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streamformatics seems not working #3

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xlinxlin opened this issue Oct 25, 2019 · 3 comments
Open

streamformatics seems not working #3

xlinxlin opened this issue Oct 25, 2019 · 3 comments

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@xlinxlin
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Hi,
I have an issue with streamformatics which works on Ubuntu 18.04.
First I set the conf.json in the sreamformatics directory:

{
  "minimap2": {
    "executable": "/home/sysgen/git/minimap2/minimap2",
    "memory": "32g",
    "threads": "100"
  },
  "speciesTyper": {
    "executable": "~/.usr/local/bin/jsa.np.rtSpeciesTyping",
    "quality": "0"
  },
  "watcher": "/home/sysgen/git/streamformatics/public/scripts/strom",
  "database": "/home/sysgen/git/streamformatics/database/refseq/sample/ref.fasta",
  "speciesIndex": "/home/sysgen/git/streamformatics/database/refseq/sample/speciesIndex"
}

Then I could see the web GUI correctly at localhost:3000. I gave the input and saw the following message on the terminal:

(base) sysgen@supermicro02:~/git/streamformatics$ npm start

> uwa_pipeline@1.0.0 start /home/sysgen/git/streamformatics
> node app.js

Listening on port 3000
Server is live at: http://::1:3000
File watcher called at Thu Oct 24 2019 10:36:57 GMT+0200 (Central European Summer Time)
minimap2 called at Thu Oct 24 2019 10:36:57 GMT+0200 (Central European Summer Time)
Species typing called at Thu Oct 24 2019 10:36:57 GMT+0200 (Central European Summer Time)
minimap2 exited 1 null at Thu Oct 24 2019 10:36:57 GMT+0200 (Central European Summer Time)
minimap2 closed 1 null at Thu Oct 24 2019 10:36:57 GMT+0200 (Central European Summer Time)

And the web page was empty with the message "Thu Oct 24 2019 10:36:22 GMT+0200 (Central European Summer Time) 0 reads have been analysed."
At first I thought it would be the minimap2 issue, but actually minimap2 worked fine:

(base) sysgen@supermicro02:~/Yan_test/20190725_SP_Metagenomics/fastq/fastq_pass$ ~/git/minimap2/minimap2 -x map-ont ~/git/streamformatics/database/refseq/sample/ref.fasta PAD55253_8725228fdceb9c3f8722715c06e9af8f6b3f4b89_989.fastq -t 100
[M::mm_idx_gen::2.830*1.44] collected minimizers
[M::mm_idx_gen::6.548*2.51] sorted minimizers
[M::main::6.548*2.51] loaded/built the index for 1494 target sequence(s)
[M::mm_mapopt_update::7.018*2.41] mid_occ = 38
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1494
[M::mm_idx_stat::7.240*2.37] distinct minimizers: 18026307 (78.33% are singletons); average occurrences: 1.491; average spacing: 5.360
232a93d7-1180-4046-82dc-4278c1f45e0a	328	266	309	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	0	tp:A:P	cm:i:8	s1:i:43	s2:i:43	dv:f:0.0149	rl:i:0
232a93d7-1180-4046-82dc-4278c1f45e0a	328	262	305	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	0	tp:A:S	cm:i:8	s1:i:43	dv:f:0.0149	rl:i:0
232a93d7-1180-4046-82dc-4278c1f45e0a	328	254	297	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	4	tp:A:P	cm:i:8	s1:i:43	s2:i:0	dv:f:0.0149	rl:i:0
232a93d7-1180-4046-82dc-4278c1f45e0a	328	258	301	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	0	tp:A:S	cm:i:8	s1:i:43	dv:f:0.0149	rl:i:0
cf15f261-b30b-4e41-94ea-9b8582ee524b	585	221	265	+	NZ_FZOB01000009.1	57122	34867	34910	42	44	2	tp:A:P	cm:i:5	s1:i:42	s2:i:0	dv:f:0.0313	rl:i:0
c90bc47d-bb57-4858-9357-62096a113035	247	75	123	-	NZ_FZOB01000009.1	57122	34867	34910	43	48	0	tp:A:P	cm:i:6	s1:i:42	s2:i:42	dv:f:0.0270	rl:i:0
c90bc47d-bb57-4858-9357-62096a113035	247	67	115	-	NZ_FZOB01000009.1	57122	34867	34910	43	48	0	tp:A:S	cm:i:6	s1:i:42	dv:f:0.0270	rl:i:0
c90bc47d-bb57-4858-9357-62096a113035	247	71	119	-	NZ_FZOB01000009.1	57122	34867	34910	43	48	0	tp:A:S	cm:i:6	s1:i:42	dv:f:0.0270	rl:i:0
c90bc47d-bb57-4858-9357-62096a113035	247	79	127	-	NZ_FZOB01000009.1	57122	34867	34910	43	48	0	tp:A:S	cm:i:6	s1:i:42	dv:f:0.0270	rl:i:0
ce9d91e1-0670-4604-b24d-0e595f70a2d8	5498	786	829	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	0	tp:A:P	cm:i:8	s1:i:43	s2:i:43	dv:f:0.0149	rl:i:0
ce9d91e1-0670-4604-b24d-0e595f70a2d8	5498	782	825	-	NZ_FZOB01000009.1	57122	34867	34910	43	43	0	tp:A:S	cm:i:8	s1:i:43	dv:f:0.0149	rl:i:0
ce9d91e1-0670-4604-b24d-0e595f70a2d8	5498	760	809	-	NZ_FZOB01000009.1	57122	34867	34910	43	49	2	tp:A:P	cm:i:6	s1:i:42	s2:i:0	dv:f:0.0341	rl:i:0
ce9d91e1-0670-4604-b24d-0e595f70a2d8	5498	764	813	-	NZ_FZOB01000009.1	57122	34867	34910	43	49	0	tp:A:S	cm:i:6	s1:i:42	dv:f:0.0341	rl:i:0
[M::worker_pipeline::7.287*2.45] mapped 4000 sequences
[M::main] Version: 2.17-r943-dirty
[M::main] CMD: /home/sysgen/git/minimap2/minimap2 -x map-ont -t 100 /home/sysgen/git/streamformatics/database/refseq/sample/ref.fasta PAD55253_8725228fdceb9c3f8722715c06e9af8f6b3f4b89_989.fastq
[M::main] Real time: 7.332 sec; CPU: 17.894 sec; Peak RSS: 1.145 GB

There are 4 output log files, I paste them below:
minimap.1571905005813.stderr is empty.
species.1571905005813.dat is empty.
species.1571905005813.stderr has the following message.

(base) sysgen@supermicro02:~/git/streamformatics/logs$ cat species.1571905005813.stderr 
[main] INFO japsa.bio.np.RealtimeSpeciesTyping - 277444   5276
[main] INFO japsa.bio.np.RealtimeSpeciesTyping - Species typing ready at Thu Oct 24 10:16:46 CEST 2019

watcher.1571905005813.stderr has the following message.

(base) sysgen@supermicro02:~/git/streamformatics/logs$ cat watcher.1571905005813.stderr 
  File "/home/sysgen/git/streamformatics/public/scripts/strom", line 33
    print 'Error'
                ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('Error')?

Can you help me? Thanks a lot!
@mbhall88
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Owner

Hi @xlinxlin ,

Apologies that you are experiencing difficulties with this repository.

Unfortunately, I have not worked on this project for several years now and am very out of touch with it. As such, it has not been maintained by myself and is likely not to be again in the future as my current work is in a somewhat different area.

Knowing the way web technologies change very rapidly, I imagine this issue is likely related to some out-dated npm/node version.

Sadly, I am unable to devote time to look into this issue. I will leave this issue open though, in case you do discover a solution, which others will no doubt find helpful.

Again, my apologies for not being able to help you.

@xlinxlin
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Hi @mbhall88 , thanks for your reply. Could you provide me some information (nodejs version, npm version etc.) about this program when it still runs stable? Thanks!

@mbhall88
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Hi @xlinxlin ,

I don't know what the exact versions were. I guess you would just need to see what versions were release when the last commit from the repository was made.

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