[2024-01-25 19:03:35,961] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:35,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:35,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference
[2024-01-25 19:03:37,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:37,146] [INFO] Task started: Prodigal
[2024-01-25 19:03:37,146] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0647c81-809f-474a-8b12-34c9a7528632/GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/cds.fna -a GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:42,488] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:42,488] [INFO] Task started: HMMsearch
[2024-01-25 19:03:42,488] [INFO] Running command: hmmsearch --tblout GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/reference_markers.hmm GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:42,686] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:42,688] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd0647c81-809f-474a-8b12-34c9a7528632/GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna.gz]
[2024-01-25 19:03:42,711] [INFO] Query marker FASTA was written to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:03:42,711] [INFO] Task started: Blastn
[2024-01-25 19:03:42,711] [INFO] Running command: blastn -query GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/reference_markers.fasta -out GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:43,157] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:43,159] [INFO] Selected 5 target genomes.
[2024-01-25 19:03:43,160] [INFO] Target genome list was writen to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:03:43,165] [INFO] Task started: fastANI
[2024-01-25 19:03:43,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0647c81-809f-474a-8b12-34c9a7528632/GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna.gz --refList GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:46,069] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:46,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:46,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:46,075] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:03:46,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:46,075] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Methanococcoides vulcani	strain=SLH 33	GCA_900111645.1	1353158	1353158	type	True	100.0	765	765	95	conclusive
Methanococcoides vulcani		GCA_900773955.1	1353158	1353158	type	True	99.9937	756	765	95	conclusive
Methanococcoides methylutens	strain=DSM 2657	GCA_000765475.1	2226	2226	type	True	89.4493	616	765	95	below_threshold
Methanococcoides methylutens		GCA_900773915.1	2226	2226	type	True	89.4412	616	765	95	below_threshold
Methanococcoides orientis	strain=LMO-1	GCA_021184045.1	2822137	2822137	type	True	89.4023	633	765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:46,076] [INFO] DFAST Taxonomy check result was written to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:03:46,077] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:46,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:46,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/checkm_data
[2024-01-25 19:03:46,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:46,106] [INFO] Task started: CheckM
[2024-01-25 19:03:46,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/checkm_input GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:04:07,656] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:07,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:07,675] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:07,675] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:07,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:04:07,677] [INFO] Task started: Blastn
[2024-01-25 19:04:07,677] [INFO] Running command: blastn -query GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0203d5-971c-4ec5-9a99-933b1a93391a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:08,129] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:08,133] [INFO] Selected 6 target genomes.
[2024-01-25 19:04:08,133] [INFO] Target genome list was writen to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:08,139] [INFO] Task started: fastANI
[2024-01-25 19:04:08,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0647c81-809f-474a-8b12-34c9a7528632/GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna.gz --refList GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:11,375] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:11,381] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:11,381] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900111645.1	s__Methanococcoides vulcani	100.0	765	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	97.94	95.89	0.92	0.84	3	conclusive
GCF_900774055.1	s__Methanococcoides sp900774055	90.2964	632	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765475.1	s__Methanococcoides methylutens	89.4531	616	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000970325.1	s__Methanococcoides methylutens_A	84.1003	573	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002508635.1	s__Methanolobus sp002508635	77.2107	53	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100715.1	s__Methanolobus vulcani	77.0647	90	765	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:11,382] [INFO] GTDB search result was written to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:11,384] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:11,386] [INFO] DFAST_QC result json was written to GCF_900111645.1_IMG-taxon_2642422537_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:04:11,386] [INFO] DFAST_QC completed!
[2024-01-25 19:04:11,387] [INFO] Total running time: 0h0m35s