[2024-01-24 11:43:25,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference
[2024-01-24 11:43:30,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stgda4a4dfa-88c6-463f-b786-f36c93c6ea79/GCF_010119975.1_ASM1011997v1_genomic.fna.gz | prodigal -d GCF_010119975.1_ASM1011997v1_genomic.fna/cds.fna -a GCF_010119975.1_ASM1011997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:07,129] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:07,130] [INFO] Task started: HMMsearch
[2024-01-24 11:44:07,130] [INFO] Running command: hmmsearch --tblout GCF_010119975.1_ASM1011997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/reference_markers.hmm GCF_010119975.1_ASM1011997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:07,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:07,510] [INFO] Found 6/6 markers.
[2024-01-24 11:44:07,580] [INFO] Query marker FASTA was written to GCF_010119975.1_ASM1011997v1_genomic.fna/markers.fasta
[2024-01-24 11:44:07,581] [INFO] Task started: Blastn
[2024-01-24 11:44:07,581] [INFO] Running command: blastn -query GCF_010119975.1_ASM1011997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/reference_markers.fasta -out GCF_010119975.1_ASM1011997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:08,166] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:08,169] [INFO] Selected 24 target genomes.
[2024-01-24 11:44:08,169] [INFO] Target genome list was writen to GCF_010119975.1_ASM1011997v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:08,187] [INFO] Task started: fastANI
[2024-01-24 11:44:08,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4a4dfa-88c6-463f-b786-f36c93c6ea79/GCF_010119975.1_ASM1011997v1_genomic.fna.gz --refList GCF_010119975.1_ASM1011997v1_genomic.fna/target_genomes.txt --output GCF_010119975.1_ASM1011997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:31,677] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:31,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:31,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:31,683] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:31,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:31,684] [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
Rhodocytophaga rosea	strain=172606-1	GCA_010119975.1	2704465	2704465	type	True	100.0	2992	2994	95	conclusive
Adhaeribacter aquaticus	strain=DSM 16391	GCA_000473365.1	299567	299567	type	True	75.9382	52	2994	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	75.676	58	2994	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	75.6194	58	2994	95	below_threshold
Sporocytophaga myxococcoides	strain=DSM 11118	GCA_000426725.1	153721	153721	type	True	75.51	54	2994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:31,689] [INFO] DFAST Taxonomy check result was written to GCF_010119975.1_ASM1011997v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:31,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:31,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:31,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/checkm_data
[2024-01-24 11:44:31,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:31,770] [INFO] Task started: CheckM
[2024-01-24 11:44:31,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119975.1_ASM1011997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119975.1_ASM1011997v1_genomic.fna/checkm_input GCF_010119975.1_ASM1011997v1_genomic.fna/checkm_result
[2024-01-24 11:46:10,373] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:10,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:10,403] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:10,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:10,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119975.1_ASM1011997v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:10,409] [INFO] Task started: Blastn
[2024-01-24 11:46:10,409] [INFO] Running command: blastn -query GCF_010119975.1_ASM1011997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60373cb2-293f-4a8a-b010-b94358711bd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119975.1_ASM1011997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:11,161] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:11,167] [INFO] Selected 28 target genomes.
[2024-01-24 11:46:11,167] [INFO] Target genome list was writen to GCF_010119975.1_ASM1011997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:11,219] [INFO] Task started: fastANI
[2024-01-24 11:46:11,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4a4dfa-88c6-463f-b786-f36c93c6ea79/GCF_010119975.1_ASM1011997v1_genomic.fna.gz --refList GCF_010119975.1_ASM1011997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119975.1_ASM1011997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:37,435] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:37,445] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:37,446] [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_010119975.1	s__Rhodocytophaga rosea	100.0	2992	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__172606-1;g__Rhodocytophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011604685.1	s__Spirosoma aureum	76.1128	60	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473365.1	s__Adhaeribacter aquaticus	75.9382	52	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	75.6194	58	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775915.1	s__Sporocytophaga myxococcoides_A	75.5206	52	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Sporocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426725.1	s__Sporocytophaga myxococcoides	75.51	54	2994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Sporocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:37,447] [INFO] GTDB search result was written to GCF_010119975.1_ASM1011997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:37,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:37,451] [INFO] DFAST_QC result json was written to GCF_010119975.1_ASM1011997v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:37,451] [INFO] DFAST_QC completed!
[2024-01-24 11:46:37,451] [INFO] Total running time: 0h3m12s