I've been trying to run metawatt for some time now and I havent had any luck getting it to bin my assemblies. I've had the program properly installed on a computing cluster and all of the depencies are installed and recognized by metawatt.
I've made the proper input (assembly.fasta and reads.fastq.gz) and output directories under the project name/ directory but when I choose that under the file/open project I dont get any results.
It seems as though it isnt running any of the modules and is missing the "profileDB'. It's my understanding that users no longer have to provide the database.
If anyone has any suggestions, I would appreciate your help!
Metawatt [INFO|10:22:42] Logging to /scratch/mstephens/metawatt/ta21/metawatt-logbook.txt
Metawatt [INFO|10:22:42] New project /scratch/mstephens/metawatt/ta21 instantiated.
Metawatt [INFO|10:22:42] Opening project from "/scratch/mstephens/metawatt/ta21"...
Metawatt [INFO|10:22:42] Adding assembly from fasta file "TA21.MPQcf.dd.norm.a5.contigs.fasta" to project
Metawatt [INFO|10:22:42] Adding readset from fastq file "TA21wgaCf.fastq.gz" to project
Metawatt [INFO|10:22:42] Creating pipeline for project...
Metawatt [INFO|10:22:43] Adding module "Update databases" to pipeline:
Metawatt [INFO|10:22:43] Adding module "Predict coverage, %GC, coding density" to pipeline:
Metawatt [INFO|10:22:44] Adding module "Classify with diamond blastx" to pipeline:
Metawatt [INFO|10:22:44] Adding module "Predict tRNAs" to pipeline:
Metawatt [INFO|10:22:45] Adding module "Six frame Pfam" to pipeline:
Metawatt [INFO|10:22:45] Adding module "Map reads to contigs" to pipeline:
Metawatt [INFO|10:22:46] Adding module "Compute N4 frequencies" to pipeline:
Metawatt [INFO|10:22:46] Adding module "Bin with tetranucleotides" to pipeline:
Metawatt [INFO|10:22:47] Adding module "Optimize bins" to pipeline:
Metawatt [INFO|10:22:47] Adding module "Polish bins" to pipeline:
Metawatt [INFO|10:22:48] Adding module "Make Bin Shortlist" to pipeline:
Metawatt [INFO|10:22:48] Adding module "Calculate bin phylogeny" to pipeline:
Metawatt [INFO|10:22:49] Adding module "Export bins" to pipeline:
Metawatt [INFO|10:22:49] Update databases: Loading data...
Metawatt [INFO|10:22:49] Predict coverage, %GC, coding density: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.properties.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Classify with diamond blastx: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.taxonomy.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Predict tRNAs: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.aragorn.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Six frame Pfam: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.codon-usage.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Map reads to contigs: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.read.mapping.results.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Compute N4 frequencies: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.n4.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Bin with tetranucleotides: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Optimize bins: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.optimized.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Polish bins: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.optimized.polished.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Make Bin Shortlist: Loading data...
Metawatt [INFO|10:22:50] Finalize bins: Processing 0 user edits...
Metawatt [INFO|10:22:50] Calculate bin phylogeny: Loading data...
Metawatt [INFO|10:22:51] Export bins: Loading data... Metawatt [INFO|10:22:51] Warning: No profileDB available - skipping bin quality assessment!
Metawatt [INFO|10:22:51] Sample "TA21.MPQcf.dd.norm.a5.contigs.fasta": Computing bin compositions...
Metawatt [INFO|10:22:51]Computing quality with profile DB "void"...
Metawatt [INFO|10:22:51] Computation completed.
Metawatt [INFO|10:22:51] High quality bins (cscg > 85%, cscg duplicated < 1.1x): 0
Medium quality bins (cscg > 75%, cscg duplicated < 1.25x): 0
Partial or duplicated bins (cscg > 50%): 0
Metawatt [INFO|10:22:51] Total time used: 0.166 minutes
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I've just start using the MetaWatt.
I had a similar issue recently - in fully automated mode the pipeline does not work as suppose.
What helped - is a runnig of every individual module manually, step by step
Last edit: Yevhen Vainshtein 2017-08-10
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I've been trying to run metawatt for some time now and I havent had any luck getting it to bin my assemblies. I've had the program properly installed on a computing cluster and all of the depencies are installed and recognized by metawatt.
I've made the proper input (assembly.fasta and reads.fastq.gz) and output directories under the project name/ directory but when I choose that under the file/open project I dont get any results.
It seems as though it isnt running any of the modules and is missing the "profileDB'. It's my understanding that users no longer have to provide the database.
If anyone has any suggestions, I would appreciate your help!
Metawatt [INFO|10:22:42] Logging to /scratch/mstephens/metawatt/ta21/metawatt-logbook.txt
Metawatt [INFO|10:22:42] New project /scratch/mstephens/metawatt/ta21 instantiated.
Metawatt [INFO|10:22:42] Opening project from "/scratch/mstephens/metawatt/ta21"...
Metawatt [INFO|10:22:42] Adding assembly from fasta file "TA21.MPQcf.dd.norm.a5.contigs.fasta" to project
Metawatt [INFO|10:22:42] Adding readset from fastq file "TA21wgaCf.fastq.gz" to project
Metawatt [INFO|10:22:42] Creating pipeline for project...
Metawatt [INFO|10:22:43] Adding module "Update databases" to pipeline:
Metawatt [INFO|10:22:43] Adding module "Predict coverage, %GC, coding density" to pipeline:
Metawatt [INFO|10:22:44] Adding module "Classify with diamond blastx" to pipeline:
Metawatt [INFO|10:22:44] Adding module "Predict tRNAs" to pipeline:
Metawatt [INFO|10:22:45] Adding module "Six frame Pfam" to pipeline:
Metawatt [INFO|10:22:45] Adding module "Map reads to contigs" to pipeline:
Metawatt [INFO|10:22:46] Adding module "Compute N4 frequencies" to pipeline:
Metawatt [INFO|10:22:46] Adding module "Bin with tetranucleotides" to pipeline:
Metawatt [INFO|10:22:47] Adding module "Optimize bins" to pipeline:
Metawatt [INFO|10:22:47] Adding module "Polish bins" to pipeline:
Metawatt [INFO|10:22:48] Adding module "Make Bin Shortlist" to pipeline:
Metawatt [INFO|10:22:48] Adding module "Calculate bin phylogeny" to pipeline:
Metawatt [INFO|10:22:49] Adding module "Export bins" to pipeline:
Metawatt [INFO|10:22:49] Update databases: Loading data...
Metawatt [INFO|10:22:49] Predict coverage, %GC, coding density: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.properties.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Classify with diamond blastx: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.taxonomy.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Predict tRNAs: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.aragorn.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Six frame Pfam: Loading data...
Metawatt [INFO|10:22:49] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.codon-usage.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:49] Map reads to contigs: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.read.mapping.results.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Compute N4 frequencies: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.n4.txt" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Bin with tetranucleotides: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Optimize bins: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.optimized.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Polish bins: Loading data...
Metawatt [INFO|10:22:50] Result file "/scratch/mstephens/metawatt/ta21/output/TA21.MPQcf.dd.norm.a5.contigs.fasta.binning.optimized.polished.sibci" (size 0) not ready: Skipping loading of module results...
Metawatt [INFO|10:22:50] Make Bin Shortlist: Loading data...
Metawatt [INFO|10:22:50] Finalize bins: Processing 0 user edits...
Metawatt [INFO|10:22:50] Calculate bin phylogeny: Loading data...
Metawatt [INFO|10:22:51] Export bins: Loading data...
Metawatt [INFO|10:22:51] Warning: No profileDB available - skipping bin quality assessment!
Metawatt [INFO|10:22:51] Sample "TA21.MPQcf.dd.norm.a5.contigs.fasta": Computing bin compositions...
Metawatt [INFO|10:22:51] Computing quality with profile DB "void"...
Metawatt [INFO|10:22:51] Computation completed.
Metawatt [INFO|10:22:51] High quality bins (cscg > 85%, cscg duplicated < 1.1x): 0
Medium quality bins (cscg > 75%, cscg duplicated < 1.25x): 0
Partial or duplicated bins (cscg > 50%): 0
Metawatt [INFO|10:22:51] Total time used: 0.166 minutes
I've just start using the MetaWatt.
I had a similar issue recently - in fully automated mode the pipeline does not work as suppose.
What helped - is a runnig of every individual module manually, step by step
Last edit: Yevhen Vainshtein 2017-08-10