 scaffold211 scaffold212 scaffold213 scaffold214 scaffold215 scaffold216 scaffold217 scaffold218 scaffold219 scaffold220 scaffold221 scaffold222 scaffold223 scaffold224 scaffold225 scaffold226 scaffold227 scaffold228 scaffold229 scaffold230 scaffold231 scaffold232 scaffold233 scaffold234 scaffold235 scaffold236 scaffold237 scaffold238 scaffold239 scaffold240 scaffold241 scaffold242 scaffold243 scaffold244 scaffold245 scaffold246 scaffold247 scaffold248 scaffold249 scaffold250 scaffold251 scaffold252 scaffold253 scaffold254 scaffold255 scaffold256 scaffold257 scaffold258 scaffold259 scaffold260 scaffold261 scaffold262 scaffold263 scaffold264 scaffold265 scaffold266 scaffold267 scaffold268 scaffold269 scaffold270 scaffold271 scaffold272 scaffold273 scaffold274 scaffold275 scaffold276 scaffold277 scaffold278 scaffold279 scaffold280 scaffold281 scaffold282 scaffold283 scaffold284 scaffold285 scaffold286 scaffold287 scaffold288 scaffold289 scaffold290 scaffold291 scaffold292 scaffold293 scaffold294 scaffold295 scaffold296 scaffold297 scaffold298 scaffold299 scaffold300 scaffold301 scaffold302 scaffold303 scaffold304 scaffold305 scaffold306 scaffold307 scaffold308 scaffold309 scaffold310 scaffold311 scaffold312 scaffold313 scaffold314 scaffold315 scaffold316 scaffold317 scaffold318 scaffold319 scaffold320 scaffold321 scaffold322 scaffold323 scaffold324 scaffold325 scaffold326 scaffold327 scaffold328 scaffold329 scaffold330 scaffold331 scaffold332 scaffold333 scaffold334 scaffold335 scaffold336 scaffold337 scaffold338 scaffold339 scaffold340 scaffold341 scaffold342 scaffold343 scaffold344 scaffold345 scaffold346 scaffold347 scaffold348 scaffold349 scaffold350 scaffold351 scaffold352 scaffold353 scaffold354 scaffold355 scaffold356 scaffold357 scaffold358 scaffold359 scaffold360 scaffold361 scaffold362 scaffold363 scaffold364 scaffold365 scaffold366 scaffold367 scaffold368 scaffold369 scaffold370 scaffold371 scaffold372 scaffold373 scaffold374 scaffold375 scaffold376 scaffold377 scaffold378 scaffold379 scaffold380 scaffold381 scaffold382 scaffold383 scaffold384 scaffold385 scaffold386 scaffold387 scaffold388 scaffold389 scaffold390 scaffold391 scaffold392 scaffold393 scaffold394 scaffold395 scaffold396 scaffold397 scaffold398 scaffold399 scaffold400 scaffold401 scaffold402 scaffold403 scaffold404 scaffold405 scaffold406 scaffold407 scaffold408 scaffold409 scaffold410 scaffold411 scaffold412 scaffold413 scaffold414 scaffold415 scaffold416 scaffold417 scaffold418 scaffold419 scaffold420 scaffold421 scaffold422 scaffold423 scaffold424 scaffold425 scaffold426 scaffold427 scaffold428 scaffold429 scaffold430 scaffold431 scaffold432 scaffold433 scaffold434 scaffold435 scaffold436 scaffold437 scaffold438 scaffold439 scaffold440 scaffold441 scaffold442 scaffold443 scaffold444 scaffold445 scaffold446 scaffold447 scaffold448 scaffold449 scaffold450 scaffold451 scaffold452 scaffold453 scaffold454 scaffold455 scaffold456 scaffold457 scaffold458 scaffold459 scaffold460 scaffold461 scaffold462 scaffold463 scaffold464 scaffold465 scaffold466 scaffold467 scaffold468 scaffold469 scaffold470 scaffold471 scaffold472 scaffold473 scaffold474 scaffold475 scaffold476 scaffold477 scaffold478 scaffold479 scaffold480 scaffold481 scaffold482 scaffold483 scaffold484 scaffold485 scaffold486 scaffold487 scaffold488 scaffold489 scaffold490 scaffold491 scaffold492 scaffold493 scaffold494 scaffold495 scaffold496 scaffold497 scaffold498 scaffold499 scaffold500 scaffold501 scaffold502 scaffold503 scaffold504 scaffold505 scaffold506 scaffold507 scaffold508 scaffold509 scaffold510 scaffold511 scaffold512 scaffold513 scaffold514 scaffold515 scaffold516 scaffold517 scaffold518 scaffold519 scaffold520 scaffold521 scaffold522 scaffold523 scaffold524 scaffold525 scaffold526 scaffold527 scaffold528 scaffold529 scaffold530 scaffold531 scaffold532 scaffold533 scaffold534 scaffold535 scaffold536 scaffold537 scaffold538 scaffold539 scaffold540 scaffold541 scaffold542 scaffold543 scaffold544 scaffold545 scaffold546 scaffold547 scaffold548 scaffold549 scaffold550 scaffold551 scaffold552 scaffold553 scaffold554 scaffold555 scaffold556 scaffold557 scaffold558 scaffold559 scaffold560 scaffold561 scaffold562 scaffold563 scaffold564 scaffold565 scaffold566 scaffold567 scaffold568 scaffold569 scaffold570 scaffold571 scaffold572 scaffold573 scaffold574 scaffold575 scaffold576 scaffold577 scaffold578 scaffold579 [20506] [2023-10-25 10:59:18.032] [GLnexus] [info] db_get_contigs GLnexus.DB [20506] [2023-10-25 10:59:18.172] [GLnexus] [info] Beginning bulk load with no range filter. [W::hts_idx_load2] The index file is older than the data file: /home/u220220932211/data/yxj_g_vcf/DWR17.g.vcf.gz.tbi [W::hts_idx_load2] The index file is older than the data file: /home/u220220932211/data/yxj_g_vcf/DWR25.g.vcf.gz.tbi [W::hts_idx_load2] The index file is older than the data file: /home/u220220932211/data/yxj_g_vcf/DWR26.g.vcf.gz.tbi [W::hts_idx_load2] The index file is older than the data file: /home/u220220932211/data/yxj_g_vcf/CCZ.g.vcf.gz.tbi [W::hts_idx_load2] The index file is older than the data file: /home/u220220932211/data/yxj_g_vcf/DWR27.g.vcf.gz.tbi [20506] [2023-10-25 12:02:24.903] [GLnexus] [info] Loaded 58 datasets with 58 samples; 2478962947064 bytes in 24132545089 BCF records (4923152 duplicate) in 5767867 buckets. Bucket max 1456928 bytes, 14021 records. 8872 BCF records skipped due to caller-specific exceptions [20506] [2023-10-25 12:02:24.905] [GLnexus] [info] Created sample set @58 [20506] [2023-10-25 12:02:24.905] [GLnexus] [info] Flushing database... [20506] [2023-10-25 12:04:31.288] [GLnexus] [info] Bulk load complete! [20506] [2023-10-25 12:04:31.340] [GLnexus] [warning] Processing full length of 605 contigs, as no --bed was provided. Providing a BED file with regions of interest, if applicable, can speed this up. [20506] [2023-10-25 12:04:31.354] [GLnexus] [info] found sample set @58 [20506] [2023-10-25 12:04:31.354] [GLnexus] [info] discovering alleles in 605 range(s) on 38 threads ./runglnexus.sh: line 2: 20506 Terminated /usr/local/cuda/.pb/binaries//bin/glnexus /home/u220220932211/data/yxj_g_vcf/BBZ.g.vcf.gz /home/u220220932211/data/yxj_g_vcf/CCZ.g.vcf.gz /home/u220220932211/pika/DCB085_L2_306306..g.vcf /home/u220220932211/data/yxj_g_vcf/DWR15.g.vcf.gz /home/u220220932211/data/yxj_g_vcf/DWR17.g.vcf.gz /home/u220220932211/pika/pika3/DWR18.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWR19.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/DWR20.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/DWR21.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWR22.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/DWR23.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWR24.sort.markdup.bam.g.vcf /home/u220220932211/data/yxj_g_vcf/DWR25.g.vcf.gz /home/u220220932211/data/yxj_g_vcf/DWR26.g.vcf.gz /home/u220220932211/data/yxj_g_vcf/DWR27.g.vcf.gz /home/u220220932211/data/yxj_g_vcf/DWR28.g.vcf.gz /home/u220220932211/pika/DWR_LS.g.vcf.gz /home/u220220932211/pika/pika3/DWRpika1.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWRpika2.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/DWRpika3.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/DWRpika4.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWRpika5.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/DWRpika6.sort.markdup.bam.g.vcf /home/u220220932211/pika/DWR_XLGL.g.vcf.gz /home/u220220932211/pika/pika3/GYpika10.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika1.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika2.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika3.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/GYpika4.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika5.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika6.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika7.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/GYpika8.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/GYpika9.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika1.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika2.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/nubrica_pika3.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika4.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika5.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika6.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/nubrica_pika7.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/OCH206.markdup.bam.g.vcf /home/u220220932211/pika/pika3/OCH240.markdup.bam.g.vcf /home/u220220932211/pika/pika3/OCH241.markdup.bam.g.vcf /home/u220220932211/pika/pika2/OCH242.markdup.bam.g.vcf /home/u220220932211/pika/pika2/plateau10.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/plateau11.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika3/plateau12.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika5/plateau13.sort.markdup.g.vcf /home/u220220932211/pika/pika5/plateau1.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika5/plateau2.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/plateau3.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika2/plateau4.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika4/plateau5.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika4/plateau6.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika4/plateau7.sort.markdup.bam.g.vcf /home/u220220932211/pika/pika4/WL15490_L4_307307.markdup.bam.g.vcf /home/u220220932211/pika/pika5/plateau8.sort.markdup.g.vcf.gz > /home/u220220932211/pika/GVCF/pika.bcf For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help Exiting... Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation

Could not run glnexus Exiting pbrun ... .

why did it occur, is it memory not enough?