failed to detect cutadapt

[Hoon Kim]

Hello,

Sorry for asking multiple questions in a few days.

I was trying to run a test, but it failed. It looks like it failed to detect the path to cutadapt, while cutadapt was on $PATH. See the below. This might be an error on my side, but I can't figure out the reason.

I wonder if you can let me know how to work around this error.

Thank you in advance,

Hoon

dqsfacpriv04:cbbio-miarma-7440692e7bb9:1122 %perl -I lib miARma Examples/basic_examples/miRNAs/Known_miRNAs/Known_miRNAs_pipeline.ini

#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Mon Jul 11 15:24:57 2016] Starting a miARma analysis for miRNA
[Mon Jul 11 15:24:57 2016] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction.
[Mon Jul 11 15:24:57 2016] Checking General-output_dir parameter ... Exists!
[Mon Jul 11 15:24:57 2016] The folder specified in (output_dir=Examples/basic_examples/miRNAs/Known_miRNAs/results/) already exists.
[Mon Jul 11 15:24:57 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise:   0
[Mon Jul 11 15:25:03 2016] Continue.
[Mon Jul 11 15:25:03 2016] All parameters are correct.
[Mon Jul 11 15:25:03 2016] Starting Quality Analysis.
[Mon Jul 11 15:27:24 2016] Quality Analysis finished.
[Mon Jul 11 15:27:24 2016] Checking if files in folder: "Examples/basic_examples/miRNAs/reads/" are in the correct fastq format.
[Mon Jul 11 15:27:24 2016] Starting a Adapter removal analysis
which: no cut_adapt in (/home/hkim6/local/fastQC/FastQC:/home/hkim6/bin:/home/hkim6/.local/bin:./bin/common/fastqc/:./bin/Linux/cutadapt/)
CUTADAPT ERROR :: system args failed: 256 : Is cutadapt installed and exported to $PATH ? at lib//CbBio/RNASeq/Adapt.pm line 783.

dqsfacpriv04:/cbbio-miarma-7440692e7bb9:1129 % which cutadapt
/home/hkim6/.local/bin/cutadapt

dqsfacpriv04:/cbbio-miarma-7440692e7bb9:1129 % cutadapt --version
1.9.1

[Eduardo Andres Leon]

Hi, The path (binaries and libraries) are handled by $miARmaPath variable in the ini file. Try to fill this variable with the full path where miARma is located. This should be fine

And please try to use miARma cutadapt. Other version installed in your computer could not be compatible (I see that you have a version in /home/hkim6/.local/bin/cutadapt) Regards

[Hoon Kim]

Thank you for your response, but I don't think I fully understood your comment.

Is "try to use miARma cutadapt" mean that 'cutadapt' should be under the path to miARma?

Thank you in advance,

Hoon

[Hoon Kim]

Hello,

Following your suggestions, I filled # "$miARmaPath" # variable in the ini file with the full path where miARma is located. I also copied a cutadapt binary file into a directory under miARmaPath; however, it failed to run with a same reason as above.

Thank you,

Hoon

[Hoon Kim]

Hello, Instead of 'https://bitbucket.org/cbbio/miarma/get/master.tar.bz2', I downloaded a source file from 'https://bitbucket.org/cbbio/miarma/get/7440692e7bb9.zip' which includes a 'cutadapt' folder. But, 'cut_adapt' does not run correctly, as shown.

dqsfacpriv04:/cbbio-miarma-7440692e7bb9:1129 % bin/Linux/cutadapt/cut_adapt --help
Traceback (most recent call last):
  File "bin/Linux/cutadapt/cut_adapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/hkim6/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/scripts/cutadapt.py", line 74, in <module>
    from cutadapt.adapters import Adapter, ColorspaceAdapter, BACK, FRONT, PREFIX, ANYWHERE
  File "/hkim6/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/adapters.py", line 4, in <module>
    from cutadapt import align, colorspace
  File "/hkim6/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/align.py", line 225, in <module>
    from cutadapt.calign import globalalign_locate


dqsfacpriv04:/cbbio-miarma-7440692e7bb9:1204 % perl -I lib miARma Examples/basic_examples/miRNAs/Known_miRNAs/Known_miRNAs_pipeline.ini
#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Tue Jul 12 16:01:51 2016] Starting a miARma analysis for miRNA
[Tue Jul 12 16:01:51 2016] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction.
[Tue Jul 12 16:01:51 2016] All parameters are correct.
[Tue Jul 12 16:01:52 2016] Starting Quality Analysis.
[Tue Jul 12 16:03:16 2016] Quality Analysis finished.
[Tue Jul 12 16:03:16 2016] Checking if files in folder: "Examples/basic_examples/miRNAs/reads/" are in the correct fastq format.
[Tue Jul 12 16:03:16 2016] Starting a Adapter removal analysis
CUTADAPT ERROR :: system args failed: 256 (mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA  -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.36663.log) at lib//CbBio/RNASeq/Adapt.pm line 851.

Your comments will be highly appreciated.

Thank you,

Hoon

[Eduardo Andres Leon]

Dear Hoon I guess that your problem must be related with python or similar.

I’ve tried a similar approach than yours and it’s working (using python 2.7.6):

So, which python version are you using ?

Regards

[Hoon Kim]

Sorry for my late response. I was away from my office for a while.

my python version is Python 2.7.8.

And, as you know, running cut_adapt does not work as follows:

dqsfacpriv01:/verhaak-data/users6/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9:1083 % bin/Linux/cutadapt/cut_adapt -help
Traceback (most recent call last):
  File "bin/Linux/cutadapt/cut_adapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/verhaak-data/users6/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/scripts/cutadapt.py", line 74, in <module>
    from cutadapt.adapters import Adapter, ColorspaceAdapter, BACK, FRONT, PREFIX, ANYWHERE
  File "/verhaak-data/users6/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/adapters.py", line 4, in <module>
    from cutadapt import align, colorspace
  File "/verhaak-data/users6/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/align.py", line 225, in <module>
    from cutadapt.calign import globalalign_locate
ImportError: /verhaak-data/users6/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/bin/Linux/cutadapt/cutadapt/calign.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8

[Hoon Kim]

Hello, Now, 'cut_adapt' works, but I have a different error when running:

perl -I lib miARma Examples/basic_examples/miRNAs/Known_miRNAs/Known_miRNAs_pipeline.ini

#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Tue Jul 19 22:00:32 2016] Starting a miARma analysis for miRNA
[Tue Jul 19 22:00:32 2016] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction.
[Tue Jul 19 22:00:32 2016] Checking General-output_dir parameter ... Exists!
[Tue Jul 19 22:00:32 2016] The folder specified in (output_dir=Examples/basic_examples/miRNAs/Known_miRNAs/results/) already exists.
[Tue Jul 19 22:00:32 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise:   0
[Tue Jul 19 22:00:38 2016] Continue.
[Tue Jul 19 22:00:38 2016] All parameters are correct.
[Tue Jul 19 22:00:38 2016] Starting Quality Analysis.
[Tue Jul 19 22:01:44 2016] Quality Analysis finished.
[Tue Jul 19 22:01:44 2016] Checking if files in folder: "Examples/basic_examples/miRNAs/reads/" are in the correct fastq format.
[Tue Jul 19 22:01:44 2016] Starting a Adapter removal analysis
Problem while running this R command:
                        source("http://valkyrie.us.es/CbBio/RNASeq/R-Scripts/AdapterGraph.R")
                        AdapterGraph("/scratch/bcb/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/Examples/basic_examples/miRNAs/Known_miRNAs/results/cutadapt_results/", "/scratch/bcb/hkim6/SH-mouse-miRNA/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/Examples/basic_examples/miRNAs/Known_miRNAs/results/cutadapt_results/SRR873382_cut.fastq.lane.report.clean.len", "SRR873382_cut")


Error:
file(filename, "r", encoding = encoding) :
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  unable to resolve 'valkyrie.us.es'
Execution halted
[hkim6@cnode204 cbbio-miarma-7440692e7bb9]$

I will appreciate for your help to resolve this issue.

thank you,

Hoon

[Hoon Kim]

I think the error comes from "source("http://valkyrie.us.es/CbBio/RNASeq/R-Scripts/AdapterGraph.R")". I found that 'AdapterGraph.R' is already present in the folder CbBio/RNASeq/R-Scripts. Is there any way to directly load 'AdapterGraph.R' rather than the link 'http://valkyrie.us.es/CbBio/RNASeq/R-Scripts/AdapterGraph.R'?

thanks,

[Hoon Kim]

sorry for multiple questions. the above R issue was solved by changing your xx.pm scripts. a next issue is as follows:

#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Tue Jul 19 22:26:21 2016] Starting a miARma analysis for miRNA
[Tue Jul 19 22:26:21 2016] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction.
[Tue Jul 19 22:26:21 2016] Checking General-output_dir parameter ... Exists!
[Tue Jul 19 22:26:21 2016] The folder specified in (output_dir=Examples/basic_examples/miRNAs/Known_miRNAs/results/) already exists.
[Tue Jul 19 22:26:21 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise:   0
[Tue Jul 19 22:26:27 2016] Continue.
[Tue Jul 19 22:26:27 2016] All parameters are correct.
[Tue Jul 19 22:26:27 2016] Starting Quality Analysis.
[Tue Jul 19 22:27:29 2016] Quality Analysis finished.
[Tue Jul 19 22:27:29 2016] Checking if files in folder: "Examples/basic_examples/miRNAs/reads/" are in the correct fastq format.
[Tue Jul 19 22:27:29 2016] Starting a Adapter removal analysis
[Tue Jul 19 22:31:07 2016] Adapter Analysis finished.
[Tue Jul 19 22:31:07 2016] Starting a Post Quality Analysis
[Tue Jul 19 22:31:57 2016] Post Quality Analysis finished.
[Tue Jul 19 22:31:57 2016] Starting a "Bowtie1" Alignment Analysis
[Tue Jul 19 22:32:27 2016] "Bowtie1" Alignment Analysis finished
[Tue Jul 19 22:32:27 2016] Starting a Readcount Analysis
[Tue Jul 19 22:32:34 2016] Readcount Analysis finished.
[Tue Jul 19 22:32:34 2016] Starting a differential expression analysis using EdgeR software(s)
Problem while running this R command:
print(resultsfiles)

Error:
print(resultsfiles) : object 'resultsfiles' not found
Execution halted
[hkim6@cnode204 cbbio-miarma-7440692e7bb9]$

Your comments will be appreciated.

Hoon

[Hoon Kim]

Finally, I figured out. The example for Known-miRNAs perfectly works. Thank you very much for your help.

Hoon

[Eduardo Andres Leon]

Nice !!!! As you see there are hundred of elements to take care of.

Regards

PS: I'll close the issue

[Eduardo Andres Leon]

The user said: Finally, I figured out. The example for Known-miRNAs perfectly works. Thank you very much for your help.