Closed katievigil closed 1 week ago
Error log: Below is my err log:
-- canu 2.2
--
-- CITATIONS
--
-- For 'standard' assemblies of PacBio or Nanopore reads:
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
--
-- Read and contig alignments during correction and consensus use:
-- Šošic M, Šikic M.
-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
-- Bioinformatics. 2017 May 1;33(9):1394-1395.
-- http://doi.org/10.1093/bioinformatics/btw753
--
-- Overlaps are generated using:
-- Berlin K, et al.
-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
-- Nat Biotechnol. 2015 Jun;33(6):623-30.
-- http://doi.org/10.1038/nbt.3238
--
-- Myers EW, et al.
-- A Whole-Genome Assembly of Drosophila.
-- Science. 2000 Mar 24;287(5461):2196-204.
-- http://doi.org/10.1126/science.287.5461.2196
--
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
-- Chin CS, et al.
-- Phased diploid genome assembly with single-molecule real-time sequencing.
-- Nat Methods. 2016 Dec;13(12):1050-1054.
-- http://doi.org/10.1038/nmeth.4035
--
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
-- Chin CS, et al.
-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
-- Nat Methods. 2013 Jun;10(6):563-9
-- http://doi.org/10.1038/nmeth.2474
--
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '22.0.1-internal' (from '/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 8 ' (from 'gnuplot') and image format 'png'.
--
-- Detected 48 CPUs and 189984 gigabytes of memory on the local machine.
--
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Slurm disabled by useGrid=false
--
-- Detected '' with 'pbsnodes' binary in /usr/bin/pbsnodes.
-- disabled by useGrid=false
--
-- Local machine mode enabled; grid support not detected or not allowed.
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | total usage algorithm
-- ------- ---------- -------- -------- -------------------- -----------------------------
-- Local: meryl 12.000 GB 4 CPUs x 12 jobs 144.000 GB 48 CPUs (k-mer counting)
-- Local: hap 8.000 GB 4 CPUs x 12 jobs 96.000 GB 48 CPUs (read-to-haplotype assignment)
-- Local: cormhap 6.000 GB 16 CPUs x 3 jobs 18.000 GB 48 CPUs (overlap detection with mhap)
-- Local: obtovl 4.000 GB 8 CPUs x 6 jobs 24.000 GB 48 CPUs (overlap detection)
-- Local: utgovl 4.000 GB 8 CPUs x 6 jobs 24.000 GB 48 CPUs (overlap detection)
-- Local: cor -.--- GB 4 CPUs x - jobs -.--- GB - CPUs (read correction)
-- Local: ovb 4.000 GB 1 CPU x 48 jobs 192.000 GB 48 CPUs (overlap store bucketizer)
-- Local: ovs 8.000 GB 1 CPU x 48 jobs 384.000 GB 48 CPUs (overlap store sorting)
-- Local: red 32.000 GB 4 CPUs x 12 jobs 384.000 GB 48 CPUs (read error detection)
-- Local: oea 32.000 GB 1 CPU x 48 jobs 1536.000 GB 48 CPUs (overlap error adjustment)
-- Local: bat 200.000 GB 4 CPUs x 1 job 200.000 GB 4 CPUs (contig construction with bogart)
-- Local: cns -.--- GB 4 CPUs x - jobs -.--- GB - CPUs (consensus)
--
-- Found untrimmed raw Nanopore reads in the input files.
--
-- Generating assembly '01_dolphin_feces_SQK-NBD114-24_barcode15' in '/ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/canu_out/01_dolphin_feces_SQK-NBD114-24_barcode15':
-- genomeSize:
-- 2000000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.3200 ( 32.00%)
-- obtOvlErrorRate 0.1600 ( 16.00%)
-- utgOvlErrorRate 0.1600 ( 16.00%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.1600 ( 16.00%)
-- utgErrorRate 0.1600 ( 16.00%)
-- cnsErrorRate 0.1600 ( 16.00%)
--
-- Stages to run:
-- correct raw reads.
-- trim corrected reads.
-- assemble corrected and trimmed reads.
--
--
-- BEGIN CORRECTION
----------------------------------------
-- Starting command on Thu Aug 29 07:35:12 2024 with 5880470.553 GB free disk space
cd .
./01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore.sh \
> ./01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore.err 2>&1
-- Finished on Thu Aug 29 07:37:36 2024 (144 seconds) with 5880456.565 GB free disk space
----------------------------------------
--
-- In sequence store './01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore':
-- Found 797209 reads.
-- Found 1115751947 bases (557.87 times coverage).
-- Histogram of raw reads:
--
-- G=1115751947 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 2447 35297 111576701 || 1000-3439 789247|---------------------------------------------------------------
-- 00020 1934 87274 223150932 || 3440-5879 7374|-
-- 00030 1657 149860 334726414 || 5880-8319 488|-
-- 00040 1471 221507 446302100 || 8320-10759 75|-
-- 00050 1332 301377 557877163 || 10760-13199 13|-
-- 00060 1227 388854 669451297 || 13200-15639 2|-
-- 00070 1149 482970 781026989 || 15640-18079 2|-
-- 00080 1089 582837 892601817 || 18080-20519 2|-
-- 00090 1040 687758 1004177769 || 20520-22959 0|
-- 00100 1000 797208 1115751947 || 22960-25399 1|-
-- 001.000x 797209 1115751947 || 25400-27839 0|
-- || 27840-30279 0|
-- || 30280-32719 2|-
-- || 32720-35159 1|-
-- || 35160-37599 0|
-- || 37600-40039 0|
-- || 40040-42479 0|
-- || 42480-44919 0|
-- || 44920-47359 0|
-- || 47360-49799 1|-
-- || 49800-52239 0|
-- || 52240-54679 0|
-- || 54680-57119 0|
-- || 57120-59559 0|
-- || 59560-61999 0|
-- || 62000-64439 0|
-- || 64440-66879 0|
-- || 66880-69319 0|
-- || 69320-71759 0|
-- || 71760-74199 0|
-- || 74200-76639 0|
-- || 76640-79079 0|
-- || 79080-81519 0|
-- || 81520-83959 0|
-- || 83960-86399 0|
-- || 86400-88839 0|
-- || 88840-91279 0|
-- || 91280-93719 0|
-- || 93720-96159 0|
-- || 96160-98599 0|
-- || 98600-101039 0|
-- || 101040-103479 0|
-- || 103480-105919 0|
-- || 105920-108359 0|
-- || 108360-110799 0|
-- || 110800-113239 0|
-- || 113240-115679 0|
-- || 115680-118119 0|
-- || 118120-120559 0|
-- || 120560-122999 1|-
--
----------------------------------------
-- Starting command on Thu Aug 29 07:37:39 2024 with 5880456.592 GB free disk space
cd correction/0-mercounts
./meryl-configure.sh \
> ./meryl-configure.err 2>&1
-- Finished on Thu Aug 29 07:37:39 2024 (lickety-split) with 5880456.592 GB free disk space
----------------------------------------
-- segments memory batches
-- -------- -------- -------
-- 01 2.35 GB 2
-- 02 1.44 GB 2
-- 04 0.72 GB 2
-- 06 0.48 GB 2
-- 08 0.36 GB 2
--
-- For 797209 reads with 1115751947 bases, limit to 11 batches.
-- Will count kmers using 01 jobs, each using 4 GB and 4 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Aug 29 07:37:40 2024 with 5880456.592 GB free disk space (1 processes; 12 concurrently)
cd correction/0-mercounts
./meryl-count.sh 1 > ./meryl-count.000001.out 2>&1
-- Finished on Thu Aug 29 07:39:08 2024 (88 seconds) with 5880445.471 GB free disk space
----------------------------------------
-- Found 1 Kmer counting (meryl) outputs.
-- Finished stage 'cor-merylCountCheck', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Aug 29 07:39:08 2024 with 5880445.471 GB free disk space (1 processes; 12 concurrently)
cd correction/0-mercounts
./meryl-process.sh 1 > ./meryl-process.000001.out 2>&1
-- Finished on Thu Aug 29 07:39:18 2024 (10 seconds) with 5880444.411 GB free disk space
----------------------------------------
-- Meryl finished successfully. Kmer frequency histogram:
--
-- 16-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 0 0.0000 0.0000
-- 2- 2 84901859 ********************************************************************** 0.5295 0.1814
-- 3- 4 48752975 **************************************** 0.7251 0.2820
-- 5- 7 16970145 ************* 0.8876 0.4026
-- 8- 11 5153508 **** 0.9522 0.4767
-- 12- 16 1866144 * 0.9750 0.5162
-- 17- 22 857680 0.9844 0.5398
-- 23- 29 477057 0.9890 0.5559
-- 30- 37 306136 0.9918 0.5683
-- 38- 46 209198 0.9936 0.5788
-- 47- 56 153468 0.9948 0.5878
-- 57- 67 118075 0.9957 0.5961
-- 68- 79 90957 0.9964 0.6037
-- 80- 92 73074 0.9970 0.6108
-- 93- 106 58842 0.9974 0.6174
-- 107- 121 47860 0.9978 0.6235
-- 122- 137 39346 0.9981 0.6293
-- 138- 154 32866 0.9983 0.6347
-- 155- 172 27457 0.9985 0.6398
-- 173- 191 22528 0.9987 0.6445
-- 192- 211 19821 0.9988 0.6489
-- 212- 232 16958 0.9990 0.6531
-- 233- 254 14718 0.9991 0.6571
-- 255- 277 12478 0.9992 0.6609
-- 278- 301 10403 0.9992 0.6644
-- 302- 326 8656 0.9993 0.6676
-- 327- 352 7403 0.9993 0.6705
-- 353- 379 6630 0.9994 0.6732
-- 380- 407 5785 0.9994 0.6758
-- 408- 436 5243 0.9995 0.6782
-- 437- 466 4744 0.9995 0.6805
-- 467- 497 4313 0.9995 0.6828
-- 498- 529 3823 0.9996 0.6850
-- 530- 562 3483 0.9996 0.6871
-- 563- 596 3214 0.9996 0.6891
-- 597- 631 2780 0.9996 0.6911
-- 632- 667 2546 0.9996 0.6929
-- 668- 704 2116 0.9997 0.6947
-- 705- 742 1982 0.9997 0.6963
-- 743- 781 1712 0.9997 0.6978
-- 782- 821 1828 0.9997 0.6992
--
-- 0 (max occurrences)
-- 935925223 (total mers, non-unique)
-- 160347383 (distinct mers, non-unique)
-- 0 (unique mers)
-- Finished stage 'meryl-process', reset canuIteration.
--
-- Removing meryl database 'correction/0-mercounts/01_dolphin_feces_SQK-NBD114-24_barcode15.ms16'.
--
-- OVERLAPPER (mhap) (correction)
--
--
-- PARAMETERS: hashes=768, minMatches=2, threshold=0.73
--
-- Given 5.4 GB, can fit 8100 reads per block.
-- For 100 blocks, set stride to 25 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 99 mhap precompute jobs.
-- Configured 243 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Aug 29 07:39:20 2024 with 5880444.315 GB free disk space (99 processes; 3 concurrently)
cd correction/1-overlapper
./precompute.sh 1 > ./precompute.000001.out 2>&1
./precompute.sh 2 > ./precompute.000002.out 2>&1
./precompute.sh 3 > ./precompute.000003.out 2>&1
./precompute.sh 4 > ./precompute.000004.out 2>&1
./precompute.sh 5 > ./precompute.000005.out 2>&1
./precompute.sh 6 > ./precompute.000006.out 2>&1
./precompute.sh 7 > ./precompute.000007.out 2>&1
./precompute.sh 8 > ./precompute.000008.out 2>&1
./precompute.sh 9 > ./precompute.000009.out 2>&1
./precompute.sh 10 > ./precompute.000010.out 2>&1
./precompute.sh 11 > ./precompute.000011.out 2>&1
./precompute.sh 12 > ./precompute.000012.out 2>&1
./precompute.sh 13 > ./precompute.000013.out 2>&1
./precompute.sh 14 > ./precompute.000014.out 2>&1
./precompute.sh 15 > ./precompute.000015.out 2>&1
./precompute.sh 16 > ./precompute.000016.out 2>&1
./precompute.sh 17 > ./precompute.000017.out 2>&1
./precompute.sh 18 > ./precompute.000018.out 2>&1
./precompute.sh 19 > ./precompute.000019.out 2>&1
./precompute.sh 20 > ./precompute.000020.out 2>&1
./precompute.sh 21 > ./precompute.000021.out 2>&1
./precompute.sh 22 > ./precompute.000022.out 2>&1
./precompute.sh 23 > ./precompute.000023.out 2>&1
./precompute.sh 24 > ./precompute.000024.out 2>&1
./precompute.sh 25 > ./precompute.000025.out 2>&1
./precompute.sh 26 > ./precompute.000026.out 2>&1
./precompute.sh 27 > ./precompute.000027.out 2>&1
./precompute.sh 28 > ./precompute.000028.out 2>&1
./precompute.sh 29 > ./precompute.000029.out 2>&1
./precompute.sh 30 > ./precompute.000030.out 2>&1
./precompute.sh 31 > ./precompute.000031.out 2>&1
./precompute.sh 32 > ./precompute.000032.out 2>&1
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./precompute.sh 40 > ./precompute.000040.out 2>&1
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./precompute.sh 46 > ./precompute.000046.out 2>&1
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./precompute.sh 48 > ./precompute.000048.out 2>&1
./precompute.sh 49 > ./precompute.000049.out 2>&1
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./precompute.sh 54 > ./precompute.000054.out 2>&1
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./precompute.sh 57 > ./precompute.000057.out 2>&1
./precompute.sh 58 > ./precompute.000058.out 2>&1
./precompute.sh 59 > ./precompute.000059.out 2>&1
./precompute.sh 60 > ./precompute.000060.out 2>&1
./precompute.sh 61 > ./precompute.000061.out 2>&1
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./precompute.sh 64 > ./precompute.000064.out 2>&1
./precompute.sh 65 > ./precompute.000065.out 2>&1
./precompute.sh 66 > ./precompute.000066.out 2>&1
./precompute.sh 67 > ./precompute.000067.out 2>&1
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./precompute.sh 70 > ./precompute.000070.out 2>&1
./precompute.sh 71 > ./precompute.000071.out 2>&1
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./precompute.sh 80 > ./precompute.000080.out 2>&1
./precompute.sh 81 > ./precompute.000081.out 2>&1
./precompute.sh 82 > ./precompute.000082.out 2>&1
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./precompute.sh 84 > ./precompute.000084.out 2>&1
./precompute.sh 85 > ./precompute.000085.out 2>&1
./precompute.sh 86 > ./precompute.000086.out 2>&1
./precompute.sh 87 > ./precompute.000087.out 2>&1
./precompute.sh 88 > ./precompute.000088.out 2>&1
./precompute.sh 89 > ./precompute.000089.out 2>&1
./precompute.sh 90 > ./precompute.000090.out 2>&1
./precompute.sh 91 > ./precompute.000091.out 2>&1
./precompute.sh 92 > ./precompute.000092.out 2>&1
./precompute.sh 93 > ./precompute.000093.out 2>&1
./precompute.sh 94 > ./precompute.000094.out 2>&1
./precompute.sh 95 > ./precompute.000095.out 2>&1
./precompute.sh 96 > ./precompute.000096.out 2>&1
./precompute.sh 97 > ./precompute.000097.out 2>&1
./precompute.sh 98 > ./precompute.000098.out 2>&1
./precompute.sh 99 > ./precompute.000099.out 2>&1
-- Finished on Thu Aug 29 07:52:54 2024 (814 seconds) with 5880404.83 GB free disk space
----------------------------------------
-- All 99 mhap precompute jobs finished successfully.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Aug 29 07:52:54 2024 with 5880404.83 GB free disk space (243 processes; 3 concurrently)
cd correction/1-overlapper
./mhap.sh 1 > ./mhap.000001.out 2>&1
./mhap.sh 2 > ./mhap.000002.out 2>&1
./mhap.sh 3 > ./mhap.000003.out 2>&1
./mhap.sh 4 > ./mhap.000004.out 2>&1
./mhap.sh 5 > ./mhap.000005.out 2>&1
./mhap.sh 6 > ./mhap.000006.out 2>&1
./mhap.sh 7 > ./mhap.000007.out 2>&1
./mhap.sh 8 > ./mhap.000008.out 2>&1
./mhap.sh 9 > ./mhap.000009.out 2>&1
./mhap.sh 10 > ./mhap.000010.out 2>&1
./mhap.sh 11 > ./mhap.000011.out 2>&1
./mhap.sh 12 > ./mhap.000012.out 2>&1
./mhap.sh 13 > ./mhap.000013.out 2>&1
./mhap.sh 14 > ./mhap.000014.out 2>&1
./mhap.sh 15 > ./mhap.000015.out 2>&1
./mhap.sh 16 > ./mhap.000016.out 2>&1
./mhap.sh 17 > ./mhap.000017.out 2>&1
./mhap.sh 18 > ./mhap.000018.out 2>&1
./mhap.sh 19 > ./mhap.000019.out 2>&1
./mhap.sh 20 > ./mhap.000020.out 2>&1
./mhap.sh 21 > ./mhap.000021.out 2>&1
./mhap.sh 22 > ./mhap.000022.out 2>&1
./mhap.sh 23 > ./mhap.000023.out 2>&1
./mhap.sh 24 > ./mhap.000024.out 2>&1
./mhap.sh 25 > ./mhap.000025.out 2>&1
./mhap.sh 26 > ./mhap.000026.out 2>&1
./mhap.sh 27 > ./mhap.000027.out 2>&1
./mhap.sh 28 > ./mhap.000028.out 2>&1
./mhap.sh 29 > ./mhap.000029.out 2>&1
./mhap.sh 30 > ./mhap.000030.out 2>&1
./mhap.sh 31 > ./mhap.000031.out 2>&1
./mhap.sh 32 > ./mhap.000032.out 2>&1
./mhap.sh 33 > ./mhap.000033.out 2>&1
./mhap.sh 34 > ./mhap.000034.out 2>&1
./mhap.sh 35 > ./mhap.000035.out 2>&1
./mhap.sh 36 > ./mhap.000036.out 2>&1
./mhap.sh 37 > ./mhap.000037.out 2>&1
./mhap.sh 38 > ./mhap.000038.out 2>&1
./mhap.sh 39 > ./mhap.000039.out 2>&1
./mhap.sh 40 > ./mhap.000040.out 2>&1
./mhap.sh 41 > ./mhap.000041.out 2>&1
./mhap.sh 42 > ./mhap.000042.out 2>&1
./mhap.sh 43 > ./mhap.000043.out 2>&1
./mhap.sh 44 > ./mhap.000044.out 2>&1
./mhap.sh 45 > ./mhap.000045.out 2>&1
./mhap.sh 46 > ./mhap.000046.out 2>&1
./mhap.sh 47 > ./mhap.000047.out 2>&1
./mhap.sh 48 > ./mhap.000048.out 2>&1
./mhap.sh 49 > ./mhap.000049.out 2>&1
./mhap.sh 50 > ./mhap.000050.out 2>&1
./mhap.sh 51 > ./mhap.000051.out 2>&1
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./mhap.sh 60 > ./mhap.000060.out 2>&1
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./mhap.sh 96 > ./mhap.000096.out 2>&1
./mhap.sh 97 > ./mhap.000097.out 2>&1
./mhap.sh 98 > ./mhap.000098.out 2>&1
./mhap.sh 99 > ./mhap.000099.out 2>&1
./mhap.sh 100 > ./mhap.000100.out 2>&1
./mhap.sh 101 > ./mhap.000101.out 2>&1
./mhap.sh 102 > ./mhap.000102.out 2>&1
./mhap.sh 103 > ./mhap.000103.out 2>&1
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-- Finished on Fri Aug 30 03:29:46 2024 (70612 seconds, like watching paint dry) with 5879138.456 GB free disk space
----------------------------------------
--
-- Mhap overlap jobs failed, retry.
-- job correction/1-overlapper/results/000015.ovb FAILED.
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--
--
-- Running jobs. Second attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Fri Aug 30 03:29:46 2024 with 5879138.456 GB free disk space (229 processes; 3 concurrently)
cd correction/1-overlapper
./mhap.sh 15 > ./mhap.000015.out 2>&1
./mhap.sh 16 > ./mhap.000016.out 2>&1
./mhap.sh 17 > ./mhap.000017.out 2>&1
./mhap.sh 18 > ./mhap.000018.out 2>&1
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-- Finished on Fri Aug 30 03:29:53 2024 (7 seconds) with 5879138.347 GB free disk space
----------------------------------------
--
-- Mhap overlap jobs failed, tried 2 times, giving up.
-- job correction/1-overlapper/results/000015.ovb FAILED.
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-- job correction/1-overlapper/results/000182.ovb FAILED.
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-- job correction/1-overlapper/results/000184.ovb FAILED.
-- job correction/1-overlapper/results/000185.ovb FAILED.
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-- job correction/1-overlapper/results/000188.ovb FAILED.
-- job correction/1-overlapper/results/000189.ovb FAILED.
-- job correction/1-overlapper/results/000190.ovb FAILED.
-- job correction/1-overlapper/results/000191.ovb FAILED.
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-- job correction/1-overlapper/results/000194.ovb FAILED.
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-- job correction/1-overlapper/results/000196.ovb FAILED.
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-- job correction/1-overlapper/results/000198.ovb FAILED.
-- job correction/1-overlapper/results/000199.ovb FAILED.
-- job correction/1-overlapper/results/000200.ovb FAILED.
-- job correction/1-overlapper/results/000201.ovb FAILED.
-- job correction/1-overlapper/results/000202.ovb FAILED.
-- job correction/1-overlapper/results/000203.ovb FAILED.
-- job correction/1-overlapper/results/000204.ovb FAILED.
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-- job correction/1-overlapper/results/000206.ovb FAILED.
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-- job correction/1-overlapper/results/000210.ovb FAILED.
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-- job correction/1-overlapper/results/000212.ovb FAILED.
-- job correction/1-overlapper/results/000213.ovb FAILED.
-- job correction/1-overlapper/results/000214.ovb FAILED.
-- job correction/1-overlapper/results/000215.ovb FAILED.
-- job correction/1-overlapper/results/000216.ovb FAILED.
-- job correction/1-overlapper/results/000217.ovb FAILED.
-- job correction/1-overlapper/results/000218.ovb FAILED.
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-- job correction/1-overlapper/results/000220.ovb FAILED.
-- job correction/1-overlapper/results/000221.ovb FAILED.
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-- job correction/1-overlapper/results/000223.ovb FAILED.
-- job correction/1-overlapper/results/000224.ovb FAILED.
-- job correction/1-overlapper/results/000225.ovb FAILED.
-- job correction/1-overlapper/results/000226.ovb FAILED.
-- job correction/1-overlapper/results/000227.ovb FAILED.
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-- job correction/1-overlapper/results/000240.ovb FAILED.
-- job correction/1-overlapper/results/000241.ovb FAILED.
-- job correction/1-overlapper/results/000242.ovb FAILED.
-- job correction/1-overlapper/results/000243.ovb FAILED.
--
ABORT:
ABORT: canu 2.2
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting. If that doesn't work, ask for help.
THANKS for your help and all you do!
I don't think memory is an issue as the jobs are only running 3 at a time using a total of 18gb and you're reserving 192 by cores. I suspect it's more likely you hit a disk quota since the initial precompute ran without issue and the first few jobs ran but everything from 15 onwards failed. What does one of the logs like correction/1-overlapper/000015.err
say?
Hi thanks for your response, but I could not find that error log.
I only found one .err log and this is what it says:
-rw-r--r-- 1 kvigil tulaneusers 9662 Aug 29 07:39 01_dolphin_feces_SQK-NBD114-24_barcode15.report
drwxr-xr-x 3 kvigil tulaneusers 4096 Aug 29 07:37 01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore
-rw-r--r-- 1 kvigil tulaneusers 962 Aug 29 07:37 01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore.err
-rwxr-xr-x 1 kvigil tulaneusers 1234 Aug 29 07:35 01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore.sh
drwxr-xr-x 2 kvigil tulaneusers 4096 Aug 29 07:35 canu-logs
drwxr-xr-x 2 kvigil tulaneusers 4096 Aug 29 07:35 canu-scripts
drwxr-xr-x 4 kvigil tulaneusers 4096 Aug 29 07:39 correction
Found perl:
/work/kvigil/.conda/envs/canu-env/bin/perl
This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi
Found java:
/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java
openjdk version "22.0.1-internal" 2024-04-16
Found canu:
/ddnB/work/kvigil/.conda/envs/canu-env/bin/canu
canu 2.2
Creating library '01_dolphin_feces_SQK-NBD114-24_barcode15' for Nanopore raw reads.
reads bases
---------- --------- ------ ------------ ------
Loaded 797209 4.2% 1115751947 10.7% /ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/fastq/01_dolphin_feces_SQK-NBD114-24_barcode15.fastq
Short 18105370 95.8% 9267004423 89.3%
All reads processed.
reads bases
---------- --------- ------ ------------ ------
Loaded 797209 4.2% 1115751947 10.7%
Short 18105370 95.8% 9267004423 89.3%
Bye.
I will move files off this drive on the HPC and rerun and let you know if I run into the same issue thanks!
The log file ends in .out not err, sorry. It should be in the correction/1-overlapper folder.
Also from this log it looks about 90% of your reads are shorter than 1kb and are being discarded. Do you expect your data to be this short? You probably need to adjust the overlap size and read length minimums to use more of the input sequences. Also take a look at the FAQ for metagenomic parameters to include if you aren't already.
Got it here you go:
(base) [kvigil@qbc1 1-overlapper]$ cat precompute.000015.out
Found perl:
/work/kvigil/.conda/envs/canu-env/bin/perl
This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi
Found java:
/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java
openjdk version "22.0.1-internal" 2024-04-16
Found canu:
/ddnB/work/kvigil/.conda/envs/canu-env/bin/canu
canu 2.2
Running job 15 based on command line options.
/ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/canu_out/01_dolphin_feces_SQK-NBD114-24_barcode15/correction/1-overlapper
Opened seqStore '../../01_dolphin_feces_SQK-NBD114-24_barcode15.seqStore' for 'raw' reads.
Dumping raw reads from 113401 to 121500 (inclusive).
Starting mhap precompute.
Running with these settings:
--filter-threshold = 1.0E-7
--help = false
--max-shift = 0.2
--min-olap-length = 500
--min-store-length = 0
--no-rc = false
--no-self = false
--no-tf = false
--num-hashes = 768
--num-min-matches = 2
--num-threads = 16
--ordered-kmer-size = 12
--ordered-sketch-size = 1536
--repeat-idf-scale = 10.0
--repeat-weight = 0.9
--settings = 0
--store-full-id = true
--supress-noise = 0
--threshold = 0.73
--version = false
-f = ../../0-mercounts/01_dolphin_feces_SQK-NBD114-24_barcode15.ms16.ignore.gz
-h = false
-k = 16
-p = ./000015.input.fasta
-q = .
-s =
Reading in filter file ../../0-mercounts/01_dolphin_feces_SQK-NBD114-24_barcode15.ms16.ignore.gz.
Read in values for repeat 0 and 0
Warning, k-mer filter file has zero elements.
Initializing
Initialized
Time (s) to read filter file: 0.049834497000000005
Read in k-mer filter for sizes: []
Processing FASTA files for binary compression...
Current # sequences loaded and processed from file: 5000...
Current # sequences loaded and processed from file: 10000...
Current # sequences loaded and processed from file: 15000...
Processed 16200 sequences (fwd and rev).
Read, hashed, and stored file ./000015.input.fasta to ./000015.input.dat.
Time (s): 23.850577403000003
Total time (s): 23.851308347
I think my reads will have low read length, because I did metagenomic sequencing of viruses from marine mammal stool and serum and oysters, mussels and seawater (~100 samples). I ended up re-basecalling everything using Nanopore's Dorado 0.7.0 super high accuracy basecaller and I am only having issues with the marine mammal dolphin and sea lion stool samples, but these samples have big fastq files so I was not sure if it was a memory thing or like you suggested a storage issue. @skoren Thanks for helping! How do you suggest I change my Canu script?
That's the previous steps, log, we want mhap.000015.out
rather than precompute.000015.out
What's your current canu command for this assembly?
(base) [kvigil@qbc1 1-overlapper]$ cat mhap.000015.out
Found perl:
/work/kvigil/.conda/envs/canu-env/bin/perl
perl: error while loading shared libraries: libcrypt.so.2: cannot open shared object file: No such file or directory
Found java:
/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java
Error occurred during initialization of VM
Found canu:
/ddnB/work/kvigil/.conda/envs/canu-env/bin/canu
perl: error while loading shared libraries: libcrypt.so.2: cannot open shared object file: No such file or directory
Running job 15 based on command line options.
Fetch blocks/000055.dat
Fetch blocks/000056.dat
Fetch blocks/000057.dat
Fetch blocks/000058.dat
Fetch blocks/000059.dat
Fetch blocks/000060.dat
Fetch blocks/000061.dat
Fetch blocks/000062.dat
Fetch blocks/000063.dat
Fetch blocks/000064.dat
Fetch blocks/000065.dat
Fetch blocks/000066.dat
Fetch blocks/000067.dat
Fetch blocks/000068.dat
Fetch blocks/000069.dat
Fetch blocks/000070.dat
Fetch blocks/000071.dat
Fetch blocks/000072.dat
Fetch blocks/000073.dat
Fetch blocks/000074.dat
Fetch blocks/000075.dat
Fetch blocks/000076.dat
Fetch blocks/000077.dat
Fetch blocks/000078.dat
Fetch blocks/000079.dat
Running block 000004 in query 000015
It looks like a issue with your compute nodes. The precompute shows everything was working fine (java, perl, etc) but now neither is able to run and if failing. That is compare this:
Found perl:
/work/kvigil/.conda/envs/canu-env/bin/perl
This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi
Found java:
/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java
openjdk version "22.0.1-internal" 2024-04-16
Found canu:
/ddnB/work/kvigil/.conda/envs/canu-env/bin/canu
canu 2.2
to this
Found perl:
/work/kvigil/.conda/envs/canu-env/bin/perl
perl: error while loading shared libraries: libcrypt.so.2: cannot open shared object file: No such file or directory
Found java:
/work/kvigil/.conda/envs/canu-env/lib/jvm/bin/java
Error occurred during initialization of VM
Found canu:
/ddnB/work/kvigil/.conda/envs/canu-env/bin/canu
perl: error while loading shared libraries: libcrypt.so.2: cannot open shared object file: No such file or directory
The fact that the same system ran jobs before implies a configuration change mid-run. Nothing in canu can change or fix that, you'd have to ask your system admins what happened.
Thank you for troubleshooting this I will consult them and re-run the samples.
Hi I am running a large dolphin feces nanopore sequencing fastq file and I am running into memory issues I think...
How much memory should I ask for to run this sample? Thanks! Katie
Canu v2.2 Using Loni HPC system "single" node see below for details:
Script:
canu report log: