Read trimming/filtering is not finding the necessary adapter file #4

holmrenser · 2015-09-06T14:43:47Z

Continued from #3

Hi Rens,

I have a problem! I'm using IOGA.py, but I keep seeing this error: OSError: [Errno 2]. Would you please help me solve this problem?

[teste] Quality trimming with BBduk

Traceback (most recent call last):

File "./IOGA.py", line 408, in main(args.reference,args.name,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)

File "./IOGA.py", line 352, in main

source,FP,RP,final_iteration = IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)

File "./IOGA.py", line 288, in IOGA_loop

forward,reverse = run_bbduk(name,forward,reverse,threads)

File "./IOGA.py", line 187, in run_bbduk subprocess.call(['bbduk.sh','ref='+adapterdir,'in='+forward,'in2='+reverse,'out='+FP,'out2='+RP,'threads='+threads,'k=25','ktrim=rl','qtrim=t','minlength=32','-Xmx10G'],stderr=fnull,stdout=fnull)

File "/usr/lib/python2.7/subprocess.py", line 522, in call

return Popen(popenargs, *kwargs).wait()

File "/usr/lib/python2.7/subprocess.py", line 710, in init

errread, errwrite)

File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child

raise child_exception

OSError: [Errno 2] No such file or directory

Best regards,

Lilian

The text was updated successfully, but these errors were encountered:

holmrenser · 2015-09-06T14:46:51Z

As I mentioned in the title, this is problem with read trimming/filtering. I will try to upload a fix in the coming days. Stay tuned!

Lilian-ufsc · 2015-09-16T15:53:45Z

Hi Mr. Holmer,

Do you have any news about the script?
Best Regards!

Lilian

holmrenser · 2015-09-21T13:57:31Z

Hi Lilian,

I am currently merging several bug fixes and feature requests into a new release, this should be finished this week.

Let's hope it is worth the wait!

Lilian-ufsc · 2015-09-21T14:03:08Z

Thank you! I will wait.

Best regards,

Lilian

2015-09-21 10:57 GMT-03:00 holmrenser [email protected]:

Hi Lilian,

I am currently merging several bug fixes and feature requests into a new
release, this should be finished this week.

Let's hope it is worth the wait!

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holmrenser · 2015-09-25T10:03:42Z

This should be fixed now, so please pull the latest code.
After pulling, do the following:

run python setup_IOGA.py in the same folder as IOGA.py
this should generate a file: IOGA_config.json

IOGA uses this file to find all the required dependencies, this should fix the problems you were having.

Please let me know if this works or does not work!

Lilian-ufsc · 2015-09-25T13:23:33Z

Dear Rens,

I've tried running the setup_IOGA.py code, but unfortunately it did not
work very well. It raises a problem when installing samtools. It seems that
the problem occurs when running the command make from the code.
I tired running it separately and it gives me the following message:

make[1]: Entering directory
/home/lilian/Documents/IOGA-master/exe/samtools-0.1.19'make[2]: Entering directory/home/lilian/Documents/IOGA-master/exe/samtools-0.1.19'gcc -c -g
-Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
-D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.oIn file included from
bgzf.c:32:0:bgzf.h:33:18: fatal error: zlib.h: No such file or
directory #include <zlib.h> ^compilation
terminated.make[2]: ** [bgzf.o] Error 1make[2]: Leaving directory
/home/lilian/Documents/IOGA-master/exe/samtools-0.1.19'make[1]: *** [lib-recur] Error 1make[1]: Leaving directory /home/lilian/Documents/IOGA-master/exe/samtools-0.1.19'make: ***
[all-recur] Error 1*

I was wondering if it is possible to exclude the samtools downloading step
from the code, since I already have samtools installed in my computer.

Thanks for your help.

Best regards,

Lilian

2015-09-25 7:03 GMT-03:00 holmrenser [email protected]:

This should be fixed now, so please pull the latest code.
After pulling, do the following:

run python setup_IOGA.py in the same folder as IOGA.py

this should generate a file: IOGA_config.json`

IOGA uses this file to find all the required dependencies, this should fix
the problems you were having.

Please let me know if this works or does not work!

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Fone(48)99767028

holmrenser · 2015-09-25T13:29:40Z

Hi Lillian,
I am update the install script so that you will get a template of the config. You can then add the samtools path yourself.
In the meantime, it looks like your missing zlib1g-dev. You could try installing that and see if it fixes the make error.

Cheers,

Rens

Lilian-ufsc · 2015-09-25T13:38:50Z

Hi Rens,

Installing the zlib1g-dev library did not solve the problem. I'll wait for
the new update then.

Thanks once again.

Best,

Lilian

2015-09-25 10:29 GMT-03:00 holmrenser [email protected]:

Hi Lillian,
I am update the install script so that you will get a template of the
config. You can then add the samtools path yourself.
In the meantime, it looks like your missing zlib1g-dev. You could try
installing that and see if it fixes the make error.

Cheers,

Rens

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Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

holmrenser · 2015-09-25T13:38:55Z

I pushed a fix, you can try that now.

Lilian-ufsc · 2015-09-25T14:49:21Z

Hi Rens,

I keep seeing this error:

/home/lilian/Documents/IOGA-master/IOGA_config.json
[teste] Quality trimming with BBduk
Iteration 1
[teste.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 113, in run_bbmap

subprocess.call([config['bbmap'],'ref='+ref,'in='+forward,'in2='+reverse,'threads='+threads,'outm='+mappedreads,'covstats='+covstats,'basecov='+basecov,'-Xmx10G','local=t','keepnames=t'],stdout=fnull,stderr=fnull)

KeyError: 'bbmap'

Regards,

Lilian

2015-09-25 10:38 GMT-03:00 holmrenser [email protected]:

I pushed a fix, you can try that now.

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holmrenser · 2015-09-25T14:51:34Z

Could you post a copy of IOGA_config.json?

EDIT: there was an error in IOGA.py. Should be fixed.

Lilian-ufsc · 2015-09-25T16:23:15Z

Following a copy of IOGA_config.jso

{
"picard.jar":
"/home/lilian/Documents/IOGA-master/exe/picard-tools-1.124/picard.jar",
"samtools": "",
"bbmap.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbmap.sh",
"bbduk.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbduk.sh",
"spades.py":
"/home/lilian/Documents/IOGA-master/exe/SPAdes-3.1.1-Linux/bin/spades.py",
"ALE": "/home/lilian/Documents/IOGA-master/exe/ALE-master/src/ALE",
"SOAPdenovo-127mer":
"/home/lilian/Documents/IOGA-master/exe/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer",

"adapters":
"/home/lilian/Documents/IOGA-master/exe/bbmap/alladapters.fa.gz",
"seqtk": "/home/lilian/Documents/IOGA-master/exe/seqtk-master/seqtk"
}

2015-09-25 11:51 GMT-03:00 holmrenser [email protected]:

Could you post a copy of IOGA_config.json?

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UFSC/CCA
Fone(48)99767028

holmrenser · 2015-09-25T16:26:34Z

Could you please check the fix?

On 25 Sep 2015, at 18:23, Lilian-ufsc <[email protected]mailto:[email protected]> wrote:

Following a copy of IOGA_config.jso

{
"picard.jar":
"/home/lilian/Documents/IOGA-master/exe/picard-tools-1.124/picard.jar",
"samtools": "",
"bbmap.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbmap.sh",
"bbduk.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbduk.sh",
"spades.py":
"/home/lilian/Documents/IOGA-master/exe/SPAdes-3.1.1-Linux/bin/spades.py",
"ALE": "/home/lilian/Documents/IOGA-master/exe/ALE-master/src/ALE",
"SOAPdenovo-127mer":
"/home/lilian/Documents/IOGA-master/exe/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer",

"adapters":
"/home/lilian/Documents/IOGA-master/exe/bbmap/alladapters.fa.gz",
"seqtk": "/home/lilian/Documents/IOGA-master/exe/seqtk-master/seqtk"
}

2015-09-25 11:51 GMT-03:00 holmrenser <[email protected]mailto:[email protected]>:

Could you post a copy of IOGA_config.json?

Reply to this email directly or view it on GitHub
#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Gen?ticos Vegetais
Laborat?rio de Fisiologia do Desenvolvimento e Gen?tica Vegetal
UFSC/CCA
Fone(48)99767028

Reply to this email directly or view it on GitHubhttps://github.com//issues/4#issuecomment-143267678.

Lilian-ufsc · 2015-09-25T16:54:02Z

Following a new error:

/home/lilian/Documents/IOGA-master/IOGA_config.json
[guabiroba] Quality trimming with BBduk
Iteration 1
[guabiroba.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 114, in run_bbmap
plot_coverage(basecov)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 121, in
plot_coverage
with open(BBmap_coverage,'rU') as infile:
IOError: [Errno 2] No such file or directory:
'/home/lilian/Documents/IOGA-master/guabiroba.1/guabiroba.1.basecov.txt'

2015-09-25 13:26 GMT-03:00 holmrenser [email protected]:

Could you please check the fix?

On 25 Sep 2015, at 18:23, Lilian-ufsc <[email protected]<mailto:
[email protected]>> wrote:

Following a copy of IOGA_config.jso

{
"picard.jar":
"/home/lilian/Documents/IOGA-master/exe/picard-tools-1.124/picard.jar",
"samtools": "",
"bbmap.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbmap.sh",
"bbduk.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbduk.sh",
"spades.py":
"/home/lilian/Documents/IOGA-master/exe/SPAdes-3.1.1-Linux/bin/spades.py",
"ALE": "/home/lilian/Documents/IOGA-master/exe/ALE-master/src/ALE",
"SOAPdenovo-127mer":

"/home/lilian/Documents/IOGA-master/exe/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer",

"adapters":
"/home/lilian/Documents/IOGA-master/exe/bbmap/alladapters.fa.gz",
"seqtk": "/home/lilian/Documents/IOGA-master/exe/seqtk-master/seqtk"
}

2015-09-25 11:51 GMT-03:00 holmrenser <[email protected]<mailto:
[email protected]>>:

Could you post a copy of IOGA_config.json?

Reply to this email directly or view it on GitHub
#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Gen?ticos Vegetais
Laborat?rio de Fisiologia do Desenvolvimento e Gen?tica Vegetal
UFSC/CCA
Fone(48)99767028

Reply to this email directly or view it on GitHub<
https://github.com/holmrenser/IOGA/issues/4#issuecomment-143267678>.

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Fone(48)99767028

holmrenser · 2015-09-25T18:07:09Z

Are you able to run the bbmap.sh and bbduk.sh that were installed?

On 25 Sep 2015, at 18:54, Lilian-ufsc <[email protected]mailto:[email protected]> wrote:

Following a new error:

/home/lilian/Documents/IOGA-master/IOGA_config.json
[guabiroba] Quality trimming with BBduk
Iteration 1
[guabiroba.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 114, in run_bbmap
plot_coverage(basecov)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 121, in
plot_coverage
with open(BBmap_coverage,'rU') as infile:
IOError: [Errno 2] No such file or directory:
'/home/lilian/Documents/IOGA-master/guabiroba.1/guabiroba.1.basecov.txt'

2015-09-25 13:26 GMT-03:00 holmrenser <[email protected]mailto:[email protected]>:

Could you please check the fix?

On 25 Sep 2015, at 18:23, Lilian-ufsc <[email protected]mailto:[email protected]<mailto:
[email protected]mailto:[email protected]>> wrote:

Following a copy of IOGA_config.jso

{
"picard.jar":
"/home/lilian/Documents/IOGA-master/exe/picard-tools-1.124/picard.jar",
"samtools": "",
"bbmap.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbmap.sh",
"bbduk.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbduk.sh",
"spades.py":
"/home/lilian/Documents/IOGA-master/exe/SPAdes-3.1.1-Linux/bin/spades.py",
"ALE": "/home/lilian/Documents/IOGA-master/exe/ALE-master/src/ALE",
"SOAPdenovo-127mer":

"/home/lilian/Documents/IOGA-master/exe/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer",

"adapters":
"/home/lilian/Documents/IOGA-master/exe/bbmap/alladapters.fa.gz",
"seqtk": "/home/lilian/Documents/IOGA-master/exe/seqtk-master/seqtk"
}

2015-09-25 11:51 GMT-03:00 holmrenser <[email protected]mailto:[email protected]<mailto:
[email protected]mailto:[email protected]>>:

Could you post a copy of IOGA_config.json?

Reply to this email directly or view it on GitHub
#4 (comment).

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Doutoranda em Recursos Gen?ticos Vegetais
Laborat?rio de Fisiologia do Desenvolvimento e Gen?tica Vegetal
UFSC/CCA
Fone(48)99767028

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Lilian-ufsc · 2015-09-25T18:18:40Z

Yes, both were installed.

2015-09-25 15:07 GMT-03:00 holmrenser [email protected]:

Are you able to run the bbmap.sh and bbduk.sh that were installed?

On 25 Sep 2015, at 18:54, Lilian-ufsc <[email protected]<mailto:
[email protected]>> wrote:

Following a new error:

/home/lilian/Documents/IOGA-master/IOGA_config.json
[guabiroba] Quality trimming with BBduk
Iteration 1
[guabiroba.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)

File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 114, in run_bbmap
plot_coverage(basecov)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 121, in
plot_coverage
with open(BBmap_coverage,'rU') as infile:
IOError: [Errno 2] No such file or directory:
'/home/lilian/Documents/IOGA-master/guabiroba.1/guabiroba.1.basecov.txt'

2015-09-25 13:26 GMT-03:00 holmrenser <[email protected]<mailto:
[email protected]>>:

Could you please check the fix?

On 25 Sep 2015, at 18:23, Lilian-ufsc <[email protected]<mailto:
[email protected]><mailto:
[email protected]mailto:[email protected]>> wrote:

Following a copy of IOGA_config.jso

{
"picard.jar":
"/home/lilian/Documents/IOGA-master/exe/picard-tools-1.124/picard.jar",
"samtools": "",
"bbmap.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbmap.sh",
"bbduk.sh": "/home/lilian/Documents/IOGA-master/exe/bbmap/bbduk.sh",
"spades.py":

"/home/lilian/Documents/IOGA-master/exe/SPAdes-3.1.1-Linux/bin/spades.py",
"ALE": "/home/lilian/Documents/IOGA-master/exe/ALE-master/src/ALE",
"SOAPdenovo-127mer":

"/home/lilian/Documents/IOGA-master/exe/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer",

"adapters":
"/home/lilian/Documents/IOGA-master/exe/bbmap/alladapters.fa.gz",
"seqtk": "/home/lilian/Documents/IOGA-master/exe/seqtk-master/seqtk"
}

2015-09-25 11:51 GMT-03:00 holmrenser <[email protected]<mailto:
[email protected]><mailto:
[email protected]mailto:[email protected]>>:

Could you post a copy of IOGA_config.json?

Reply to this email directly or view it on GitHub
#4 (comment).

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Doutoranda em Recursos Gen?ticos Vegetais
Laborat?rio de Fisiologia do Desenvolvimento e Gen?tica Vegetal
UFSC/CCA
Fone(48)99767028

Reply to this email directly or view it on GitHub<
https://github.com/holmrenser/IOGA/issues/4#issuecomment-143267678>.

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holmrenser · 2015-09-25T18:19:49Z

Can you tell me what files are in the folder guabiroba.1, and what the exact command is that you used?

Lilian-ufsc · 2015-09-25T18:28:14Z

Sure!

Just one file.The file in the folder guabi.1 is guabi.1.temp.fasta.

Commands:

root@bioinfo-Precision-Tower-5810:/home/lilian/Documents/IOGA-master#
IOGA.py -n guabi -r chloroplast.reference.fasta -1
CampomanesiaXanthocarpa_S6_L001_R1_001.fastq -2
CampomanesiaXanthocarpa_S6_L001_R2 -i 300 -t 8
/home/lilian/Documents/IOGA-master/IOGA_config.json
/home/lilian/Documents/IOGA-master/IOGA_config.json
[guabi] Quality trimming with BBduk
Folder /home/lilian/Documents/IOGA-master/guabi.1 exists, overwriting
Iteration 1
[guabi.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 114, in run_bbmap
plot_coverage(basecov)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 121, in
plot_coverage
with open(BBmap_coverage,'rU') as infile:
IOError: [Errno 2] No such file or directory:
'/home/lilian/Documents/IOGA-master/guabi.1/guabi.1.basecov.txt'
root@bioinfo-Precision-Tower-5810:/home/lilian/Documents/IOGA-master#

2015-09-25 15:19 GMT-03:00 holmrenser [email protected]:

Can you tell me what files are in the folder guabiroba.1, and what the
exact command is that you used?

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holmrenser · 2015-09-25T18:37:43Z

I suspect the problem is in your IOGA.py command.

You typed: IOGA.py -n guabi -r chloroplast.reference.fasta -1 CampomanesiaXanthocarpa_S6_L001_R1_001.fastq -2 CampomanesiaXanthocarpa_S6_L001_R2 -i 300 -t 8.

The second readfile probably should be CampomanesiaXanthocarpa_S6_L001_R2_001.fastq ?

Lilian-ufsc · 2015-09-25T18:43:13Z

Unfortunately not, I fixed the command but I still get the same error.

root@bioinfo-Precision-Tower-5810:/home/lilian/Documents/IOGA-master#
IOGA.py -n guabi -r chloroplast.reference.fasta -1
CampomanesiaXanthocarpa_S6_L001_R1_001.fastq -2
CampomanesiaXanthocarpa_S6_L001_R2_001.fastq -i 300 -t 8
/home/lilian/Documents/IOGA-master/IOGA_config.json
/home/lilian/Documents/IOGA-master/IOGA_config.json
[guabi] Quality trimming with BBduk
Folder /home/lilian/Documents/IOGA-master/guabi.1 exists, overwriting
Iteration 1
[guabi.1] BBmap
Traceback (most recent call last):
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 432, in
main(args.reference,args.name
,args.forward,args.reverse,args.threads,args.insertsize,args.maxrounds,args.verbose)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 377, in main
source,FP,RP,final_iteration =
IOGA_loop(name,ref,forward,reverse,insertsize,threads,maxrounds)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 344, in IOGA_loop
samfile = run_bbmap(folder,prefix,ref,forward,reverse,threads)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 114, in run_bbmap
plot_coverage(basecov)
File "/home/lilian/Documents/IOGA-master/IOGA.py", line 121, in
plot_coverage
with open(BBmap_coverage,'rU') as infile:
IOError: [Errno 2] No such file or directory:
'/home/lilian/Documents/IOGA-master/guabi.1/guabi.1.basecov.txt'

2015-09-25 15:37 GMT-03:00 holmrenser [email protected]:

I suspect the problem is in your IOGA.py command.

You typed: IOGA.py -n guabi -r chloroplast.reference.fasta -1
CampomanesiaXanthocarpa_S6_L001_R1_001.fastq -2
CampomanesiaXanthocarpa_S6_L001_R2 -i 300 -t 8.

The second readfile probably should be
CampomanesiaXanthocarpa_S6_L001_R2_001.fastq ?

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Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

holmrenser · 2015-10-08T14:39:59Z

Do you still have these issues?

So far I have been unable to reproduce these errors. Do you have java7?

For sure I will work on more informative logging and error messages.

holmrenser · 2015-10-08T15:04:34Z

Also I fixed an error with the adapters.
I think it should work now...

Lilian-ufsc · 2015-10-09T17:50:18Z

Hi Rens,

I installed java 7 but it's not working. So, I installed java 8 and I
trying to run.
Typical runtime on 4 threads is ~20minutes, but I used 2 threads and it's
taking sometime. Is it right?

Regards

Lilian

2015-10-08 12:04 GMT-03:00 holmrenser [email protected]:

Also I fixed an error with the adapters.
I think it should work now...

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#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

Lilian-ufsc · 2015-10-09T18:57:20Z

Java error - threads error

Here are thread error messages:

lilian@bioinfo-Precision-Tower-5810:~/Downloads/IOGA-master$ ./IOGA.py -r
chloroplast.reference.fasta -n teste -1
/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R1_001.fastq
-2
/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R2_001.fastq
-i 300 -t 4 -v
/home/lilian/Downloads/IOGA-master/IOGA_config.json
/home/lilian/Downloads/IOGA-master/IOGA_config.json
[teste] Quality trimming with BBduk
java -ea -Xmx10G -cp /home/lilian/Downloads/IOGA-master/exe/bbmap/current/
jgi.BBDukF
ref=/home/lilian/Downloads/IOGA-master/exe/bbmap/alladapters.fa.gz
in=/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R1_001.fastq
in2=/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R2_001.fastq
out=teste.temp.filtered.R1.fastq out2=teste.temp.filtered.R2.fastq
threads=4 k=25 ktrim=rl qtrim=t minlength=32 -Xmx10G
Executing jgi.BBDukF
[ref=/home/lilian/Downloads/IOGA-master/exe/bbmap/alladapters.fa.gz,
in=/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R1_001.fastq,
in2=/home/lilian/Documents/Guabiroba/CampomanesiaXanthocarpa_S6_L001_R2_001.fastq,
out=teste.temp.filtered.R1.fastq, out2=teste.temp.filtered.R2.fastq,
threads=4, k=25, ktrim=rl, qtrim=t, minlength=32, -Xmx10G]

Initial:
Memory: free=486m, used=18m

Exception in thread "Thread-8" java.lang.AssertionError: 0, 238296, 2
at stream.FastaReadInputStream.nextHeader(FastaReadInputStream.java:317)
at stream.FastaReadInputStream.fillList(FastaReadInputStream.java:205)
at stream.FastaReadInputStream.hasMore(FastaReadInputStream.java:137)
at
stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:746)
at
stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:738)

Would you help me, please?
Thank you!

2015-10-09 14:50 GMT-03:00 Lilian Machado [email protected]:

Hi Rens,

I installed java 7 but it's not working. So, I installed java 8 and I
trying to run.
Typical runtime on 4 threads is ~20minutes, but I used 2 threads and it's
taking sometime. Is it right?

Regards

Lilian

2015-10-08 12:04 GMT-03:00 holmrenser [email protected]:

Also I fixed an error with the adapters.
I think it should work now...

—
Reply to this email directly or view it on GitHub
#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

holmrenser · 2015-10-09T19:01:29Z

This is proving to be an excellent test case! Thanks for sticking with me. I think your latest error is a result of a bug in the adapter sequences for read trimming. This should be fixed now, so please make sure you do a git pull and check again.

If that doesn't fix things, please check in again!

Lilian-ufsc · 2015-10-09T19:14:51Z

Have you update the script on the github page? I haven't found any new
files there, today.

Cheers.

2015-10-09 16:01 GMT-03:00 holmrenser [email protected]:

This is proving to be an excellent test case! Thanks for sticking with me.
I think your latest error is a result of a bug in the adapter sequences for
read trimming. This should be fixed now, so please make sure you do a git
pull and check again.

If that doesn't fix things, please check in again!

—
Reply to this email directly or view it on GitHub
#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

holmrenser · 2015-10-10T09:17:57Z

No new files, but they have changed ;-)

Lilian-ufsc · 2015-10-14T00:10:07Z

Dear Rens,

Great sucess, problem solved!

Thank you so much :)

Cheers,

Lilian

2015-10-10 6:17 GMT-03:00 holmrenser [email protected]:

No new files, but they have changed ;-)

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#4 (comment).

Lilian de Oliveira Machado
Doutoranda em Recursos Genéticos Vegetais
Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal
UFSC/CCA
Fone(48)99767028

holmrenser · 2015-10-14T07:57:15Z

Hurray! Thank you a lot for working this out with me!

holmrenser mentioned this issue Sep 6, 2015

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Closed

holmrenser closed this as completed Oct 14, 2015

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Read trimming/filtering is not finding the necessary adapter file #4

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