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mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
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Unable to compute haplogroup. Exit - No annotation.csv found. Exit #96

Open moldach opened 3 years ago

moldach commented 3 years ago

I'm getting an error when running MToolBox which seems to be cause due to missing dependency when installing.

As I'm working on cluster with no outgoing internet connection I needed to download and run the install.sh script to build MToolBox locally (laptop) then tar czvf the folder, transfer to secure cluster, then unzip manually supply paths for all the tools in the conf.sh script.

One curious thing was that I initially got errors when supplying the path to thesamtools-1.3.1 dependency which was installed within the RUFUS directory (samtoolsexe=/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools)

First error

/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3/samtools: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory
Skip Indel Realigner...
Skipping Mark Duplicates...

It seems like libtinfow.so.6 is a dependency issue so next I tried supplying a path for a working samtools-1.3.1 version I had installed previously on the cluster:(samtoolsexe=/project/M-mtgraovac182840/tools/samtools-1.3.1/samtools)

conf.sh

######################################MTOOLBOX CONFIG FILE#####################################################
##If the default installation of MToolBox was used (install.sh), the user should specify 
##only the MANDATORY parameters. To enable other options, please remove the # before the OPTIONAL parameters
## and assign them the correct value. 
##
##
##to get support, please write to 
##claudia.calabrese23 at gmail.com 
#or to 
##dome.simone at gmail.com 
##or to 
##roberto.preste at gmail.com
##
##or open a new github issue.
######################SET PATH TO MTOOLBOX EXECUTABLES########################################################
##
##OPTIONAL. If MToolBox default installation (install.sh) was used, samtoolsexe path is $MTOOLBOX_BIN/samtools-{samtools_version}/samtools. Otherwise please specify the FULL PATH to samtools executables.
##
samtoolsexe=/project/M-mtgraovac182840/tools/samtools-1.3.1/samtools
##
##OPTIONAL. If MToolBox default installation (install.sh) was used, samtools_version is 1.3
##
#samtools_version=1.3
##
##OPTIONAL. If MToolBox default installation (install.sh) was used, musclexe path is $MTOOLBOX_BIN/muscle3.8.31_i86linux64. Otherwise, please specify the FULL PATH to muscle executables.
##
muscleexe=/project/M-mtgraovac182840/tools/MToolBox/bin/muscle3.8.31_i86linux64
##
#OPTIONAL. If MToolBox default installation (install.sh) was used, gsnapexe path is $MTOOLBOX_BIN/gmap/bin/gsnap. Otherwise, please specify the FULL PATH to gsnap executables.
##
gsnapexe=/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap
##
#####################SET FILE NAMES OF REFERENCE SEQUENCE AND DATABASE TO BE USED FOR THE MAPPING STEP#######
##
#OPTIONAL. If MToolBox default installation (install.sh) was used, fasta_path is $MTOOLBOX_DIR/genome_fasta/. Otherwise, please specify the FULL PATH to fasta and fasta.fai reference sequences to be used in the mapping step.
##
fasta_path=/project/M-mtgraovac182840/tools/MToolBox/genome_fasta/
##
#OPTIONAL. If MToolBox default installation (install.sh) was used, gsnapdb is $MTOOLBOX_DIR/gmapdb/. Otherwise, please specify the FULL PATH to gsnap/gmap database executables
##
gsnapdb=/project/M-mtgraovac182840/tools/MToolBox/gmapdb/
##
##OPTIONAL. If MToolBox default installation (install.sh) was used, mtdb_fasta is chrRSRS.fa (RSRS). To use rCRS sequence as reference, please set mtdb_fasta=chrM.fa Otherwise, please specify the file name of the mitochondrial reference fasta sequence you want to use.
##
mtdb_fasta=chrM.fa
##
##OPTIONAL. If MToolBox default installation (install.sh) was used, hg19_fasta is hg19RSRS.fa (corresponding to the GCh37/hg19 reference multifasta including the RSRS sequence). To use the nuclear multifasta including the rCRS reference sequence, please set hg19_fasta=hg19RCRS.fa. Otherwise, please specify the file name of the nuclear reference sequence you want to use.
##
hg19_fasta=hg19RCRS.fa
##
#OPTIONAL. If MToolBox dafault installation (install.sh) was used, mtdb is chrRSRS. To use the rCRS database, please set mtdb=chrM Otherwise, please specify the name of the mitochondrial gsnap database you want to use.
##
mtdb=chrM
##
#OPTIONAL. If MToolBox default installation (install.sh) was used, the default GSNAP database for nuclear DNA is hg19RSRS. To use the one with rCRS, please set humandb=hg19RCRS, which refers to hg19 nuclear genome + rCRS mitochondrial database. Otherwise, please specify the name of the nuclear (+mitochondrial) gsnap database you want to use.
##
humandb=hg19RCRS
##
######################SET PATH TO INPUT/OUTPUT and PRE/POST PROCESSING PARAMETERS############################
##
##OPTIONAL. Specify the FULL PATH of the input directory. Default is the current working directory
##
input_path=/project/M-mtgraovac182840/CombGene/CG00010/
##
##OPTIONAL. Specify the FULL PATH of the output directory. Default is the current working directory
##
output_name=/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output
##
##OPTIONAL. Specify the list name of files to be analyzed if input_path was not defined. Default is use all the files with the specified file format extension 
##in the current working directory and skip this option
##
#list=
##
##OPTIONAL. Specifiy the name to assign to the VCF file. If not specified, filename will be set to `unknown_sample_name.vcf`
vcf_name=CG00010
##
##MANDATORY. Specify the input file format extension. [fasta | bam | sam | fastq ]
##
input_type=fastq
##
##MANDATORY. Specify the mitochondrial reference to be used for the mapping step with mapExome. [RCRS | RSRS; DEFAULT is RSRS]
ref=RCRS
##
##OPTIONAL. Specify if duplicate removal by MarkDuplicates should be set on. [false | true; DEFAULT is false]
UseMarkDuplicates=false
##
##OPTIONAL. Specify if realignment around ins/dels should be set on. [false | true; DEFAULT is false]
UseIndelRealigner=false
##
##OPTIONAL: specify if to exctract only mitochondrial reads from bam file provided as input. [false | true; DEFAULT is false]
MitoExtraction=false
##
##OPTIONAL: specificy the minumum level of heteroplasmy for the alternative allele(s) for consensus generation [DEFAULT is 0.2]
hf_min=0.2
##
##OPTIONAL: specify the maximum level of heteroplasmy for the alternative allele(s) for consensus generation [DEFAULT is 0.8]
hf_max=0.8
##
##OPTIONAL: specify the minimum read depth per position [DEFAULT is 5]
minrd=5
##
##OPTIONAL: specify the minimum quality score per allele [DEFAULT is 25]
minqual=25
##

log


setting up MToolBox environment variables...
...done

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

CG00010 will be used as vcf file name...

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.
output files will be placed in /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output

##### EXECUTING READ MAPPING WITH MAPEXOME...

mapExome for sample CG00010F_R1, files found: CG00010F_R1.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010F_R1.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R1/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R1/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R1/OUT.sam.
Done.
mapExome for sample CG00010F_R2, files found: CG00010F_R2.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010F_R2.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R2/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R2/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R2/OUT.sam.
Done.
mapExome for sample CG00010P_R1, files found: CG00010P_R1.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010P_R1.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R1/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R1/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R1/OUT.sam.
Done.
mapExome for sample CG00010P_R2, files found: CG00010P_R2.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010P_R2.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R2/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R2/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R2/OUT.sam.
Done.
mapExome for sample CG00010M_R1, files found: CG00010M_R1.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010M_R1.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R1/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R1/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R1/OUT.sam.
Done.
mapExome for sample CG00010M_R2, files found: CG00010M_R2.fastq.gz
Mapping onto mtDNA...
/project/M-mtgraovac182840/tools/MToolBox/bin/gmap/bin/gsnap -D /project/M-mtgraovac182840/tools/MToolBox/gmapdb/ --gunzip -d chrM -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 CG00010M_R2.fastq.gz > /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R2/outmt.sam 2> /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R2/logmt.txt
Extracting FASTQ from SAM...
Reading Results...
Filtering reads...
Outfile saved on /project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R2/OUT.sam.
Done.

SAM files post-processing...

##### SORTING OUT.sam FILES WITH PICARDTOOLS...

[Wed Feb 10 10:58:20 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:20 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:20 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:20 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:20 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:20 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:20 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:20 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:21 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:21 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:21 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:21 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:21 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:21 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:21 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:21 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:22 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:22 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:22 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:22 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:22 MST 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:22 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
INFO    2021-02-10 10:58:22 SortSam Finished reading inputs, merging and writing to output now.
[Wed Feb 10 10:58:22 MST 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
Success.

Skip Indel Realigner...
Skipping Mark Duplicates...
[Wed Feb 10 10:58:24 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:24 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:24 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010F_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:25 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:25 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010M_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:25 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:25 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R1/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:25 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:26 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336
[Wed Feb 10 10:58:26 MST 2021] net.sf.picard.sam.SamFormatConverter INPUT=OUT.sam.bam.marked.bam OUTPUT=OUT.sam.bam.marked.bam.marked.sam TMP_DIR=[/project/M-mtgraovac182840/matthew/tool-testing/MTG_human_genomics_pipeline/mtoolbox-output/OUT_CG00010P_R2/tmp]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Feb 10 10:58:26 MST 2021] Executing as moldach@sg1 on Linux 4.18.0-193.28.1.el8_2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_272-b10; Picard version: 1.98(1547)
[Wed Feb 10 10:58:26 MST 2021] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336

##### 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
<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

##### GENERATING VCF OUTPUT...
Reference sequence used for VCF: RCRS

##### PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...

Haplogroup predictions based on RSRS Phylotree build 17
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010F_R1-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010F_R2-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010M_R1-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010M_R2-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010P_R1-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is  mt_classification_best_results.csv

Loading contig sequences from file CG00010P_R2-contigs.fasta
Parsing pathogenicity table...
Parsing variability data...
Parsing info about haplogroup-defining sites...
Parsing info about haplogroup assignments...
No annotation.csv found. Exit

Take away

Note: I was able to fix the samtools-1.3 depency issue, within the MToolBox directory by re-running the following command (below), then switiching back the samtoolsexe path in conf.sh; however, I get the same No annotation.csv found error, so it appears like there is downstream issue (of samtools) going on here.

$  ./configure --enable-plugins --enable-libcurl --prefix=/project/M-mtgraovac182840/tools/MToolBox/bin/samtools-1.3
$  make all all-htslib
$  make install install-htslib