search

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
90 stars 38 forks source link

TypeError: unhashable type: 'list' #19

Closed maojn closed 7 years ago

maojn commented 8 years ago

Hi,

I installed version 0.3.3 using the install.sh and when I run test using the files in the test directory, I received error1. I saw an early issue here which has the same error. So I modified the code in assembleMTgenome.py and tried again, but then I got another error2. Please help. Thank you.

ERROR1 [/XX/MToolBox/test]$ MToolBox.sh -i ../my_config.sh

setting up MToolBox environment variables... [+] Loading samtools 1.3 ... [-] Unloading Zlib 1.2.8 ... [+] Loading Zlib 1.2.8 ... ...done

setting up MToolBox variables in config file ... ...done

Check python version... (2.7 required) OK.

Checking files to be used in MToolBox execution...

Checking mapExome parameters... OK.

Checking assembleMTgenome parameters... OK.

Checking mt-classifier parameters... OK. Input type is fastq.

EXECUTING READ MAPPING WITH MAPEXOME...

mapExome for sample simulation100X, files found: simulation100X.R1.fastq simulation100X.R2.fastq Mapping onto mtDNA... /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-

dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-

platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2>

OUT_simulation100X/logmt.txt Extracting FASTQ from SAM... Mapping onto complete human genome...single reads Mapping onto complete human genome...pair reads Reading Results... Filtering reads... Outfile saved on OUT_simulation100X/OUT.sam. Done.

SAM files post-processing...

SORTING OUT.sam FILES WITH PICARDTOOLS...

[Mon Aug 15 13:33:51 EDT 2016] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate

TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false

VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false

CREATE_MD5_FILE=false [Mon Aug 15 13:33:51 EDT 2016] Executing as maoj@cn0315 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM

1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) INFO 2016-08-15 13:33:51 SortSam Finished reading inputs, merging and writing to output now. [Mon Aug 15 13:33:52 EDT 2016] net.sf.picard.sam.SortSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2025848832 Success.

Skip Indel Realigner... Skipping Mark Duplicates... [Mon Aug 15 13:33:53 EDT 2016] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam

OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp]

VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000

CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 15 13:33:53 EDT 2016] Executing as maoj@cn0315 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM

1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) [Mon Aug 15 13:33:55 EDT 2016] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2025848832

ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...

WARNING: values of tail < 5 are deprecated and will be replaced with 5

[mpileup] 1 samples in 1 input files

Set max per-file depth to 8000 Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/assembleMTgenome.py", line 441, in mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail) File "/spin1/scratch/maoj/MToolBox/MToolBox/mtVariantCaller.py", line 911, in mtvcf_main_analysis Indels[name2]=[] TypeError: unhashable type: 'list' ##### GENERATING VCF OUTPUT... Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/VCFoutput.py", line 31, in VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read()) IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp' ##### PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS... Haplogroup predictions based on RSRS Phylotree build 16 Your best results file is mt_classification_best_results.csv Loading contig sequences from file simulation100X-contigs.fasta Unable to compute haplogroup. ExitSuccess. Heteroplasmy data file ('VCF_dict_tmp') not found. HF will not be reported in the output. Parsing pathogenicity table... Parsing variability data... Parsing info about haplogroup-defining sites... Parsing info about haplogroup assignments... Success. ls: cannot access OUT__/_annotation.csv: No such file or directory ls: cannot access OUT__/_annotation.csv: No such file or directory Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/prioritization.py", line 12, in raw_file=open(sys.argv[1],"r").readlines() IOError: [Errno 2] No such file or directory: 'priority_tmp.txt' rm: cannot remove `priority_tmp.txt': No such file or directory Prioritization analysis done. cat: _coverage.txt: No such file or directory awk: fatal: cannot open file `_annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file `*annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file`*annotation.csv' for reading (No such file or directory) Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/summary.py", line 26, in var_number=open("variant_number.txt", "r").readlines() IOError: [Errno 2] No such file or directory: 'variant_number.txt' rm: cannot remove `variant_number.txt': No such file or directory awk: cmd. line:1: fatal: cannot open file`prioritized_variants.txt' for reading (No such file or directory) # Analysis completed! ERROR2 $ MToolBox.sh -i ../jean_config.sh setting up MToolBox environment variables... [+] Loading samtools 1.3 ... [+] Loading Zlib 1.2.8 ... ...done setting up MToolBox variables in config file ... ...done Check python version... (2.7 required) OK. Checking files to be used in MToolBox execution... Checking mapExome parameters... OK. Checking assembleMTgenome parameters... OK. Checking mt-classifier parameters... OK. Input type is fastq. ##### EXECUTING READ MAPPING WITH MAPEXOME... mapExome for sample simulation100X, files found: simulation100X.R1.fastq simulation100X.R2.fastq Mapping onto mtDNA... /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2> OUT_simulation100X/logmt.txt sh: line 1: 15683 Illegal instruction /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2> OUT_simulation100X/logmt.txt Extracting FASTQ from SAM... Reading Results... Filtering reads... Outfile saved on OUT_simulation100X/OUT.sam. Done. SAM files post-processing... ##### SORTING OUT.sam FILES WITH PICARDTOOLS... [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 16 13:23:33 EDT 2016] Executing as maoj@cn2793 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) INFO 2016-08-16 13:23:33 SortSam Finished reading inputs, merging and writing to output now. [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1138753536 Success. Skip Indel Realigner... Skipping Mark Duplicates... [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 16 13:23:33 EDT 2016] Executing as maoj@cn2793 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1138753536 ##### ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME... WARNING: values of tail < 5 are deprecated and will be replaced with 5 [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 ##### GENERATING VCF OUTPUT... Reference sequence used for VCF: RSRS ##### PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS... Haplogroup predictions based on RSRS Phylotree build 16 Your best results file is mt_classification_best_results.csv Loading contig sequences from file simulation100X-contigs.fasta Unable to compute haplogroup. ExitSuccess. Parsing pathogenicity table... Parsing variability data... Parsing info about haplogroup-defining sites... Parsing info about haplogroup assignments... Success. ls: cannot access OUT__/_annotation.csv: No such file or directory ls: cannot access OUT__/_annotation.csv: No such file or directory Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/prioritization.py", line 12, in raw_file=open(sys.argv[1],"r").readlines() IOError: [Errno 2] No such file or directory: 'priority_tmp.txt' rm: cannot remove `priority_tmp.txt': No such file or directory Prioritization analysis done. awk: fatal: cannot open file `*annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file`_annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file `_annotation.csv' for reading (No such file or directory) Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/summary.py", line 26, in var_number=open("variant_number.txt", "r").readlines() IOError: [Errno 2] No such file or directory: 'variant_number.txt' rm: cannot remove `variant_number.txt': No such file or directory awk: cmd. line:1: fatal: cannot open file`prioritized_variants.txt' for reading (No such file or directory) Analysis completed!
clody23 commented 7 years ago

Please upgrade to version 1.0 of the tool. Versions < 1.0 are deprecated. This error should be fixed in the latest version of MToolBox.

Best, C

EricDeveaud commented 7 years ago

Hello,

where one can find the version >=1.0 ? can you provide a release tag please.

regards

Eric

clody23 commented 7 years ago

Hi,

version 0.3.3 does not require any installation, but the user has to provide full path to dependancies used by MToolBox. The install.sh script should be used only used with version v 1.0 (the current one). Please read changelog of 3 June 2016 https://github.com/mitoNGS/MToolBox/blob/master/changelog.md for further info.

Version 0.3.3 is deprecated because since then there have been many bugs fixed, so I would recommend to move to version 1.0.

However, if you want to use 0.3.3 you can have a look at the REAME.txt included in the package or visit https://sourceforge.net/projects/mtoolbox/files/?source=navbar

Best, C

2016-08-16 18:27 GMT+01:00 maojn notifications@github.com:

Hi, I installed version 0.3.3 using the install.sh and when I run test using the files in the test directory, I received error1. I saw an early issue here which has the same error. So I modified the code in assembleMTgenome.py and tried again, but then I got another error2. Please help. Thank you.

ERROR1 [/XX/MToolBox/test]$ MToolBox.sh -i ../my_config.sh

setting up MToolBox environment variables... [+] Loading samtools 1.3 ... [-] Unloading Zlib 1.2.8 ... [+] Loading Zlib 1.2.8 ... ...done

setting up MToolBox variables in config file ... ...done

Check python version... (2.7 required) OK.

Checking files to be used in MToolBox execution...

Checking mapExome parameters... OK.

Checking assembleMTgenome parameters... OK.

Checking mt-classifier parameters... OK. Input type is fastq. EXECUTING READ MAPPING WITH MAPEXOME...

mapExome for sample simulation100X, files found: simulation100X.R1.fastq simulation100X.R2.fastq Mapping onto mtDNA... /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-

dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-

platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2>

OUT_simulation100X/logmt.txt Extracting FASTQ from SAM... Mapping onto complete human genome...single reads Mapping onto complete human genome...pair reads Reading Results... Filtering reads... Outfile saved on OUT_simulation100X/OUT.sam. Done.

SAM files post-processing... SORTING OUT.sam FILES WITH PICARDTOOLS...

[Mon Aug 15 13:33:51 EDT 2016] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate

TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false

VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false

CREATE_MD5_FILE=false [Mon Aug 15 13:33:51 EDT 2016] Executing as maoj@cn0315 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM

1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) INFO 2016-08-15 13:33:51 SortSam Finished reading inputs, merging and writing to output now. [Mon Aug 15 13:33:52 EDT 2016] net.sf.picard.sam.SortSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2025848832 Success.

Skip Indel Realigner... Skipping Mark Duplicates... [Mon Aug 15 13:33:53 EDT 2016] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam

OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/scratch/maoj/ MToolBox/test/OUT_simulation100X/tmp]

VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000

CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 15 13:33:53 EDT 2016] Executing as maoj@cn0315 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM

1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) [Mon Aug 15 13:33:55 EDT 2016] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2025848832 ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...

WARNING: values of tail < 5 are deprecated and will be replaced with 5

[mpileup] 1 samples in 1 input files Set max per-file depth to 8000 Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/assembleMTgenome.py", line 441, in mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail) File "/spin1/scratch/maoj/MToolBox/MToolBox/mtVariantCaller.py", line 911, in mtvcf_main_analysis Indels[name2]=[] TypeError: unhashable type: 'list' GENERATING VCF OUTPUT...

Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/VCFoutput.py", line 31, in VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read()) IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp' PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...

Haplogroup predictions based on RSRS Phylotree build 16 Your best results file is mt_classification_best_results.csv

Loading contig sequences from file simulation100X-contigs.fasta Unable to compute haplogroup. ExitSuccess.

Heteroplasmy data file ('VCF_dict_tmp') not found. HF will not be reported in the output. Parsing pathogenicity table... Parsing variability data... Parsing info about haplogroup-defining sites... Parsing info about haplogroup assignments... Success.

ls: cannot access OUT/annotation.csv: No such file or directory ls: cannot access OUT/annotation.csv: No such file or directory Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/prioritization.py", line 12, in raw_file=open(sys.argv[1],"r").readlines() IOError: [Errno 2] No such file or directory: 'priority_tmp.txt' rm: cannot remove `priority_tmp.txt': No such file or directory

Prioritization analysis done.

cat: coverage.txt: No such file or directory awk: fatal: cannot open file `annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file annotation.csv' for reading (No such file or directory) awk: fatal: cannot open fileannotation.csv' for reading (No such file or directory) Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/summary.py", line 26, in var_number=open("variant_number.txt", "r").readlines() IOError: [Errno 2] No such file or directory: 'variant_number.txt' rm: cannot remove variant_number.txt': No such file or directory awk: cmd. line:1: fatal: cannot open fileprioritized_variants.txt' for reading (No such file or directory) Analysis completed!

ERROR2 $ MToolBox.sh -i ../jean_config.sh

setting up MToolBox environment variables... [+] Loading samtools 1.3 ... [+] Loading Zlib 1.2.8 ... ...done

setting up MToolBox variables in config file ... ...done

Check python version... (2.7 required) OK.

Checking files to be used in MToolBox execution...

Checking mapExome parameters... OK.

Checking assembleMTgenome parameters... OK.

Checking mt-classifier parameters... OK. Input type is fastq. EXECUTING READ MAPPING WITH MAPEXOME...

mapExome for sample simulation100X, files found: simulation100X.R1.fastq simulation100X.R2.fastq Mapping onto mtDNA... /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2> OUT_simulation100X/logmt.txt sh: line 1: 15683 Illegal instruction /spin1/scratch/maoj/MToolBox/bin/gmap/bin/gsnap -D /scratch/maoj/MToolBox/gmapdb/ --gunzip -d chrRSRS -A sam --nofails --pairmax-dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-platform=sample -n 1 -Q -O -t 8 simulation100X.R1.fastq simulation100X.R2.fastq > OUT_simulation100X/outmt.sam 2> OUT_simulation100X/logmt.txt Extracting FASTQ from SAM... Reading Results... Filtering reads... Outfile saved on OUT_simulation100X/OUT.sam. Done.

SAM files post-processing... SORTING OUT.sam FILES WITH PICARDTOOLS...

[Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/scratch/maoj/ MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 16 13:23:33 EDT 2016] Executing as maoj@cn2793 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) INFO 2016-08-16 13:23:33 SortSam Finished reading inputs, merging and writing to output now. [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1138753536 Success.

Skip Indel Realigner... Skipping Mark Duplicates... [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/scratch/maoj/MToolBox/test/OUT_simulation100X/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 16 13:23:33 EDT 2016] Executing as maoj@cn2793 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_04_15_00_02-b00; Picard version: 1.98(1547) [Tue Aug 16 13:23:33 EDT 2016] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1138753536 ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...

WARNING: values of tail < 5 are deprecated and will be replaced with 5

[mpileup] 1 samples in 1 input files Set max per-file depth to 8000 GENERATING VCF OUTPUT...

Reference sequence used for VCF: RSRS PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...

Haplogroup predictions based on RSRS Phylotree build 16 Your best results file is mt_classification_best_results.csv

Loading contig sequences from file simulation100X-contigs.fasta Unable to compute haplogroup. ExitSuccess.

Parsing pathogenicity table... Parsing variability data... Parsing info about haplogroup-defining sites... Parsing info about haplogroup assignments... Success.

ls: cannot access OUT/annotation.csv: No such file or directory ls: cannot access OUT/annotation.csv: No such file or directory Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/prioritization.py", line 12, in raw_file=open(sys.argv[1],"r").readlines() IOError: [Errno 2] No such file or directory: 'priority_tmp.txt' rm: cannot remove `priority_tmp.txt': No such file or directory

Prioritization analysis done.

awk: fatal: cannot open file annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file annotation.csv' for reading (No such file or directory) awk: fatal: cannot open file `*annotation.csv' for reading (No such file or directory) Traceback (most recent call last): File "/scratch/maoj/MToolBox/MToolBox/summary.py", line 26, in var_number=open("variant_number.txt", "r").readlines() IOError: [Errno 2] No such file or directory: 'variant_number.txt' rm: cannot remove variant_number.txt': No such file or directory awk: cmd. line:1: fatal: cannot open fileprioritized_variants.txt' for reading (No such file or directory)

Analysis completed!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mitoNGS/MToolBox/issues/19, or mute the thread https://github.com/notifications/unsubscribe-auth/AAh5zU0-TwDuIWz6Ikob4Kf78Cm-DEZYks5qgfMQgaJpZM4Jlp7n .

-- Claudia

clody23 commented 7 years ago

Hi Eric,

git clone git@github.com:mitoNGS/MToolBox.git to get the MToolBox v.1.0 which is the latest one.

There is no other upgraded version of MToolBox at the moment....

EricDeveaud commented 7 years ago

would it be possible for you to have a tagged relelase for this one.

our install policy is to use tagged versions preferentialy to git clone and keep track of the commit tag. it allow us easier versioning and ease re-installation for any given versions, when reproducibility problems arise

regards

Eric

clody23 commented 6 years ago

Hi there,

we've released tagged version 1.0 of MToolBox.

https://github.com/mitoNGS/MToolBox/releases/tag/v.1.0

Best, C

2017-10-24 14:50 GMT+01:00 Eric Deveaud notifications@github.com:

would it be possible for you to have a tagged relelase for this one.

our install policy is to use tagged versions preferentialy to git clone and keep track of the commit tag. it allow us easier versioning and ease re-installation for any given versions, when reproducibility problems arise

regards

Eric

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/mitoNGS/MToolBox/issues/19#issuecomment-338996593, or mute the thread https://github.com/notifications/unsubscribe-auth/AAh5zTHKneugS0C-9ffAM6LCMjBTW7YVks5svesIgaJpZM4Jlp7n .

-- Claudia