maestsi / ontrack Goto Github PK
View Code? Open in Web Editor NEWA MinION-based pipeline for tracking species biodiversity
License: GNU General Public License v3.0
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Installer takes for ages
Hi all,
I am trying to install the ONTrack pipeline, but the installer takes for ages and seems to hang:
I am able to install other conda environments easily.
Kind regards,
T.
Long run time
Hi,
I've been trying to use ONTrack for my analysis.
I have extracted DNA from a mock community and used MinION sequencing.
First, i was only using one barcode so i could test wether ONTrack is suitable for us.
I used MetatONTrack.sh and at first i received an blast database error saying not valid version 4 database.
I think is solved that one by updating Blast to version 2.10.1
Now when I start running Ontrack with one barcode (3.5 gigabyte) it looks like it is doing something, however after 8 hours it is still te same. When i cancel the command i only have a BC01_top_Blast_hits_tmp.txt file but nothing else.
Is it normal that ONTrack takes this amount of time for only one barcode?
Kind regards
Contaminants inspection analysis; bedtools Segmentation fault: 11
Hi there,
I'm trying to run the code for the contaminants inspection analysis, and am running into a 'segmentation fault' error when I do.
SAMPLE_NAME=BC08
ANALYSIS_DIR=/path/to/BC08/files
PIPELINE_DIR=/path/to/ONTrack
source activate ONTrack_env
cd $ANALYSIS_DIR
$PIPELINE_DIR"/Calculate_mapping_rate.sh" $SAMPLE_NAME".fastq" $SAMPLE_NAME"/"$SAMPLE_NAME"_decont.fastq" $SAMPLE_NAME".contigs.fasta"
if [ ! -d "contaminants_analysis" ]; then
mkdir contaminants_analysis
fi
samtools view -f4 -b $SAMPLE_NAME"_reads_on_contig.bam" > "contaminants_analysis/"$SAMPLE_NAME"_unmapped.bam"
bedtools bamtofastq -i "contaminants_analysis/"$SAMPLE_NAME"_unmapped.bam" -fq "contaminants_analysis/"$SAMPLE_NAME".fastq"
Segmentation fault: 11
I checked for the error online, and found amongst others this thread. However, I checked the bedtools version, and since it's one of the latest versions I assume it's fine?
bedtools --version
bedtools v2.29.0
The folder is created, the bam file has information in it, but the fastq file is not 'filled', so to say:
My question: how do I solve this error? Is there any way to update the bedtools in the virtual environment? Thanks in advance!
Error: No fasta files in directory
Hi,
I'm getting an error message when running the ONTrack.R script with the following command:
(ONTrack_env) $ Rscript ONTrack.R /fasta_directory/
Error: No fasta files in directory /fasta_directory/
Execution halted
Initially I thought it was an issue with the reads being in FASTQ format but converting to FASTA didn't resolve it. Any help would be greatly appreciated!
parameters metaontrack
hello simone,
i was wondering if you could explain what these parameters for the metaontrack mean?
"change cut -d" " -f2,3 (line 47) and cut -d" " -f2 (line 48) to cut -d" " -f1,2 and cut -d" " -f1 respectively"
kind regards, Imane
No fasta files error
I've just installed (I think successfully) ONTrack but can't get it to work properly.
Running,
Rscript ONTrack.R /path/to/fasta/file
returns
Error: No fasta files in directory /path/to/fasta/file Execution halted
There is both a fasta and fastq file in the directory that I pointed to. Am I missing something basic?
Thanks for any help you can offer!
ONTrack2 pipeline available
Dear @chewbeckie, @hoohugokim, @chrbrn,@Jwebster89, @Vikash84, @howard-ryan, @denise0593, @ieknot, @lpoorvin, @george-githinji and @devindrown, you may be interested in checking out ONTrack2, a NextFlow implementation of ONTrack pipeline, with support for R10.4.1 polishing.
Best,
Simone
file input error
Hi,
Thanks for developing this pipeline, but I encountered some error.
[E::stk_subseq] failed to open the input file/stream
mkdir: cannot create directory ‘/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq’: Not a directory
mv: failed to access '/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq': Not a directory
mv: failed to access '/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq': Not a directory
mv: failed to access '/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq': Not a directory
mv: failed to access '/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq': Not a directory
mv: failed to access '/media/swaggyp1985/HDD6T/VT_Projects_2020/Tools_testing/ONTrack/ping_endopyte/F1-6-copy/filtered_BC01.fastq/decontam_tmp_filtered_BC01.fastq': Not a directory
WARNING: Only 0 reads available for sample filtered_BC01.fastq after contaminants removal
sh: 1: cannot create ./filtered_BC01.fastq/filtered_BC01.fastq_draft_0_reads_1.fastq: Directory nonexistent
sh: 1: cannot create ./filtered_BC01.fastq/filtered_BC01.fastq_draft_0_reads_1.fasta: Directory nonexistent
sh: 1: cannot create ./filtered_BC01.fastq/filtered_BC01.fastq_draft_0_reads_1.mfa: Directory nonexistent
Create a consensus sequence from a multiple alignment
Error: Failed to open filename './filtered_BC01.fastq/filtered_BC01.fastq_draft_0_reads_1.mfa'
Error: Unable to read sequence './filtered_BC01.fastq/filtered_BC01.fastq_draft_0_reads_1.mfa'
Died: cons terminated: Bad value for '-sequence' and no prompt
sh: 1: cannot create ./filtered_BC01.fastq/filtered_BC01.fastq_non_polished.contig_1_tmp2.fasta: Directory nonexistent
Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") :
cannot open file './filtered_BC01.fastq/filtered_BC01.fastq_non_polished.contig_1_tmp2.fasta'
Calls: readDNAStringSet ... lapply -> lapply -> FUN -> new_input_filexp -> .Call2
In addition: Warning message:
In dir.create(sample_dir) : './filtered_BC01.fastq' already exists
Execution halted
I did change the line 101 in the ONTrack.R to accommodate the our file names fasta_files <- list.files(path = home_dir, pattern = "filtered_BC\\d+\\.fastq.fasta", full.names = TRUE)
also what decontamination algorithm you used? seems like 0 reads after contaminants removal?
There are some error when I activate the conda environment as well, not sure if they have something to do with the above errors:
source activate ONTrack_env
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-c++
ERROR: deactivate-gxx_linux-64.sh failed, see above for details
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
INFO: deactivate-gfortran_linux-64.sh made the following environmental changes:
-HOST=x86_64-conda_cos6-linux-gnu
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-cc
ERROR: deactivate-gcc_linux-64.sh failed, see above for details
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-cc
ERROR: activate-gcc_linux-64.sh failed, see above for details
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
INFO: activate-gfortran_linux-64.sh made the following environmental changes:
+HOST=x86_64-conda_cos6-linux-gnu
ERROR: This cross-compiler package contains no program /media/swaggyp1985/SSD1T/Software/miniconda3/envs/ONTrack_env/bin/x86_64-conda_cos6-linux-gnu-c++
ERROR: activate-gxx_linux-64.sh failed, see above for details
Thanks,
Running on non-multiplexed data
Hello!
I was just wondering if this pipeline is hard-coded to only work with data from multiplexing protocols.
We have PromethION data that contain multiple samples in a single pool, and were wondering if we might still use your pipeline.
Best
Michael
add the the percent identity (%) column to the Blast search results
Hello ONTrack developer-
I have successfully ran ONTrack on my dataset, but I want to add the 'percent identity(%)' to my BLAST search results generated by ONTrack. Is there a specific way to manage this?
Thanks,
~DD
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