skoren
commented
1 month ago What's the version of canu you're using? Can you post the full log (the report) from the run?
Closed swcho-HYBigLab closed 3 weeks ago
skoren
commented
1 month ago What's the version of canu you're using? Can you post the full log (the report) from the run?
swcho-HYBigLab
commented
1 month ago My version is 2.2 and this is my log
2024-07-11 14:59:40 - Starting Error correction
-- 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:
-- ?o?ic M, ?ikic 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 '13.0.1' (from '/share/apps/programs/java/jdk-13.0.1/bin/java') without -d64 support.
--
-- WARNING:
-- WARNING: Failed to run gnuplot using command 'gnuplot'.
-- WARNING: Plots will be disabled.
-- WARNING:
--
--
-- Detected 40 CPUs and 661 gigabytes of memory on the local machine.
--
-- Detected PBSPro '14.1.0' with 'pbsnodes' binary in /opt/pbs/bin/pbsnodes.
-- PBSPro disabled by useGrid=false
--
-- Local machine mode enabled; grid support not detected or not allowed.
--
-- Job limits:
-- 40 gigabytes memory (maxMemory option).
-- 40 CPUs (maxThreads option).
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | total usage algorithm
-- ------- ---------- -------- -------- -------------------- -----------------------------
-- Local: meryl 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (k-mer counting)
-- Local: hap 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (read-to-haplotype assignment)
-- Local: cormhap 20.000 GB 16 CPUs x 2 jobs 40.000 GB 32 CPUs (overlap detection with mhap)
-- Local: obtovl 20.000 GB 8 CPUs x 2 jobs 40.000 GB 16 CPUs (overlap detection)
-- Local: utgovl 20.000 GB 8 CPUs x 2 jobs 40.000 GB 16 CPUs (overlap detection)
-- Local: cor 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (read correction)
-- Local: ovb 20.000 GB 1 CPU x 2 jobs 40.000 GB 2 CPUs (overlap store bucketizer)
-- Local: ovs 20.000 GB 1 CPU x 2 jobs 40.000 GB 2 CPUs (overlap store sorting)
-- Local: red 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (read error detection)
-- Local: oea 20.000 GB 1 CPU x 2 jobs 40.000 GB 2 CPUs (overlap error adjustment)
-- Local: bat 20.000 GB 4 CPUs x 1 job 20.000 GB 4 CPUs (contig construction with bogart)
-- Local: cns 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (consensus)
--
-- Found Nanopore reads in 'S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore':
-- Libraries:
-- Nanopore: 1
-- Reads:
-- Raw: 820000922
--
--
-- Generating assembly 'S23-10097_targeted_long_read_ERBB2.trimmed_Q7' in '/lustre/export/home/swcho/1_ecDNA/3_data_for_WGS/nanopore_targeted/canu_results_trimmed_Q7':
-- genomeSize:
-- 4100000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.5000 ( 50.00%)
-- obtOvlErrorRate 0.1200 ( 12.00%)
-- utgOvlErrorRate 0.1200 ( 12.00%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.5000 ( 50.00%)
-- obtErrorRate 0.1200 ( 12.00%)
-- utgErrorRate 0.1200 ( 12.00%)
-- cnsErrorRate 0.1200 ( 12.00%)
--
-- Stages to run:
-- only correct raw reads.
--
--
-- BEGIN CORRECTION
--
-- Correction jobs estimated to need at most 1.659 GB for computation.
-- Correction jobs will request 20 GB each.
--
-- Local: cor 20.000 GB 4 CPUs x 2 jobs 40.000 GB 8 CPUs (read correction)
--
--
-- Configuring correction jobs:
-- Reads estimated to need at most 1.659 GB for computation.
-- Jobs will request 20 GB each.
----------------------------------------
-- Starting command on Thu Jul 11 14:59:40 2024 with 182482.537 GB free disk space
cd correction/2-correction
./correctReadsPartition.sh \
> ./correctReadsPartition.err 2>&1
-- Finished on Thu Jul 11 15:01:21 2024 (101 seconds) with 182451.866 GB free disk space
----------------------------------------
-- Finished stage 'cor-generateCorrectedReadsConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Thu Jul 11 15:01:21 2024 with 182451.866 GB free disk space (64 processes; 2 concurrently)
cd correction/2-correction
./correctReads.sh 1 > ./correctReads.000001.out 2>&1
./correctReads.sh 2 > ./correctReads.000002.out 2>&1
./correctReads.sh 3 > ./correctReads.000003.out 2>&1
./correctReads.sh 4 > ./correctReads.000004.out 2>&1
./correctReads.sh 5 > ./correctReads.000005.out 2>&1
./correctReads.sh 6 > ./correctReads.000006.out 2>&1
./correctReads.sh 7 > ./correctReads.000007.out 2>&1
./correctReads.sh 8 > ./correctReads.000008.out 2>&1
./correctReads.sh 9 > ./correctReads.000009.out 2>&1
./correctReads.sh 10 > ./correctReads.000010.out 2>&1
./correctReads.sh 11 > ./correctReads.000011.out 2>&1
./correctReads.sh 12 > ./correctReads.000012.out 2>&1
./correctReads.sh 13 > ./correctReads.000013.out 2>&1
./correctReads.sh 14 > ./correctReads.000014.out 2>&1
./correctReads.sh 15 > ./correctReads.000015.out 2>&1
./correctReads.sh 16 > ./correctReads.000016.out 2>&1
./correctReads.sh 17 > ./correctReads.000017.out 2>&1
./correctReads.sh 18 > ./correctReads.000018.out 2>&1
./correctReads.sh 19 > ./correctReads.000019.out 2>&1
./correctReads.sh 20 > ./correctReads.000020.out 2>&1
./correctReads.sh 21 > ./correctReads.000021.out 2>&1
./correctReads.sh 22 > ./correctReads.000022.out 2>&1
./correctReads.sh 23 > ./correctReads.000023.out 2>&1
./correctReads.sh 24 > ./correctReads.000024.out 2>&1
./correctReads.sh 25 > ./correctReads.000025.out 2>&1
./correctReads.sh 26 > ./correctReads.000026.out 2>&1
./correctReads.sh 27 > ./correctReads.000027.out 2>&1
./correctReads.sh 28 > ./correctReads.000028.out 2>&1
./correctReads.sh 29 > ./correctReads.000029.out 2>&1
./correctReads.sh 30 > ./correctReads.000030.out 2>&1
./correctReads.sh 31 > ./correctReads.000031.out 2>&1
./correctReads.sh 32 > ./correctReads.000032.out 2>&1
./correctReads.sh 33 > ./correctReads.000033.out 2>&1
./correctReads.sh 34 > ./correctReads.000034.out 2>&1
./correctReads.sh 35 > ./correctReads.000035.out 2>&1
./correctReads.sh 36 > ./correctReads.000036.out 2>&1
./correctReads.sh 37 > ./correctReads.000037.out 2>&1
./correctReads.sh 38 > ./correctReads.000038.out 2>&1
./correctReads.sh 39 > ./correctReads.000039.out 2>&1
./correctReads.sh 40 > ./correctReads.000040.out 2>&1
./correctReads.sh 41 > ./correctReads.000041.out 2>&1
./correctReads.sh 42 > ./correctReads.000042.out 2>&1
./correctReads.sh 43 > ./correctReads.000043.out 2>&1
./correctReads.sh 44 > ./correctReads.000044.out 2>&1
./correctReads.sh 45 > ./correctReads.000045.out 2>&1
./correctReads.sh 46 > ./correctReads.000046.out 2>&1
./correctReads.sh 47 > ./correctReads.000047.out 2>&1
./correctReads.sh 48 > ./correctReads.000048.out 2>&1
./correctReads.sh 49 > ./correctReads.000049.out 2>&1
./correctReads.sh 50 > ./correctReads.000050.out 2>&1
./correctReads.sh 51 > ./correctReads.000051.out 2>&1
./correctReads.sh 52 > ./correctReads.000052.out 2>&1
./correctReads.sh 53 > ./correctReads.000053.out 2>&1
./correctReads.sh 54 > ./correctReads.000054.out 2>&1
./correctReads.sh 55 > ./correctReads.000055.out 2>&1
./correctReads.sh 56 > ./correctReads.000056.out 2>&1
./correctReads.sh 57 > ./correctReads.000057.out 2>&1
./correctReads.sh 58 > ./correctReads.000058.out 2>&1
./correctReads.sh 59 > ./correctReads.000059.out 2>&1
./correctReads.sh 60 > ./correctReads.000060.out 2>&1
./correctReads.sh 61 > ./correctReads.000061.out 2>&1
./correctReads.sh 62 > ./correctReads.000062.out 2>&1
./correctReads.sh 63 > ./correctReads.000063.out 2>&1
./correctReads.sh 64 > ./correctReads.000064.out 2>&1
-- Finished on Fri Jul 12 07:30:39 2024 (59358 seconds, at least I didn't crash) with 175671.08 GB free disk space
----------------------------------------
-- Found 64 read correction output files.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
-- Found 64 read correction output files.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
--
-- Loading corrected reads into corStore and seqStore.
----------------------------------------
-- Starting command on Fri Jul 12 07:30:39 2024 with 175671.08 GB free disk space
cd correction
/lustre/export/home/swcho/4_DNA_analysis_practice/tools/canu-2.2/bin/loadCorrectedReads \
-S ../S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore \
-C ./S23-10097_targeted_long_read_ERBB2.trimmed_Q7.corStore \
-L ./2-correction/corjob.files \
> ./S23-10097_targeted_long_read_ERBB2.trimmed_Q7.loadCorrectedReads.log \
2> ./S23-10097_targeted_long_read_ERBB2.trimmed_Q7.loadCorrectedReads.err
-- Finished on Fri Jul 12 07:34:07 2024 (208 seconds) with 175656.176 GB free disk space
----------------------------------------
--
-- In sequence store './S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore':
-- Found 889131 reads.
-- Found 694634880 bases (169.42 times coverage).
-- Histogram of corrected reads:
--
-- G=694634880 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 2873 20246 69465471 || 200-1261 797156|---------------------------------------------------------------
-- 00020 1383 63135 138928297 || 1262-2323 70311|------
-- 00030 1183 117776 208391117 || 2324-3385 2984|-
-- 00040 1041 180390 277854107 || 3386-4447 18597|--
-- 00050 920 251393 347318104 || 4448-5509 57|-
-- 00060 801 332206 416781093 || 5510-6571 5|-
-- 00070 680 426248 486244899 || 6572-7633 15|-
-- 00080 568 538095 555708422 || 7634-8695 1|-
-- 00090 435 676722 625171663 || 8696-9757 1|-
-- 00100 200 889130 694634880 || 9758-10819 1|-
-- 001.000x 889131 694634880 || 10820-11881 0|
-- || 11882-12943 0|
-- || 12944-14005 0|
-- || 14006-15067 0|
-- || 15068-16129 0|
-- || 16130-17191 0|
-- || 17192-18253 0|
-- || 18254-19315 0|
-- || 19316-20377 0|
-- || 20378-21439 0|
-- || 21440-22501 0|
-- || 22502-23563 0|
-- || 23564-24625 0|
-- || 24626-25687 0|
-- || 25688-26749 0|
-- || 26750-27811 1|-
-- || 27812-28873 0|
-- || 28874-29935 0|
-- || 29936-30997 0|
-- || 30998-32059 0|
-- || 32060-33121 0|
-- || 33122-34183 0|
-- || 34184-35245 1|-
-- || 35246-36307 0|
-- || 36308-37369 0|
-- || 37370-38431 0|
-- || 38432-39493 0|
-- || 39494-40555 0|
-- || 40556-41617 0|
-- || 41618-42679 0|
-- || 42680-43741 0|
-- || 43742-44803 0|
-- || 44804-45865 0|
-- || 45866-46927 0|
-- || 46928-47989 0|
-- || 47990-49051 0|
-- || 49052-50113 0|
-- || 50114-51175 0|
-- || 47990-49051 0|
-- || 49052-50113 0|
-- || 50114-51175 0|
-- || 51176-52237 0|
-- || 52238-53299 1|-
--
--
-- Purging correctReads output after loading into stores.
-- Purged 64 .cns outputs.
-- Purged 128 .out job log outputs.
--
-- No corrected reads generated, overlaps used for correction saved.
-- Finished stage 'cor-loadCorrectedReads', reset canuIteration.
----------------------------------------
-- Starting command on Fri Jul 12 07:34:32 2024 with 175704.653 GB free disk space
cd .
/lustre/export/home/swcho/4_DNA_analysis_practice/tools/canu-2.2/bin/sqStoreDumpFASTQ \
-corrected \
-S ./S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore \
-o ./S23-10097_targeted_long_read_ERBB2.trimmed_Q7.correctedReads.gz \
-fasta \
-nolibname \
> S23-10097_targeted_long_read_ERBB2.trimmed_Q7.correctedReads.fasta.err 2>&1
-- Finished on Fri Jul 12 07:34:59 2024 (27 seconds) with 175724.334 GB free disk space
----------------------------------------
--
-- Corrected reads saved in 'S23-10097_targeted_long_read_ERBB2.trimmed_Q7.correctedReads.fasta.gz'.
-- Finished stage 'cor-dumpCorrectedReads', reset canuIteration.
--
-- Trimming skipped; not enabled.
--
-- Unitigging skipped; not enabled.
--
-- Bye.That looks like a restart run so it doesn't have all the info on the previous steps, there should be a report file that has the full information, can you share that? The reads are pretty short so you probably don't want to reduce the mhap sensitivity, I think you want MhapSensitivity=high.
swcho-HYBigLab
commented
1 month ago Sorry, I have only this prefix.report in may canu_results folder.
[CORRECTION/READS]
--
-- In sequence store './S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore':
-- Found 921717 reads.
-- Found 820000922 bases (200 times coverage).
-- Histogram of raw reads:
--
-- G=820000922 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 2008 25667 82000684 || 200-2994 901655|---------------------------------------------------------------
-- 00020 1411 77345 164000530 || 2995-5789 20037|--
-- 00030 1232 139864 246000829 || 5790-8584 19|-
-- 00040 1108 210150 328001135 || 8585-11379 2|-
-- 00050 999 288134 410000887 || 11380-14174 0|
-- 00060 900 374599 492000658 || 14175-16969 0|
-- 00070 794 471471 574001082 || 16970-19764 0|
-- 00080 676 583092 656000937 || 19765-22559 0|
-- 00090 536 718330 738001185 || 22560-25354 0|
-- 00100 200 921716 820000922 || 25355-28149 1|-
-- 001.000x 921717 820000922 || 28150-30944 0|
-- || 30945-33739 0|
-- || 33740-36534 1|-
-- || 36535-39329 0|
-- || 39330-42124 0|
-- || 42125-44919 0|
-- || 44920-47714 0|
-- || 47715-50509 0|
-- || 50510-53304 0|
-- || 53305-56099 1|-
-- || 56100-58894 0|
-- || 58895-61689 0|
-- || 61690-64484 0|
-- || 64485-67279 0|
-- || 67280-70074 0|
-- || 70075-72869 0|
-- || 72870-75664 0|
-- || 75665-78459 0|
-- || 78460-81254 0|
-- || 81255-84049 0|
-- || 84050-86844 0|
-- || 86845-89639 0|
-- || 89640-92434 0|
-- || 92435-95229 0|
-- || 95230-98024 0|
-- || 98025-100819 0|
-- || 100820-103614 0|
-- || 103615-106409 0|
-- || 106410-109204 0|
-- || 109205-111999 0|
-- || 112000-114794 0|
-- || 114795-117589 0|
-- || 117590-120384 0|
-- || 120385-123179 0|
-- || 123180-125974 0|
-- || 125975-128769 0|
-- || 128770-131564 0|
-- || 131565-134359 0|
-- || 134360-137154 0|
-- || 137155-139949 1|-
--
[CORRECTION/MERS]
--
-- 16-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 0 0.0000 0.0000
-- 2- 2 32955094 ********************************************************************** 0.5035 0.0986
-- 3- 4 18758270 *************************************** 0.6980 0.1557
-- 5- 7 6386875 ************* 0.8394 0.2158
-- 8- 11 2408429 ***** 0.9010 0.2564
-- 12- 16 1242505 ** 0.9296 0.2850
-- 17- 22 796618 * 0.9460 0.3088
-- 23- 29 577780 * 0.9572 0.3309
-- 30- 37 443972 0.9655 0.3527
-- 38- 46 354538 0.9720 0.3745
-- 47- 56 279734 0.9772 0.3963
-- 57- 67 225712 0.9813 0.4174
-- 68- 79 177945 0.9847 0.4380
-- 80- 92 142449 0.9873 0.4573
-- 93- 106 113894 0.9895 0.4753
-- 107- 121 95023 0.9912 0.4920
-- 122- 137 79417 0.9926 0.5080
-- 138- 154 64942 0.9938 0.5233
-- 155- 172 51230 0.9948 0.5373
-- 173- 191 41661 0.9955 0.5496
-- 192- 211 34539 0.9962 0.5609
-- 212- 232 28216 0.9967 0.5712
-- 233- 254 22850 0.9971 0.5804
-- 255- 277 18388 0.9975 0.5887
-- 278- 301 15720 0.9977 0.5959
-- 302- 326 13521 0.9980 0.6027
-- 327- 352 11734 0.9982 0.6090
-- 353- 379 9174 0.9984 0.6149
-- 380- 407 7964 0.9985 0.6199
-- 408- 436 6851 0.9986 0.6246
-- 437- 466 5915 0.9987 0.6289
-- 467- 497 5382 0.9988 0.6329
-- 498- 529 4683 0.9989 0.6367
-- 530- 562 4214 0.9990 0.6403
-- 563- 596 3874 0.9990 0.6437
-- 597- 631 3439 0.9991 0.6471
-- 632- 667 3043 0.9991 0.6502
-- 668- 704 2824 0.9992 0.6532
-- 705- 742 2492 0.9992 0.6561
-- 743- 781 2298 0.9993 0.6588
-- 782- 821 2121 0.9993 0.6614
--
-- 0 (max occurrences)
-- 668734055 (total mers, non-unique)
-- 65449213 (distinct mers, non-unique)
-- 0 (unique mers)
[CORRECTION/LAYOUT]
-- original original
-- raw reads raw reads
-- category w/overlaps w/o/overlaps
-- -------------------- ------------- -------------
-- Number of Reads 900598 31168169
-- Number of Bases 807155152 2035357
-- Coverage 196.867 0.496
-- Median 812 0
-- Mean 896 0
-- N50 1004 678
-- Minimum 200 0
-- Maximum 139903 2054
--
-- --------corrected--------- ----------rescued----------
-- evidence expected expected
-- category reads raw corrected raw corrected
-- -------------------- ------------- ------------- ------------- ------------- -------------
-- Number of Reads 904089 900597 900597 0 0
-- Number of Bases 809155029 807015249 783595700 0 0
-- Coverage 197.355 196.833 191.121 0.000 0.000
-- Median 811 812 789 0 0
-- Mean 894 896 870 0 0
-- N50 1003 1004 993 0 0
-- Minimum 200 200 4 0 0
-- Maximum 139903 53354 53353 0 0
--
-- --------uncorrected--------
-- expected
-- category raw corrected
-- -------------------- ------------- -------------
-- Number of Reads 31168170 31168170
-- Number of Bases 2175260 133073
-- Coverage 0.531 0.032
-- Median 0 0
-- Mean 0 0
-- N50 716 0
-- Minimum 0 0
-- Maximum 139903 133073
--
-- Maximum Memory 1782103604
[TRIMMING/READS]
--
-- In sequence store './S23-10097_targeted_long_read_ERBB2.trimmed_Q7.seqStore':
-- Found 889131 reads.
-- Found 694634880 bases (169.42 times coverage).
-- Histogram of corrected reads:
--
-- G=694634880 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 2873 20246 69465471 || 200-1261 797156|---------------------------------------------------------------
-- 00020 1383 63135 138928297 || 1262-2323 70311|------
-- 00030 1183 117776 208391117 || 2324-3385 2984|-
-- 00040 1041 180390 277854107 || 3386-4447 18597|--
-- 00050 920 251393 347318104 || 4448-5509 57|-
-- 00060 801 332206 416781093 || 5510-6571 5|-
-- 00070 680 426248 486244899 || 6572-7633 15|-
-- 00080 568 538095 555708422 || 7634-8695 1|-
-- 00090 435 676722 625171663 || 8696-9757 1|-
-- 00100 200 889130 694634880 || 9758-10819 1|-
-- 001.000x 889131 694634880 || 10820-11881 0|
-- || 11882-12943 0|
-- || 12944-14005 0|
-- || 14006-15067 0|
-- || 15068-16129 0|
-- || 16130-17191 0|
-- || 17192-18253 0|
-- || 18254-19315 0|
-- || 19316-20377 0|
-- || 20378-21439 0|
-- || 21440-22501 0|
-- || 22502-23563 0|
-- || 23564-24625 0|
-- || 24626-25687 0|
-- || 25688-26749 0|
-- || 26750-27811 1|-
-- || 27812-28873 0|
-- || 28874-29935 0|
-- || 29936-30997 0|
-- || 30998-32059 0|
-- || 32060-33121 0|
-- || 33122-34183 0|
-- || 34184-35245 1|-
-- || 35246-36307 0|
-- || 36308-37369 0|
-- || 37370-38431 0|
-- || 38432-39493 0|
-- || 39494-40555 0|
-- || 40556-41617 0|
-- || 41618-42679 0|
-- || 42680-43741 0|
-- || 43742-44803 0|
-- || 44804-45865 0|
-- || 45866-46927 0|
-- || 46928-47989 0|
-- || 47990-49051 0|
-- || 49052-50113 0|
-- || 50114-51175 0|
-- || 51176-52237 0|
-- || 52238-53299 1|-
--Ah you're hitting the max input coverage, which defaults to 200x so the 170x of corrected data makes sense given that. Add maxInputCoverage=10000 (I don't recall if it also supports all or not you could try it). The report should update to show a much higher coverage than 200x (the first read length report).
swcho-HYBigLab
commented
1 month ago Thank you!
So, you mean that there's no problem with genomeSize=4.1m?
I though it was a matter with read count calling, since the documentation said it affects corOutCoverage and MhapSensitivity.
As you mentioned, I will run it by adjusting MhapSensitivity=high and maxInputCoverage=10000.
Thanks again.
skoren
commented
1 month ago The genome size doesn't matter much, it affects those two settings plus maxInputCoverage but not the correction itself. So if you explicitly set the sensitivity and coverages, then the genome size essentially doesn't matter.
swcho-HYBigLab
commented
1 month ago Thank you for your comment! It was great help for my research
Hello, I am a BI graduate student in South Korea dealing with ONT long-read sequencing data for the first time. I am working on a project to align and analyze targeted long-read sqeuencing data, and plan to use CANU to error correct trimmed fastq.
Actually, there was no major problem with running progress, but the data scale of corrected reads fasta changed significantly. (trimmed 32,365,275 reads -> corrected 889,131 reads)
Compared to existing trimmed data, the number of reads of data that underwent correction was greatly reduced. I want to solve the above situation and to get as much as reads possible.
Targeted long-read sequencing data was sequenced using a 4.1Mb panel, and the code used is as follows:
Thank you