katievigil
commented
2 years ago Closed katievigil closed 1 year ago
katievigil
commented
2 years ago katievigil
commented
2 years ago I am wondering why this failed? Thanks!
skoren
commented
2 years ago I'm going to guess you either have no overlaps or some corruption of a file from an earlier step. Do you have the report file from this run and/or are you able to share the input data?
katievigil
commented
2 years ago Serum Canu Report
[CORRECTION/READS]
--
-- In sequence store './serumcanu.seqStore':
-- Found 382922 reads.
-- Found 480001210 bases (100 times coverage).
-- Histogram of raw reads:
--
-- G=480001210 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 1665 24963 48001009 || 1000-1110 126794|---------------------------------------------------------------
-- 00020 1486 55585 96000820 || 1111-1221 90455|---------------------------------------------
-- 00030 1353 89625 144000889 || 1222-1332 68023|----------------------------------
-- 00040 1281 126179 192000846 || 1333-1443 34456|------------------
-- 00050 1223 164523 240001313 || 1444-1554 21504|-----------
-- 00060 1169 204674 288001466 || 1555-1665 16831|---------
-- 00070 1121 246622 336001242 || 1666-1776 10389|------
-- 00080 1078 290314 384001958 || 1777-1887 4382|---
-- 00090 1036 335751 432001593 || 1888-1998 3009|--
-- 00100 1000 382921 480001210 || 1999-2109 2481|--
-- 001.000x 382922 480001210 || 2110-2220 1525|-
-- || 2221-2331 944|-
-- || 2332-2442 671|-
-- || 2443-2553 409|-
-- || 2554-2664 307|-
-- || 2665-2775 232|-
-- || 2776-2886 157|-
-- || 2887-2997 107|-
-- || 2998-3108 67|-
-- || 3109-3219 49|-
-- || 3220-3330 41|-
-- || 3331-3441 23|-
-- || 3442-3552 13|-
-- || 3553-3663 6|-
-- || 3664-3774 5|-
-- || 3775-3885 6|-
-- || 3886-3996 5|-
-- || 3997-4107 7|-
-- || 4108-4218 7|-
-- || 4219-4329 3|-
-- || 4330-4440 3|-
-- || 4441-4551 0|
-- || 4552-4662 2|-
-- || 4663-4773 2|-
-- || 4774-4884 1|-
-- || 4885-4995 1|-
-- || 4996-5106 1|-
-- || 5107-5217 1|-
-- || 5218-5328 1|-
-- || 5329-5439 0|
-- || 5440-5550 1|-
-- || 5551-5661 0|
-- || 5662-5772 0|
-- || 5773-5883 0|
-- || 5884-5994 0|
-- || 5995-6105 0|
-- || 6106-6216 0|
-- || 6217-6327 0|
-- || 6328-6438 0|
-- || 6439-6549 1|-
--
[CORRECTION/MERS]
--
-- 16-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 0 0.0000 0.0000
-- 2- 2 9990280 ********************************************************************** 0.4944 0.0500
-- 3- 4 4955187 ********************************** 0.6588 0.0749
-- 5- 7 2081543 ************** 0.7878 0.1034
-- 8- 11 1038265 ******* 0.8601 0.1283
-- 12- 16 595342 **** 0.9018 0.1499
-- 17- 22 376314 ** 0.9275 0.1691
-- 23- 29 248845 * 0.9444 0.1863
-- 30- 37 173551 * 0.9558 0.2018
-- 38- 46 128081 0.9639 0.2158
-- 47- 56 96658 0.9700 0.2289
-- 57- 67 75814 0.9746 0.2411
-- 68- 79 60263 0.9783 0.2527
-- 80- 92 48711 0.9812 0.2635
-- 93- 106 39944 0.9835 0.2739
-- 107- 121 33331 0.9855 0.2838
-- 122- 137 27361 0.9871 0.2931
-- 138- 154 22822 0.9884 0.3019
-- 155- 172 19684 0.9895 0.3102
-- 173- 191 17479 0.9905 0.3182
-- 192- 211 15356 0.9914 0.3261
-- 212- 232 12976 0.9921 0.3338
-- 233- 254 11341 0.9927 0.3409
-- 255- 277 10062 0.9933 0.3478
-- 278- 301 8979 0.9938 0.3545
-- 302- 326 7835 0.9942 0.3610
-- 327- 352 7267 0.9946 0.3671
-- 353- 379 6662 0.9950 0.3733
-- 380- 407 6287 0.9953 0.3793
-- 408- 436 5594 0.9956 0.3855
-- 437- 466 5268 0.9959 0.3914
-- 467- 497 4759 0.9961 0.3974
-- 498- 529 4433 0.9964 0.4031
-- 530- 562 4103 0.9966 0.4088
-- 563- 596 3828 0.9968 0.4144
-- 597- 631 3466 0.9970 0.4199
-- 632- 667 3169 0.9972 0.4252
-- 668- 704 2993 0.9973 0.4303
-- 705- 742 2629 0.9975 0.4355
-- 743- 781 2509 0.9976 0.4403
-- 782- 821 2324 0.9977 0.4450
--
-- 0 (max occurrences)
-- 399656845 (total mers, non-unique)
-- 20205073 (distinct mers, non-unique)
-- 0 (unique mers)
[CORRECTION/LAYOUT]
-- original original
-- raw reads raw reads
-- category w/overlaps w/o/overlaps
-- -------------------- ------------- -------------
-- Number of Reads 361303 1702042
-- Number of Bases 454030373 22542732
-- Coverage 94.590 4.696
-- Median 1188 0
-- Mean 1256 13
-- N50 1226 1186
-- Minimum 1000 0
-- Maximum 6521 3071
--
-- --------corrected--------- ----------rescued----------
-- evidence expected expected
-- category reads raw corrected raw corrected
-- -------------------- ------------- ------------- ------------- ------------- -------------
-- Number of Reads 318627 132637 132637 40085 40085
-- Number of Bases 409419087 194997824 192000015 43875749 43160967
-- Coverage 85.296 40.625 40.000 9.141 8.992
-- Median 1226 1384 1364 1088 1070
-- Mean 1284 1470 1447 1094 1076
-- N50 1262 1416 1397 1091 1073
-- Minimum 1000 1215 1214 1002 1001
-- Maximum 6521 5253 4800 2346 1213
--
-- --------uncorrected--------
-- expected
-- category raw corrected
-- -------------------- ------------- -------------
-- Number of Reads 1890623 1890623
-- Number of Bases 237699532 160846564
-- Coverage 49.521 33.510
-- Median 0 0
-- Mean 125 85
-- N50 1128 1085
-- Minimum 0 0
-- Maximum 6521 5527
--
-- Maximum Memory 584196650
[TRIMMING/READS]
--
-- In sequence store './serumcanu.seqStore':
-- Found 147016 reads.
-- Found 192828947 bases (40.17 times coverage).
-- Histogram of corrected reads:
--
-- G=192828947 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 1658 10440 19283228 || 1000-1066 17436|---------------------------------------
-- 00020 1523 22614 38566448 || 1067-1133 13344|------------------------------
-- 00030 1414 35709 57849021 || 1134-1200 12513|----------------------------
-- 00040 1346 49702 77132110 || 1201-1267 28367|---------------------------------------------------------------
-- 00050 1293 64345 96414912 || 1268-1334 23150|----------------------------------------------------
-- 00060 1259 79469 115698203 || 1335-1401 14514|---------------------------------
-- 00070 1225 94998 134981300 || 1402-1468 7796|------------------
-- 00080 1164 111069 154264172 || 1469-1535 8861|--------------------
-- 00090 1071 128381 173546935 || 1536-1602 6713|---------------
-- 00100 1000 147015 192828947 || 1603-1669 4802|-----------
-- 001.000x 147016 192828947 || 1670-1736 3721|---------
-- || 1737-1803 1459|----
-- || 1804-1870 884|--
-- || 1871-1937 691|--
-- || 1938-2004 851|--
-- || 2005-2071 576|--
-- || 2072-2138 363|-
-- || 2139-2205 300|-
-- || 2206-2272 153|-
-- || 2273-2339 123|-
-- || 2340-2406 111|-
-- || 2407-2473 57|-
-- || 2474-2540 54|-
-- || 2541-2607 47|-
-- || 2608-2674 24|-
-- || 2675-2741 29|-
-- || 2742-2808 13|-
-- || 2809-2875 17|-
-- || 2876-2942 5|-
-- || 2943-3009 12|-
-- || 3010-3076 8|-
-- || 3077-3143 6|-
-- || 3144-3210 4|-
-- || 3211-3277 2|-
-- || 3278-3344 4|-
-- || 3345-3411 1|-
-- || 3412-3478 3|-
-- || 3479-3545 0|
-- || 3546-3612 0|
-- || 3613-3679 1|-
-- || 3680-3746 0|
-- || 3747-3813 0|
-- || 3814-3880 0|
-- || 3881-3947 0|
-- || 3948-4014 0|
-- || 4015-4081 0|
-- || 4082-4148 0|
-- || 4149-4215 0|
-- || 4216-4282 0|
-- || 4283-4349 1|-
--
[TRIMMING/MERS]
--
-- 22-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 0 0.0000 0.0000
-- 2- 2 569303 ********************************************************************** 0.3344 0.0061
-- 3- 4 390439 ************************************************ 0.4805 0.0102
-- 5- 7 203463 ************************* 0.6170 0.0157
-- 8- 11 117542 ************** 0.7058 0.0212
-- 12- 16 76175 ********* 0.7628 0.0266
-- 17- 22 49273 ****** 0.8028 0.0320
-- 23- 29 36363 **** 0.8296 0.0370
-- 30- 37 28343 *** 0.8499 0.0420
-- 38- 46 23960 ** 0.8660 0.0471
-- 47- 56 20917 ** 0.8794 0.0524
-- 57- 67 18118 ** 0.8914 0.0582
-- 68- 79 15775 * 0.9018 0.0642
-- 80- 92 16686 ** 0.9109 0.0704
-- 93- 106 13662 * 0.9206 0.0781
-- 107- 121 10840 * 0.9284 0.0853
-- 122- 137 9151 * 0.9346 0.0918
-- 138- 154 10084 * 0.9401 0.0984
-- 155- 172 7447 0.9460 0.1064
-- 173- 191 6606 0.9504 0.1130
-- 192- 211 4666 0.9540 0.1191
-- 212- 232 4945 0.9568 0.1242
-- 233- 254 4553 0.9596 0.1301
-- 255- 277 4475 0.9623 0.1361
-- 278- 301 3406 0.9649 0.1425
-- 302- 326 3221 0.9669 0.1477
-- 327- 352 3397 0.9688 0.1532
-- 353- 379 2713 0.9708 0.1594
-- 380- 407 2292 0.9724 0.1647
-- 408- 436 3074 0.9737 0.1696
-- 437- 466 2550 0.9755 0.1766
-- 467- 497 2495 0.9770 0.1828
-- 498- 529 1890 0.9785 0.1892
-- 530- 562 2176 0.9796 0.1945
-- 563- 596 1488 0.9808 0.2008
-- 597- 631 1743 0.9817 0.2055
-- 632- 667 1068 0.9827 0.2112
-- 668- 704 1383 0.9834 0.2149
-- 705- 742 1473 0.9842 0.2200
-- 743- 781 1092 0.9850 0.2258
-- 782- 821 805 0.9857 0.2303
--
-- 0 (max occurrences)
-- 185527350 (total mers, non-unique)
-- 1702670 (distinct mers, non-unique)
-- 0 (unique mers)Serum report
[CORRECTION/READS]
--
-- In sequence store './serum.seqStore':
-- Found 383198 reads.
-- Found 480000209 bases (100 times coverage).
-- Histogram of raw reads:
--
-- G=480000209 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 1661 25025 48000363 || 1000-1119 136049|---------------------------------------------------------------
-- 00020 1485 55687 96001101 || 1120-1239 94118|--------------------------------------------
-- 00030 1352 89755 144001065 || 1240-1359 66027|-------------------------------
-- 00040 1280 126339 192000604 || 1360-1479 30394|---------------
-- 00050 1223 164701 240000978 || 1480-1599 22848|-----------
-- 00060 1168 204870 288000581 || 1600-1719 15258|--------
-- 00070 1120 246850 336000474 || 1720-1839 6897|----
-- 00080 1077 290572 384001145 || 1840-1959 3557|--
-- 00090 1036 336022 432000756 || 1960-2079 3022|--
-- 00100 1000 383197 480000209 || 2080-2199 1789|-
-- 001.000x 383198 480000209 || 2200-2319 1135|-
-- || 2320-2439 670|-
-- || 2440-2559 464|-
-- || 2560-2679 316|-
-- || 2680-2799 202|-
-- || 2800-2919 141|-
-- || 2920-3039 81|-
-- || 3040-3159 60|-
-- || 3160-3279 62|-
-- || 3280-3399 27|-
-- || 3400-3519 21|-
-- || 3520-3639 16|-
-- || 3640-3759 4|-
-- || 3760-3879 9|-
-- || 3880-3999 5|-
-- || 4000-4119 4|-
-- || 4120-4239 6|-
-- || 4240-4359 2|-
-- || 4360-4479 3|-
-- || 4480-4599 0|
-- || 4600-4719 1|-
-- || 4720-4839 1|-
-- || 4840-4959 1|-
-- || 4960-5079 1|-
-- || 5080-5199 1|-
-- || 5200-5319 2|-
-- || 5320-5439 0|
-- || 5440-5559 0|
-- || 5560-5679 0|
-- || 5680-5799 1|-
-- || 5800-5919 0|
-- || 5920-6039 0|
-- || 6040-6159 1|-
-- || 6160-6279 0|
-- || 6280-6399 0|
-- || 6400-6519 0|
-- || 6520-6639 1|-
-- || 6640-6759 0|
-- || 6760-6879 0|
-- || 6880-6999 1|-
-- What are the two different reports? One looks like it made it past the correction step.
katievigil
commented
2 years ago I am doing viral metagenomics and do now know what my genome size is or what parameters to use. My FASTQ sequencing file size is 17,647,403,666. However, my other 2 sequencing files that are 18,000,000,000 in size , this default code worked: canu -p fecesRNA -d /lustre/project/taw/ONRPan/canu/fecesRNA genomeSize=4.8m maxInputCoverage=100 –nanopore fecesRNA.fastq
skoren
commented
2 years ago There are metagenomic parameters suggested on the FAQ: https://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak
katievigil
commented
2 years ago Ok thanks I will try that! My other 2 large files worked with the code I listed up there, I am not sure what is up with this file, but I will check the FAQ.
katievigil
commented
2 years ago (/lustre/project/taw/share/conda-envs/ONRviral) [kvigil@cypress01-055 fastq_concat]$ canu -p serum -d /lustre/project/taw/ONRPan/canu/serum genomeSize=4.8m maxInputCoverage=10000 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 redMemory=32 oeaMemory=32 batMemory=200 correctedErrorRate=0.12 -nanopore serum.fastq
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
-- 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 '10.0.2' (from '/lustre/project/taw/share/conda-envs/ONRviral/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 3 ' (from 'gnuplot') and image format 'png'.
--
-- Detected 20 CPUs and 64000 gigabytes of memory on the local machine.
--
-- Detected Slurm with 'sinfo' binary in /cm/shared/apps/slurm/14.03.0/bin/sinfo.
-- Detected Slurm with task IDs up to 1000 allowed.
--
-- Slurm support detected. Resources available:
-- 30 hosts with 20 cores and 62 GB memory.
-- 49 hosts with 20 cores and 124 GB memory.
-- 41 hosts with 20 cores and 249 GB memory.
--
-- (tag)Threads
-- (tag)Memory |
-- (tag) | | algorithm
-- ------- ---------- -------- -----------------------------
-- Grid: meryl 12.000 GB 4 CPUs (k-mer counting)
-- Grid: hap 8.000 GB 4 CPUs (read-to-haplotype assignment)
-- Grid: cormhap 6.000 GB 10 CPUs (overlap detection with mhap)
-- Grid: obtovl 4.000 GB 5 CPUs (overlap detection)
-- Grid: utgovl 4.000 GB 5 CPUs (overlap detection)
-- Grid: cor -.--- GB 4 CPUs (read correction)
-- Grid: ovb 4.000 GB 1 CPU (overlap store bucketizer)
-- Grid: ovs 8.000 GB 1 CPU (overlap store sorting)
-- Grid: red 32.000 GB 4 CPUs (read error detection)
-- Grid: oea 32.000 GB 1 CPU (overlap error adjustment)
-- Grid: bat 200.000 GB 4 CPUs (contig construction with bogart)
-- Grid: cns -.--- GB 4 CPUs (consensus)
--
-- Found Nanopore reads in 'serum.seqStore':
-- Libraries:
-- Nanopore: 1
-- Reads:
-- Raw: 480000209
--
--
-- Generating assembly 'serum' in '/lustre/project/taw/ONRPan/canu/serum':
-- genomeSize:
-- 4800000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.3200 ( 32.00%)
-- obtOvlErrorRate 0.1200 ( 12.00%)
-- utgOvlErrorRate 0.1200 ( 12.00%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.1200 ( 12.00%)
-- utgErrorRate 0.1200 ( 12.00%)
-- cnsErrorRate 0.1200 ( 12.00%)
--
-- Stages to run:
-- correct raw reads.
-- trim corrected reads.
-- assemble corrected and trimmed reads.
--
--
-- BEGIN CORRECTION
----------------------------------------
-- Starting command on Tue Aug 30 10:58:24 2022 with 239809.235 GB free disk space
cd correction
/lustre/project/taw/share/conda-envs/ONRviral/bin/ovStoreConfig \
-S ../serum.seqStore \
-M 4-8 \
-L ./1-overlapper/ovljob.files \
-create ./serum.ovlStore.config \
> ./serum.ovlStore.config.txt \
2> ./serum.ovlStore.config.err
sh: line 6: 55138 Segmentation fault /lustre/project/taw/share/conda-envs/ONRviral/bin/ovStoreConfig -S ../serum.seqStore -M 4-8 -L ./1-overlapper/ovljob.files -create ./serum.ovlStore.config > ./serum.ovlStore.config.txt 2> ./serum.ovlStore.config.err
-- Finished on Tue Aug 30 10:58:24 2022 (fast as lightning) with 239809.235 GB free disk space
----------------------------------------
ERROR:
ERROR: Failed with exit code 139. (rc=35584)
ERROR:
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.
ABORT:
ABORT: failed to configure the overlap store.
ABORT:
ABORT: Disk space available: 239809.235 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (correction/serum.ovlStore.config.err):
ABORT:
ABORT:
ABORT: Finding number of overlaps per read and per file.
ABORT:
ABORT: Moverlaps
ABORT: ------------ ----------------------------------------
ABORT:
ABORT: Failed with 'Segmentation fault'; backtrace (libbacktrace):
ABORT:
(/lustre/project/taw/share/conda-envs/ONRviral) [kvigil@cypress01-055 fastq_concat]$ canu -p serum -d /lustre/project/taw/ONRPan/canu/serum genomeSize=4.8m maxInputCoverage=10000 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 redMemory=32 oeaMemory=32 batMemory=200 correctedErrorRate=0.16 -nanopore serum.fastq
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
-- 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 '10.0.2' (from '/lustre/project/taw/share/conda-envs/ONRviral/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 3 ' (from 'gnuplot') and image format 'png'.
--
-- Detected 20 CPUs and 64000 gigabytes of memory on the local machine.
--
-- Detected Slurm with 'sinfo' binary in /cm/shared/apps/slurm/14.03.0/bin/sinfo.
-- Detected Slurm with task IDs up to 1000 allowed.
--
-- Slurm support detected. Resources available:
-- 30 hosts with 20 cores and 62 GB memory.
-- 41 hosts with 20 cores and 249 GB memory.
-- 49 hosts with 20 cores and 124 GB memory.
--
-- (tag)Threads
-- (tag)Memory |
-- (tag) | | algorithm
-- ------- ---------- -------- -----------------------------
-- Grid: meryl 12.000 GB 4 CPUs (k-mer counting)
-- Grid: hap 8.000 GB 4 CPUs (read-to-haplotype assignment)
-- Grid: cormhap 6.000 GB 10 CPUs (overlap detection with mhap)
-- Grid: obtovl 4.000 GB 5 CPUs (overlap detection)
-- Grid: utgovl 4.000 GB 5 CPUs (overlap detection)
-- Grid: cor -.--- GB 4 CPUs (read correction)
-- Grid: ovb 4.000 GB 1 CPU (overlap store bucketizer)
-- Grid: ovs 8.000 GB 1 CPU (overlap store sorting)
-- Grid: red 32.000 GB 4 CPUs (read error detection)
-- Grid: oea 32.000 GB 1 CPU (overlap error adjustment)
-- Grid: bat 200.000 GB 4 CPUs (contig construction with bogart)
-- Grid: cns -.--- GB 4 CPUs (consensus)
--
-- Found Nanopore reads in 'serum.seqStore':
-- Libraries:
-- Nanopore: 1
-- Reads:
-- Raw: 480000209
--
--
-- Generating assembly 'serum' in '/lustre/project/taw/ONRPan/canu/serum':
-- genomeSize:
-- 4800000
--
-- 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 Tue Aug 30 10:59:16 2022 with 239807.059 GB free disk space
cd correction
/lustre/project/taw/share/conda-envs/ONRviral/bin/ovStoreConfig \
-S ../serum.seqStore \
-M 4-8 \
-L ./1-overlapper/ovljob.files \
-create ./serum.ovlStore.config \
> ./serum.ovlStore.config.txt \
2> ./serum.ovlStore.config.err
sh: line 6: 55247 Segmentation fault /lustre/project/taw/share/conda-envs/ONRviral/bin/ovStoreConfig -S ../serum.seqStore -M 4-8 -L ./1-overlapper/ovljob.files -create ./serum.ovlStore.config > ./serum.ovlStore.config.txt 2> ./serum.ovlStore.config.err
-- Finished on Tue Aug 30 10:59:16 2022 (fast as lightning) with 239807.059 GB free disk space
----------------------------------------
ERROR:
ERROR: Failed with exit code 139. (rc=35584)
ERROR:
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.
ABORT:
ABORT: failed to configure the overlap store.
ABORT:
ABORT: Disk space available: 239807.059 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (correction/serum.ovlStore.config.err):
ABORT:
ABORT:
ABORT: Finding number of overlaps per read and per file.
ABORT:
ABORT: Moverlaps
ABORT: ------------ ----------------------------------------
ABORT:
ABORT: Failed with 'Segmentation fault'; backtrace (libbacktrace):I added these metagenomics parameters and still got an error.
canu -p serum -d /lustre/project/taw/ONRPan/canu/serum genomeSize=4.8m maxInputCoverage=10000 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 redMemory=32 oeaMemory=32 batMemory=200 correctedErrorRate=0.12 -nanopore serum.fastq
skoren
commented
2 years ago You want to make sure you remove the full output folder before re-trying. What was the difference between serum and serumcanu?
katievigil
commented
2 years ago Hi I deleted all my previous files from my last Canu runs and looks like no error! I will keep you posted on if it generates a complete fasta file!
skoren
commented
1 year ago Idle, open a new issue if you git an error on the new run.