[2024-01-24 11:19:55,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference
[2024-01-24 11:19:56,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,506] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg33daaa79-7d40-4647-9ce6-f5e8534953aa/GCF_027554905.1_ASM2755490v1_genomic.fna.gz | prodigal -d GCF_027554905.1_ASM2755490v1_genomic.fna/cds.fna -a GCF_027554905.1_ASM2755490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:01,073] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:01,073] [INFO] Task started: HMMsearch
[2024-01-24 11:20:01,074] [INFO] Running command: hmmsearch --tblout GCF_027554905.1_ASM2755490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/reference_markers.hmm GCF_027554905.1_ASM2755490v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:01,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:01,282] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg33daaa79-7d40-4647-9ce6-f5e8534953aa/GCF_027554905.1_ASM2755490v1_genomic.fna.gz]
[2024-01-24 11:20:01,302] [INFO] Query marker FASTA was written to GCF_027554905.1_ASM2755490v1_genomic.fna/markers.fasta
[2024-01-24 11:20:01,302] [INFO] Task started: Blastn
[2024-01-24 11:20:01,302] [INFO] Running command: blastn -query GCF_027554905.1_ASM2755490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/reference_markers.fasta -out GCF_027554905.1_ASM2755490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:01,789] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:01,793] [INFO] Selected 4 target genomes.
[2024-01-24 11:20:01,793] [INFO] Target genome list was writen to GCF_027554905.1_ASM2755490v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:01,795] [INFO] Task started: fastANI
[2024-01-24 11:20:01,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg33daaa79-7d40-4647-9ce6-f5e8534953aa/GCF_027554905.1_ASM2755490v1_genomic.fna.gz --refList GCF_027554905.1_ASM2755490v1_genomic.fna/target_genomes.txt --output GCF_027554905.1_ASM2755490v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:03,671] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:03,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:03,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:03,677] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:03,677] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:20:03,677] [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 thermautotrophicus	strain=Delta H	GCA_000008645.1	145262	145262	type	True	99.9612	583	583	95	inconclusive
Methanothermobacter defluvii	strain=DSM 7466	GCA_003385755.1	49339	49339	type	True	97.4686	539	583	95	inconclusive
Methanothermobacter marburgensis	strain=Marburg	GCA_000145295.1	145263	145263	type	True	82.7452	420	583	95	below_threshold
Methanothermobacter wolfeii	strain=DSM 2970	GCA_025397995.1	145261	145261	type	True	81.0884	386	583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:03,680] [INFO] DFAST Taxonomy check result was written to GCF_027554905.1_ASM2755490v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:03,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:03,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:03,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/checkm_data
[2024-01-24 11:20:03,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:03,708] [INFO] Task started: CheckM
[2024-01-24 11:20:03,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027554905.1_ASM2755490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027554905.1_ASM2755490v1_genomic.fna/checkm_input GCF_027554905.1_ASM2755490v1_genomic.fna/checkm_result
[2024-01-24 11:20:25,513] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:25,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,539] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:25,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:25,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027554905.1_ASM2755490v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:25,540] [INFO] Task started: Blastn
[2024-01-24 11:20:25,541] [INFO] Running command: blastn -query GCF_027554905.1_ASM2755490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607d9c0e-72ba-48e8-802a-48ebf2cd2a20/dqc_reference/reference_markers_gtdb.fasta -out GCF_027554905.1_ASM2755490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:26,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:26,104] [INFO] Selected 5 target genomes.
[2024-01-24 11:20:26,104] [INFO] Target genome list was writen to GCF_027554905.1_ASM2755490v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:26,109] [INFO] Task started: fastANI
[2024-01-24 11:20:26,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg33daaa79-7d40-4647-9ce6-f5e8534953aa/GCF_027554905.1_ASM2755490v1_genomic.fna.gz --refList GCF_027554905.1_ASM2755490v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027554905.1_ASM2755490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:28,380] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:28,386] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:28,387] [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	99.9612	583	583	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	94.5576	502	583	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	91.2645	511	583	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	82.7452	420	583	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	81.046	375	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	99.47	99.15	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:28,390] [INFO] GTDB search result was written to GCF_027554905.1_ASM2755490v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:28,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:28,394] [INFO] DFAST_QC result json was written to GCF_027554905.1_ASM2755490v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:28,394] [INFO] DFAST_QC completed!
[2024-01-24 11:20:28,394] [INFO] Total running time: 0h0m33s