[2024-01-24 13:40:35,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference
[2024-01-24 13:40:36,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,473] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg27f8b285-24e2-4265-b543-8361916cead9/GCF_004745425.1_ASM474542v1_genomic.fna.gz | prodigal -d GCF_004745425.1_ASM474542v1_genomic.fna/cds.fna -a GCF_004745425.1_ASM474542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:43,316] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:43,317] [INFO] Task started: HMMsearch
[2024-01-24 13:40:43,317] [INFO] Running command: hmmsearch --tblout GCF_004745425.1_ASM474542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/reference_markers.hmm GCF_004745425.1_ASM474542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:43,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:43,578] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg27f8b285-24e2-4265-b543-8361916cead9/GCF_004745425.1_ASM474542v1_genomic.fna.gz]
[2024-01-24 13:40:43,603] [INFO] Query marker FASTA was written to GCF_004745425.1_ASM474542v1_genomic.fna/markers.fasta
[2024-01-24 13:40:43,603] [INFO] Task started: Blastn
[2024-01-24 13:40:43,603] [INFO] Running command: blastn -query GCF_004745425.1_ASM474542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/reference_markers.fasta -out GCF_004745425.1_ASM474542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:44,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:44,104] [INFO] Selected 7 target genomes.
[2024-01-24 13:40:44,104] [INFO] Target genome list was writen to GCF_004745425.1_ASM474542v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:44,109] [INFO] Task started: fastANI
[2024-01-24 13:40:44,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f8b285-24e2-4265-b543-8361916cead9/GCF_004745425.1_ASM474542v1_genomic.fna.gz --refList GCF_004745425.1_ASM474542v1_genomic.fna/target_genomes.txt --output GCF_004745425.1_ASM474542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:48,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:48,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:48,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:48,148] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:48,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:48,148] [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
Methanolobus halotolerans	strain=SY-01	GCA_004745425.1	2052935	2052935	type	True	100.0	843	845	95	conclusive
Methanolobus zinderi	strain=DSM 21339	GCA_013388255.1	536044	536044	type	True	80.4569	477	845	95	below_threshold
Methanolobus psychrotolerans	strain=YSF-03	GCA_002243045.1	1874706	1874706	type	True	77.9747	191	845	95	below_threshold
Methanolobus vulcani	strain=PL 12/M	GCA_900100715.1	38026	38026	type	True	77.7628	161	845	95	below_threshold
Methanolobus bombayensis	strain=DSM 7082	GCA_017873415.1	38023	38023	type	True	77.6964	174	845	95	below_threshold
Methanomethylovorans hollandica	strain=DSM 15978	GCA_000328665.1	101192	101192	type	True	76.547	56	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:48,150] [INFO] DFAST Taxonomy check result was written to GCF_004745425.1_ASM474542v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:48,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:48,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:48,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/checkm_data
[2024-01-24 13:40:48,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:48,192] [INFO] Task started: CheckM
[2024-01-24 13:40:48,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004745425.1_ASM474542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004745425.1_ASM474542v1_genomic.fna/checkm_input GCF_004745425.1_ASM474542v1_genomic.fna/checkm_result
[2024-01-24 13:41:14,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:14,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,529] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:14,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:14,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004745425.1_ASM474542v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:14,530] [INFO] Task started: Blastn
[2024-01-24 13:41:14,530] [INFO] Running command: blastn -query GCF_004745425.1_ASM474542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bfb3184-5dd4-4e50-b7da-d0076af0d224/dqc_reference/reference_markers_gtdb.fasta -out GCF_004745425.1_ASM474542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:15,038] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:15,041] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:15,041] [INFO] Target genome list was writen to GCF_004745425.1_ASM474542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:15,081] [INFO] Task started: fastANI
[2024-01-24 13:41:15,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f8b285-24e2-4265-b543-8361916cead9/GCF_004745425.1_ASM474542v1_genomic.fna.gz --refList GCF_004745425.1_ASM474542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004745425.1_ASM474542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:19,077] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,084] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:19,084] [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_004745425.1	s__Methanolobus sp004745425	100.0	843	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013388255.1	s__Methanolobus zinderi	80.4528	477	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	96.85	96.85	0.87	0.87	2	-
GCA_002508635.1	s__Methanolobus sp002508635	80.3595	324	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932675.1	s__Methanolobus sp016932675	79.9311	356	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278365.1	s__Methanolobus sp016278365	78.1029	270	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243045.1	s__Methanolobus psychrotolerans	77.9667	192	845	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	77.7628	161	845	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,086] [INFO] GTDB search result was written to GCF_004745425.1_ASM474542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:19,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:19,089] [INFO] DFAST_QC result json was written to GCF_004745425.1_ASM474542v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:19,089] [INFO] DFAST_QC completed!
[2024-01-24 13:41:19,089] [INFO] Total running time: 0h0m44s