Hi
I am using canu v1.7 +75 , having a similar issue like @ptranvan
The memory (job size) configuration in my canu run is
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | total usage algorithm
-- ------- ------ -------- -------- ----------------- -----------------------------
-- Local: meryl 64 GB 16 CPUs x 1 job 64 GB 16 CPUs (k-mer counting)
-- Local: cormhap 32 GB 16 CPUs x 6 jobs 192 GB 96 CPUs (overlap detection with mhap)
-- Local: obtmhap 32 GB 16 CPUs x 6 jobs 192 GB 96 CPUs (overlap detection with mhap)
-- Local: utgmhap 32 GB 16 CPUs x 6 jobs 192 GB 96 CPUs (overlap detection with mhap)
-- Local: ovb 4 GB 1 CPU x 96 jobs 384 GB 96 CPUs (overlap store bucketizer)
-- Local: ovs 16 GB 1 CPU x 63 jobs 1008 GB 63 CPUs (overlap store sorting)
-- Local: red 8 GB 4 CPUs x 24 jobs 192 GB 96 CPUs (read error detection)
-- Local: oea 4 GB 1 CPU x 96 jobs 384 GB 96 CPUs (overlap error adjustment)
-- Local: bat 256 GB 16 CPUs x 1 job 256 GB 16 CPUs (contig construction)
-- Local: gfa 16 GB 16 CPUs x 1 job 16 GB 16 CPUs (GFA alignment and processing)
--
-- In 'epauciflora.gkpStore', found Nanopore reads:
-- Raw: 0
-- Corrected: 477295
-- Trimmed: 477295
--
-- Generating assembly 'ep' in '/home/ashutosh/canu_assembly'
--
-- Parameters:
--
-- genomeSize 500000000
The job is stopped at the following point after 477295 red.sh
-- Starting 'red' concurrent execution on Sun May 20 03:15:50 2018 with 6287.189 GB free disk space(477295 processes; 24 concurrently)
cd unitigging/3-overlapErrorAdjustment
./red.sh 1 > ./red.000001.out 2>&1
./red.sh 2 > ./red.000002.out 2>&1
./red.sh 3 > ./red.000003.out 2>&1
.
.
.
./red.sh 474655 > ./red.474655.out 2>&1
./red.sh 475704 > ./red.475704.out 2>&1
./red.sh 476813 > ./red.476813.out 2>&1
-- Finished on Thu May 31 04:46:20 2018 (955830 seconds) with 29331.671 GB free disk space
----------------------------------------
--
-- Read error detection jobs failed, retry.
-- job 00737.red FAILED.
-- job 02142.red FAILED.
-- job 02256.red FAILED.
-- job 02521.red FAILED.
In my run redMemory is 8gb and probably oeaMemory is 4gb. I added AS_UTL_closeFile() in "ovStoreFile.C" as shown in 6bb19fc commit.
I renamed the 3-overlapErrorAdjustment directory and rerun CANU, it still shows 477295 red processes, as I remember it took 11 days (955830 seconds) to finish 477295 red processes
Can I rerun the canu by keeping these files or need to delete the 3-overlapErrorAdjustment directory
Please advise me, how I can get rid of the issue
Thanks in advance
Hi
I am using canu v1.7 +75 , having a similar issue like @ptranvan
The memory (job size) configuration in my canu run is
The job is stopped at the following point after 477295 red.sh
In my run redMemory is 8gb and probably oeaMemory is 4gb. I added AS_UTL_closeFile() in "ovStoreFile.C" as shown in 6bb19fc commit.
I renamed the 3-overlapErrorAdjustment directory and rerun CANU, it still shows 477295 red processes, as I remember it took 11 days (955830 seconds) to finish 477295 red processes
Can I rerun the canu by keeping these files or need to delete the 3-overlapErrorAdjustment directory
Please advise me, how I can get rid of the issue
Thanks in advance