[2024-01-25 18:13:20,697] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference
[2024-01-25 18:13:21,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,805] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,805] [INFO] Running command: gunzip -c /var/lib/cwl/stge3462272-6b7e-4a7c-8b6b-432151b82081/GCF_003385755.1_ASM338575v1_genomic.fna.gz | prodigal -d GCF_003385755.1_ASM338575v1_genomic.fna/cds.fna -a GCF_003385755.1_ASM338575v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:25,724] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:25,725] [INFO] Task started: HMMsearch
[2024-01-25 18:13:25,725] [INFO] Running command: hmmsearch --tblout GCF_003385755.1_ASM338575v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/reference_markers.hmm GCF_003385755.1_ASM338575v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:25,868] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:25,869] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge3462272-6b7e-4a7c-8b6b-432151b82081/GCF_003385755.1_ASM338575v1_genomic.fna.gz]
[2024-01-25 18:13:25,889] [INFO] Query marker FASTA was written to GCF_003385755.1_ASM338575v1_genomic.fna/markers.fasta
[2024-01-25 18:13:25,889] [INFO] Task started: Blastn
[2024-01-25 18:13:25,889] [INFO] Running command: blastn -query GCF_003385755.1_ASM338575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/reference_markers.fasta -out GCF_003385755.1_ASM338575v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:26,343] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:26,345] [INFO] Selected 4 target genomes.
[2024-01-25 18:13:26,346] [INFO] Target genome list was writen to GCF_003385755.1_ASM338575v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:26,350] [INFO] Task started: fastANI
[2024-01-25 18:13:26,350] [INFO] Running command: fastANI --query /var/lib/cwl/stge3462272-6b7e-4a7c-8b6b-432151b82081/GCF_003385755.1_ASM338575v1_genomic.fna.gz --refList GCF_003385755.1_ASM338575v1_genomic.fna/target_genomes.txt --output GCF_003385755.1_ASM338575v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:28,150] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:28,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:28,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:28,155] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:13:28,155] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:13:28,155] [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
Methanothermobacter defluvii	strain=DSM 7466	GCA_003385755.1	49339	49339	type	True	100.0	567	567	95	inconclusive
Methanothermobacter thermautotrophicus	strain=Delta H	GCA_000008645.1	145262	145262	type	True	97.4208	534	567	95	inconclusive
Methanothermobacter marburgensis	strain=Marburg	GCA_000145295.1	145263	145263	type	True	82.8052	415	567	95	below_threshold
Methanothermobacter wolfeii	strain=DSM 2970	GCA_025397995.1	145261	145261	type	True	81.2046	385	567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:28,159] [INFO] DFAST Taxonomy check result was written to GCF_003385755.1_ASM338575v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:28,159] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:28,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:28,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/checkm_data
[2024-01-25 18:13:28,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:28,182] [INFO] Task started: CheckM
[2024-01-25 18:13:28,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385755.1_ASM338575v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385755.1_ASM338575v1_genomic.fna/checkm_input GCF_003385755.1_ASM338575v1_genomic.fna/checkm_result
[2024-01-25 18:13:46,707] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:46,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:46,745] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:46,745] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:46,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385755.1_ASM338575v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:46,746] [INFO] Task started: Blastn
[2024-01-25 18:13:46,746] [INFO] Running command: blastn -query GCF_003385755.1_ASM338575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48f5a558-b44f-4fa9-a895-c7117b41313a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385755.1_ASM338575v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:47,230] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:47,232] [INFO] Selected 6 target genomes.
[2024-01-25 18:13:47,233] [INFO] Target genome list was writen to GCF_003385755.1_ASM338575v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:47,240] [INFO] Task started: fastANI
[2024-01-25 18:13:47,240] [INFO] Running command: fastANI --query /var/lib/cwl/stge3462272-6b7e-4a7c-8b6b-432151b82081/GCF_003385755.1_ASM338575v1_genomic.fna.gz --refList GCF_003385755.1_ASM338575v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385755.1_ASM338575v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:49,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:49,868] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:49,868] [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_000008645.1	s__Methanothermobacter thermautotrophicus	97.4208	534	567	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.55	96.65	0.96	0.94	7	conclusive
GCF_000828575.1	s__Methanothermobacter sp000828575	94.4708	493	567	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014889545.1	s__Methanothermobacter thermautotrophicus_A	91.3627	502	567	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145295.1	s__Methanothermobacter marburgensis	82.8367	413	567	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.04	96.76	0.96	0.96	3	-
GCA_900095815.1	s__Methanothermobacter wolfeii	81.2361	385	567	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	99.47	99.15	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:49,870] [INFO] GTDB search result was written to GCF_003385755.1_ASM338575v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:49,870] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:49,873] [INFO] DFAST_QC result json was written to GCF_003385755.1_ASM338575v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:49,873] [INFO] DFAST_QC completed!
[2024-01-25 18:13:49,873] [INFO] Total running time: 0h0m29s