error in get nd.asm.p.fasta
ucassee opened this issue · comments
Hi,
I met the following error。
Error message
/data/software/NextDenovo/bin/nextgraph -a 1 -f /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.seqs /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
[INFO] 2017-01-28 06:12:13 Initialize graph and reading...
[INFO] 2017-01-28 06:12:13 Initial Node(s): 0, Edge(s): 0
[INFO] 2017-01-28 06:12:13 Depth stat, Mid: 0.000 Max: 0.000 Repeat: 0.000 L:N:H: -nan:-nan:-nan
[INFO] 2017-01-28 06:12:13 Outdegree stat, Mid: 0.000 Max: 0.000 Repeat: 0.000 L:N:H: -nan:-nan:-nan
[INFO] 2017-01-28 06:12:13 Chimeric node ratio: 0.000% (candidate: 0.000%)
[INFO] 2017-01-28 06:12:13 Assembly done and outputting...
[INFO] 2017-01-28 06:12:14 CMD:
time /data/software/NextDenovo/bin/nextgraph -a 1 -f /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.seqs /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
[INFO] 2021-01-28 16:17:56 Initialize graph and reading...
nextgraph: asg.c:1387: update_graph: Assertion `mode == 10' failed.
Aborted
Genome characteristics
genome size：2.1G
Input data
pacbio
Operating system
Which operating system and version are you using?
PBS
GCC
What version of GCC are you using?
gcc version 4.8.5 20150623 (Red Hat 4.8.5-39) (GCC)
Python
What version of Python are you using?
Python 2.7.16
NextDenovo
What version of NextDenovo are you using?
nextDenovo v2.3.1
It seems files in /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.ovls are empty, so you can check subjobs which produced files in /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/03.ctg_graph/01.ctg_graph.input.ovls, it should be /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/./02.cns_align/02.cns_align.sh.work/*/nextDenovo.sh.e
Hi @moold,
There are 464 subtasks in 02.cns_align.sh.work.
I attach one of them:
-bash: module: line 1: syntax error: unexpected end of file
-bash: error importing function definition for `BASH_FUNC_module'
hostname
+ hostname
cd /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/02.cns_align.sh.work/cns_align1/cns_align463
+ cd /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/02.cns_align.sh.work/cns_align1/cns_align463
time /data/software/NextDenovo/bin/minimap2-nd -I 150G --step 2 --dual=yes -x ava-pb -t 20 -k17 -w17 --minlen 326 --maxhan1 1633 /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns28/cns.fasta /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns29/cns.fasta -o cns.filt.dovt.ovl;
+ /data/software/NextDenovo/bin/minimap2-nd -I 150G --step 2 --dual=yes -x ava-pb -t 20 -k17 -w17 --minlen 326 --maxhan1 1633 /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns28/cns.fasta /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns29/cns.fasta -o cns.filt.dovt.ovl
[M::mm_idx_gen::41.284*1.54] collected minimizers
[M::mm_idx_gen::45.329*2.10] sorted minimizers
[M::main::45.329*2.10] loaded/built the index for 136742 target sequence(s)
[M::mm_mapopt_update::45.883*2.08] mid_occ = 3248
[M::mm_idx_stat] kmer size: 17; skip: 17; is_hpc: 1; #seq: 136742
[M::mm_idx_stat::46.033*2.08] distinct minimizers: 13247957 (21.83% are singletons); average occurrences: 17.252; average spacing: 11.324
[M::worker_pipeline::18501.270*18.43] mapped 26635 sequences
[M::worker_pipeline::37619.023*18.57] mapped 27116 sequences
[M::worker_pipeline::55303.135*18.85] mapped 26493 sequences
[M::worker_pipeline::72974.940*18.96] mapped 26280 sequences
[M::worker_pipeline::92255.365*18.88] mapped 26556 sequences
[M::worker_pipeline::94815.828*18.76] mapped 2999 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: /data/software/NextDenovo/bin/minimap2-nd -I 150G --step 2 --dual=yes -x ava-pb -t 20 -k17 -w17 --minlen 326 --maxhan1 1633 -o cns.filt.dovt.ovl /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns28/cns.fasta /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns29/cns.fasta
[M::main] Real time: 94817.060 sec; CPU: 1778686.225 sec; Peak RSS: 41.675 GB
real 1580m17.676s
user 29599m3.687s
sys 45m43.060s
touch /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/02.cns_align.sh.work/cns_align1/cns_align463/nextDenovo.sh.done
+ touch /data/Project/3.fish/01.assmbly/01_rundir_gonad_seed3266/02.cns_align/02.cns_align.sh.work/cns_align1/cns_align463/nextDenovo.sh.done
Could you check all ovl files? The log shows that at least one ovl file is empty.
Hi @moold,
It seems no ovl file is empty with du -h cns_align*/cns_align*/cns.filt.dovt.ovl.
163M cns_align0/cns_align000/cns.filt.dovt.ovl
320M cns_align0/cns_align001/cns.filt.dovt.ovl
319M cns_align0/cns_align002/cns.filt.dovt.ovl
318M cns_align0/cns_align003/cns.filt.dovt.ovl
320M cns_align0/cns_align004/cns.filt.dovt.ovl
322M cns_align0/cns_align005/cns.filt.dovt.ovl
318M cns_align0/cns_align006/cns.filt.dovt.ovl
318M cns_align0/cns_align007/cns.filt.dovt.ovl
319M cns_align0/cns_align008/cns.filt.dovt.ovl
316M cns_align0/cns_align009/cns.filt.dovt.ovl
320M cns_align0/cns_align010/cns.filt.dovt.ovl
321M cns_align0/cns_align011/cns.filt.dovt.ovl
318M cns_align0/cns_align012/cns.filt.dovt.ovl
321M cns_align0/cns_align013/cns.filt.dovt.ovl
317M cns_align0/cns_align014/cns.filt.dovt.ovl
318M cns_align0/cns_align015/cns.filt.dovt.ovl
319M cns_align0/cns_align016/cns.filt.dovt.ovl
316M cns_align0/cns_align017/cns.filt.dovt.ovl
322M cns_align0/cns_align018/cns.filt.dovt.ovl
323M cns_align0/cns_align019/cns.filt.dovt.ovl
320M cns_align0/cns_align020/cns.filt.dovt.ovl
321M cns_align0/cns_align021/cns.filt.dovt.ovl
323M cns_align0/cns_align022/cns.filt.dovt.ovl
321M cns_align0/cns_align023/cns.filt.dovt.ovl
316M cns_align0/cns_align024/cns.filt.dovt.ovl
390M cns_align0/cns_align025/cns.filt.dovt.ovl
317M cns_align0/cns_align026/cns.filt.dovt.ovl
319M cns_align0/cns_align027/cns.filt.dovt.ovl
320M cns_align0/cns_align028/cns.filt.dovt.ovl
317M cns_align0/cns_align029/cns.filt.dovt.ovl
163M cns_align0/cns_align030/cns.filt.dovt.ovl
318M cns_align0/cns_align031/cns.filt.dovt.ovl
320M cns_align0/cns_align032/cns.filt.dovt.ovl
321M cns_align0/cns_align033/cns.filt.dovt.ovl
323M cns_align0/cns_align034/cns.filt.dovt.ovl
319M cns_align0/cns_align035/cns.filt.dovt.ovl
319M cns_align0/cns_align036/cns.filt.dovt.ovl
320M cns_align0/cns_align037/cns.filt.dovt.ovl
316M cns_align0/cns_align038/cns.filt.dovt.ovl
320M cns_align0/cns_align039/cns.filt.dovt.ovl
321M cns_align0/cns_align040/cns.filt.dovt.ovl
320M cns_align0/cns_align041/cns.filt.dovt.ovl
319M cns_align0/cns_align042/cns.filt.dovt.ovl
318M cns_align0/cns_align043/cns.filt.dovt.ovl
320M cns_align0/cns_align044/cns.filt.dovt.ovl
318M cns_align0/cns_align045/cns.filt.dovt.ovl
320M cns_align0/cns_align046/cns.filt.dovt.ovl
323M cns_align0/cns_align047/cns.filt.dovt.ovl
323M cns_align0/cns_align048/cns.filt.dovt.ovl
322M cns_align0/cns_align049/cns.filt.dovt.ovl
321M cns_align0/cns_align050/cns.filt.dovt.ovl
324M cns_align0/cns_align051/cns.filt.dovt.ovl
321M cns_align0/cns_align052/cns.filt.dovt.ovl
318M cns_align0/cns_align053/cns.filt.dovt.ovl
391M cns_align0/cns_align054/cns.filt.dovt.ovl
318M cns_align0/cns_align055/cns.filt.dovt.ovl
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321M cns_align0/cns_align057/cns.filt.dovt.ovl
318M cns_align0/cns_align058/cns.filt.dovt.ovl
161M cns_align0/cns_align059/cns.filt.dovt.ovl
316M cns_align0/cns_align060/cns.filt.dovt.ovl
317M cns_align0/cns_align061/cns.filt.dovt.ovl
318M cns_align0/cns_align062/cns.filt.dovt.ovl
317M cns_align0/cns_align063/cns.filt.dovt.ovl
314M cns_align0/cns_align064/cns.filt.dovt.ovl
318M cns_align0/cns_align065/cns.filt.dovt.ovl
313M cns_align0/cns_align066/cns.filt.dovt.ovl
317M cns_align0/cns_align067/cns.filt.dovt.ovl
318M cns_align0/cns_align068/cns.filt.dovt.ovl
316M cns_align0/cns_align069/cns.filt.dovt.ovl
318M cns_align0/cns_align070/cns.filt.dovt.ovl
314M cns_align0/cns_align071/cns.filt.dovt.ovl
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320M cns_align0/cns_align075/cns.filt.dovt.ovl
320M cns_align0/cns_align076/cns.filt.dovt.ovl
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318M cns_align0/cns_align080/cns.filt.dovt.ovl
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388M cns_align0/cns_align082/cns.filt.dovt.ovl
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314M cns_align0/cns_align086/cns.filt.dovt.ovl
164M cns_align0/cns_align087/cns.filt.dovt.ovl
322M cns_align0/cns_align088/cns.filt.dovt.ovl
323M cns_align0/cns_align089/cns.filt.dovt.ovl
319M cns_align0/cns_align090/cns.filt.dovt.ovl
319M cns_align0/cns_align091/cns.filt.dovt.ovl
320M cns_align0/cns_align092/cns.filt.dovt.ovl
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319M cns_align0/cns_align094/cns.filt.dovt.ovl
321M cns_align0/cns_align095/cns.filt.dovt.ovl
320M cns_align0/cns_align096/cns.filt.dovt.ovl
322M cns_align0/cns_align097/cns.filt.dovt.ovl
318M cns_align0/cns_align098/cns.filt.dovt.ovl
319M cns_align0/cns_align099/cns.filt.dovt.ovl
320M cns_align0/cns_align100/cns.filt.dovt.ovl
320M cns_align0/cns_align101/cns.filt.dovt.ovl
324M cns_align0/cns_align102/cns.filt.dovt.ovl
324M cns_align0/cns_align103/cns.filt.dovt.ovl
323M cns_align0/cns_align104/cns.filt.dovt.ovl
321M cns_align0/cns_align105/cns.filt.dovt.ovl
324M cns_align0/cns_align106/cns.filt.dovt.ovl
321M cns_align0/cns_align107/cns.filt.dovt.ovl
318M cns_align0/cns_align108/cns.filt.dovt.ovl
393M cns_align0/cns_align109/cns.filt.dovt.ovl
319M cns_align0/cns_align110/cns.filt.dovt.ovl
320M cns_align0/cns_align111/cns.filt.dovt.ovl
323M cns_align0/cns_align112/cns.filt.dovt.ovl
317M cns_align0/cns_align113/cns.filt.dovt.ovl
163M cns_align0/cns_align114/cns.filt.dovt.ovl
322M cns_align0/cns_align115/cns.filt.dovt.ovl
320M cns_align0/cns_align116/cns.filt.dovt.ovl
318M cns_align0/cns_align117/cns.filt.dovt.ovl
318M cns_align0/cns_align118/cns.filt.dovt.ovl
316M cns_align0/cns_align119/cns.filt.dovt.ovl
319M cns_align0/cns_align120/cns.filt.dovt.ovl
322M cns_align0/cns_align121/cns.filt.dovt.ovl
318M cns_align0/cns_align122/cns.filt.dovt.ovl
322M cns_align0/cns_align123/cns.filt.dovt.ovl
315M cns_align0/cns_align124/cns.filt.dovt.ovl
319M cns_align0/cns_align125/cns.filt.dovt.ovl
318M cns_align0/cns_align126/cns.filt.dovt.ovl
319M cns_align0/cns_align127/cns.filt.dovt.ovl
321M cns_align0/cns_align128/cns.filt.dovt.ovl
324M cns_align0/cns_align129/cns.filt.dovt.ovl
321M cns_align0/cns_align130/cns.filt.dovt.ovl
321M cns_align0/cns_align131/cns.filt.dovt.ovl
324M cns_align0/cns_align132/cns.filt.dovt.ovl
322M cns_align0/cns_align133/cns.filt.dovt.ovl
318M cns_align0/cns_align134/cns.filt.dovt.ovl
390M cns_align0/cns_align135/cns.filt.dovt.ovl
317M cns_align0/cns_align136/cns.filt.dovt.ovl
318M cns_align0/cns_align137/cns.filt.dovt.ovl
321M cns_align0/cns_align138/cns.filt.dovt.ovl
318M cns_align0/cns_align139/cns.filt.dovt.ovl
165M cns_align0/cns_align140/cns.filt.dovt.ovl
321M cns_align0/cns_align141/cns.filt.dovt.ovl
320M cns_align0/cns_align142/cns.filt.dovt.ovl
321M cns_align0/cns_align143/cns.filt.dovt.ovl
315M cns_align0/cns_align144/cns.filt.dovt.ovl
321M cns_align0/cns_align145/cns.filt.dovt.ovl
321M cns_align0/cns_align146/cns.filt.dovt.ovl
321M cns_align0/cns_align147/cns.filt.dovt.ovl
323M cns_align0/cns_align148/cns.filt.dovt.ovl
317M cns_align0/cns_align149/cns.filt.dovt.ovl
322M cns_align0/cns_align150/cns.filt.dovt.ovl
320M cns_align0/cns_align151/cns.filt.dovt.ovl
320M cns_align0/cns_align152/cns.filt.dovt.ovl
324M cns_align0/cns_align153/cns.filt.dovt.ovl
324M cns_align0/cns_align154/cns.filt.dovt.ovl
323M cns_align0/cns_align155/cns.filt.dovt.ovl
322M cns_align0/cns_align156/cns.filt.dovt.ovl
325M cns_align0/cns_align157/cns.filt.dovt.ovl
322M cns_align0/cns_align158/cns.filt.dovt.ovl
320M cns_align0/cns_align159/cns.filt.dovt.ovl
394M cns_align0/cns_align160/cns.filt.dovt.ovl
320M cns_align0/cns_align161/cns.filt.dovt.ovl
321M cns_align0/cns_align162/cns.filt.dovt.ovl
322M cns_align0/cns_align163/cns.filt.dovt.ovl
319M cns_align0/cns_align164/cns.filt.dovt.ovl
161M cns_align0/cns_align165/cns.filt.dovt.ovl
315M cns_align0/cns_align166/cns.filt.dovt.ovl
318M cns_align0/cns_align167/cns.filt.dovt.ovl
314M cns_align0/cns_align168/cns.filt.dovt.ovl
317M cns_align0/cns_align169/cns.filt.dovt.ovl
319M cns_align0/cns_align170/cns.filt.dovt.ovl
316M cns_align0/cns_align171/cns.filt.dovt.ovl
319M cns_align0/cns_align172/cns.filt.dovt.ovl
312M cns_align0/cns_align173/cns.filt.dovt.ovl
316M cns_align0/cns_align174/cns.filt.dovt.ovl
316M cns_align0/cns_align175/cns.filt.dovt.ovl
315M cns_align0/cns_align176/cns.filt.dovt.ovl
320M cns_align0/cns_align177/cns.filt.dovt.ovl
320M cns_align0/cns_align178/cns.filt.dovt.ovl
318M cns_align0/cns_align179/cns.filt.dovt.ovl
317M cns_align0/cns_align180/cns.filt.dovt.ovl
320M cns_align0/cns_align181/cns.filt.dovt.ovl
319M cns_align0/cns_align182/cns.filt.dovt.ovl
315M cns_align0/cns_align183/cns.filt.dovt.ovl
388M cns_align0/cns_align184/cns.filt.dovt.ovl
315M cns_align0/cns_align185/cns.filt.dovt.ovl
317M cns_align0/cns_align186/cns.filt.dovt.ovl
319M cns_align0/cns_align187/cns.filt.dovt.ovl
314M cns_align0/cns_align188/cns.filt.dovt.ovl
159M cns_align0/cns_align189/cns.filt.dovt.ovl
315M cns_align0/cns_align190/cns.filt.dovt.ovl
312M cns_align0/cns_align191/cns.filt.dovt.ovl
317M cns_align0/cns_align192/cns.filt.dovt.ovl
318M cns_align0/cns_align193/cns.filt.dovt.ovl
314M cns_align0/cns_align194/cns.filt.dovt.ovl
318M cns_align0/cns_align195/cns.filt.dovt.ovl
312M cns_align0/cns_align196/cns.filt.dovt.ovl
316M cns_align0/cns_align197/cns.filt.dovt.ovl
314M cns_align0/cns_align198/cns.filt.dovt.ovl
316M cns_align0/cns_align199/cns.filt.dovt.ovl
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317M cns_align0/cns_align205/cns.filt.dovt.ovl
315M cns_align0/cns_align206/cns.filt.dovt.ovl
388M cns_align0/cns_align207/cns.filt.dovt.ovl
314M cns_align0/cns_align208/cns.filt.dovt.ovl
317M cns_align0/cns_align209/cns.filt.dovt.ovl
317M cns_align0/cns_align210/cns.filt.dovt.ovl
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Try this command:
ls cns_align*/cns_align*/cns.filt.dovt.ovl|while read line;do echo $line;/data/software/NextDenovo/bin/ovl_cvt -m 1 $line|head -5;done;
to check which file has an error?
I don't know how to check the output. So I attached it.
check.log
It seems everything is ok, so just retry or download the latest version and retry.
I retried several times, got the same error reported before.
If I use the latest version, can I restart from the step that met the error?
Hi @moold,
I have another question. If the sequencing depth of the genome is 100x, should I change the seed_depth to 100x, or just the default parameter?
I retried several times, got the same error reported before.
If I use the latest version, can I restart from the step that met the error?
YES
Hi @moold,
I have another question. If the sequencing depth of the genome is 100x, should I change theseed_depthto 100x, or just the default parameter?
default
I just realized what is the seed_cutoff in your config file or log file?
I set seed_cutoff as 3266.
I rerun it with the latest version with the following error.
[INFO] 2021-02-01 14:54:37,370 skip step: db_split
[INFO] 2021-02-01 14:54:37,584 skip step: raw_align
[INFO] 2021-02-01 14:54:37,603 skip step: sort_align
[INFO] 2021-02-01 14:54:37,628 skip step: seed_cns
[INFO] 2021-02-01 14:54:37,629 seed_cns finished, and final corrected reads file:
[INFO] 2021-02-01 14:54:37,629 /data/Project/3.fish/01.assmbly/./01_rundir_gonad_seed3266/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta
[INFO] 2021-02-01 14:54:37,809 skip step: cns_align
[INFO] 2021-02-01 14:54:37,815 skip step: ctg_graph
[ERROR] failed to find seq file type or empty file
- It seems the ctg_graph task has finished but the result file is an empty file, so you need remove the ctg_graph directory
03.ctg_graph. - The reason maybe is: the seed_cutoff is too short, and NextDenovo will filter almost all reads by default, because NextDenovo is optimized for assembly with seed_cutoff >= 10kb, see here. So I do not suggest you to try again...
okay, I will use the default seed_depth to rerun the whole program.
minimap2-nd step is really slow. So I set -I 6G to -I 150G to speed up. Is this modification also okay?
yes，it is ok