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cns_1_al_vol_0.sh: line 16: 35702 Bus error #57

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QichengMa opened this issue Aug 3, 2023 · 6 comments
Open

cns_1_al_vol_0.sh: line 16: 35702 Bus error #57

QichengMa opened this issue Aug 3, 2023 · 6 comments

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@QichengMa
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Dear Chuan-Le,

When I run "necat.pl correct my_config.txt", I got the error message:

"cns_1_al_vol_0.sh: line 16: 35702 Bus error

... ...

/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh: line 16: 35702 Bus error /home/kggx609/software/NECAT/Linux-amd64/bin/oc2pmov -a 1000 -b 2000 -k 15 -t 1 -q 500 -i 1 -d 0.25 -n 500 -z 10 -m 500 -j
0 -s 3 -u 1 -e 0.5 -t 1 /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData 0 /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData/pm_result_02023-08-03 01:53:33 [Warning] Failed to run script, 135, /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_
1_al_vol_0.sh
2023-08-03 01:53:33 [Error] Reached to maximum number of script errors
"

I appreciate if you could help me to configure out where I did wrong.

Thanks,
@lemene
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lemene commented Aug 3, 2023

Hi, @QichengMa

I read your mail and GENOME_SIZE was set to 7000 and PREP_OUTPUT_COVERAGE was set to 40. We haven't tested on such a small genome before. You can try increasing the two parameters, for example, PREP_OUTPUT_COVERAGE=200.

Is it convenient to provide the file size in 1-consensus/cns_iter1?

@QichengMa
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I increased the values, but I still get the same error:

(base) [kggx609@seskscpn075 fastq_pass]$ more my_config.txt
PROJECT=gr1_gfp
ONT_READ_LIST=read_list.txt
GENOME_SIZE=600000
THREADS=1
MIN_READ_LENGTH=1500
PREP_OUTPUT_COVERAGE=200
OVLP_FAST_OPTIONS=-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000
OVLP_SENSITIVE_OPTIONS=-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000
CNS_FAST_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
CNS_SENSITIVE_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
TRIM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400
ASM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400
NUM_ITER=2
CNS_OUTPUT_COVERAGE=30
CLEANUP=1
USE_GRID=false
GRID_NODE=0
GRID_OPTIONS=
SMALL_MEMORY=0
FSA_OL_FILTER_OPTIONS=
FSA_ASSEMBLE_OPTIONS=
FSA_CTG_BRIDGE_OPTIONS=
POLISH_CONTIGS=true
(base) [kggx609@seskscpn075 fastq_pass]$

(base) [kggx609@seskscpn075 fastq_pass]$ tail nohup.out
2023-08-03 23:58:20 [Info] Skip filtering reads for consensus for outputs are newer.
2023-08-03 23:58:20 [Info] Start correcting iteratively for cns 1..
2023-08-03 23:58:20 [Info] Start aliging for cns 1.
2023-08-03 23:58:20 [Info] Skip making vol for cns 1 for outputs are newer.
2023-08-03 23:58:20 [Info] Start aligning vol for cns 1.
2023-08-03 23:58:20 [Info] Parallelly start aligning vol 0 for cns 1.
2023-08-03 23:58:20 [Info] Run script: /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh 2>&1 |tee /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh.log
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh: line 16: 8202 Bus error /home/kggx609/software/NECAT/Linux-amd64/bin/oc2pmov -e 0.5 -m 500 -a 1000 -u 1 -j 0 -k 15 -b 2000 -i 1 -d 0.25 -t 1 -q 500 -s 3 -n 500 -z 10 -t 1 /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData 0 /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData/pm_result_0
2023-08-03 23:58:38 [Warning] Failed to run script, 135, /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh
2023-08-03 23:58:38 [Error] Reached to maximum number of script errors
(base) [kggx609@seskscpn075 fastq_pass]$

(base) [kggx609@seskscpn075 fastq_pass]$ cd -
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1
(base) [kggx609@seskscpn075 cns_iter1]$ ls -ltr
total 1
drwxrwx--- 2 kggx609 xaz-scp-rd 4096 Aug 3 01:53 PackedData
(base) [kggx609@seskscpn075 cns_iter1]$ pwd
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1
(base) [kggx609@seskscpn075 cns_iter1]$ ls
PackedData
(base) [kggx609@seskscpn075 cns_iter1]$ cd PackedData
(base) [kggx609@seskscpn075 PackedData]$ ls
reads_info.txt vol0 volume_names.txt
(base) [kggx609@seskscpn075 PackedData]$ ls -ltr
total 129
-rw-rw---- 1 kggx609 xaz-scp-rd 75091 Aug 3 01:53 vol0
-rw-rw---- 1 kggx609 xaz-scp-rd 92 Aug 3 01:53 volume_names.txt
-rw-rw---- 1 kggx609 xaz-scp-rd 4 Aug 3 01:53 reads_info.txt
(base) [kggx609@seskscpn075 PackedData]$ more reads_info.txt
1 3
(base) [kggx609@seskscpn075 PackedData]$ more volume_names.txt
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData/vol0 0 3
(base) [kggx609@seskscpn075 PackedData]$ file vol0
vol0: data
(base) [kggx609@seskscpn075 PackedData]$

Vol0 is a binary file.

@lemene
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lemene commented Aug 4, 2023 via email

@QichengMa
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I deleted it:

$ /bin/rm -rf gr1_gfp nohup.out
$ nohup bash tt &

But I still get errors:

Smartmatch is experimental at /home/kggx609/software/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263.
2023-08-04 00:30:25 [Info] Found Slurm, which is /usr/bin/sinfo
2023-08-04 00:30:25 [Info] Start correcting rawreads.
2023-08-04 00:30:25 [Info] Start filtering reads for consensus.
2023-08-04 00:30:25 [Info] Run script: /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_pprr.sh 2>&1 |tee
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_pprr.sh.log
2023-08-04 00:30:25 [INFO] Start
2023-08-04 00:30:25 [INFO] Arguments:
cmd = longest
ifname = read_list.txt
size = 0
block_size = 0
base_size = 120000000
ofname = /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/raw_reads/filtered_raw_reads.fasta
thread_size = 1
names =
min_length = 1500
genome_size = 0
id2name =
discard_illegal_read = 1

2023-08-04 00:30:35 [INFO] length size = 523144
2023-08-04 00:30:35 [INFO] min_length = 2238
2023-08-04 00:30:37 [INFO] End
2023-08-04 00:30:54 [Info] End filtering reads for consensus.
2023-08-04 00:30:54 [Info] Start correcting iteratively for cns 1..
2023-08-04 00:30:54 [Info] Start aliging for cns 1.
2023-08-04 00:30:54 [Info] Start making vol for cns 1.
2023-08-04 00:30:54 [Info] Run script: /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_mk_vol.sh 2>&1 |
tee /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_mk_vol.sh.log
file_list: /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/raw_reads/raw_read_list.txt
[Fri Aug 4 00:30:55 2023] INFO: pack /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/raw_reads/filtered_
raw_reads.fasta.gz: 49156 reads, 120105871 bps (makedb/main.c, 44)
2023-08-04 00:30:55 [Info] End making vol for cns 1.
2023-08-04 00:30:55 [Info] Start aligning vol for cns 1.
2023-08-04 00:30:55 [Info] Parallelly start aligning vol 0 for cns 1.
2023-08-04 00:30:55 [Info] Run script: /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh 2>&1
|tee /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh.log
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_1_al_vol_0.sh: line 16: 18375 Killed /ho
me/kggx609/software/NECAT/Linux-amd64/bin/oc2pmov -u 1 -z 10 -s 3 -n 500 -k 15 -j 0 -b 2000 -d 0.25 -i 1 -a 1000 -e 0.5
-m 500 -t 1 -q 500 -t 1 /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData 0 /home/kgg
x609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData/pm_result_0
2023-08-04 00:33:14 [Warning] Failed to run script, 137, /home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/scripts/cns_
1_al_vol_0.sh
2023-08-04 00:33:14 [Error] Reached to maximum number of script errors
(base) [kggx609@seskscpn075 fastq_pass]$

BUT, this time, the file vol0 is MUCH larger,

(base) [kggx609@seskscpn075 PackedData]$ pwd
/home/kggx609/projects/gr1_gfp/fastq_pass/gr1_gfp/1-consensus/cns_iter1/PackedData
(base) [kggx609@seskscpn075 PackedData]$ ls -ltr
total 32641
-rw-rw---- 1 kggx609 xaz-scp-rd 33418287 Aug 4 00:30 vol0
-rw-rw---- 1 kggx609 xaz-scp-rd 96 Aug 4 00:30 volume_names.txt
-rw-rw---- 1 kggx609 xaz-scp-rd 8 Aug 4 00:30 reads_info.txt
(base) [kggx609@seskscpn075 PackedData]$

Thanks again!

@lemene
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lemene commented Aug 4, 2023

Hi, @QichengMa
I corrected a dataset of similar size, but there were no errors. Have you used NECAT to correct other datasets before, or is this your first time using it? Could you provide the version of NECAT and the operating system?

@QichengMa
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This is the first time that I use NECAT.
This is the latest version of NECAT which I downloaded last week.
This is the OS version I used:
Linux seskscpn084.prim.scp 3.10.0-1160.11.1.el7.x86_64 #1 SMP Fri Dec 18 16:34:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

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@lemene @QichengMa