[2024-01-25 19:06:35,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:35,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:35,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference
[2024-01-25 19:06:36,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:36,764] [INFO] Task started: Prodigal
[2024-01-25 19:06:36,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg8caabca0-145f-4fd7-8912-9fd631ab682f/GCF_000259075.1_ASM25907v1_genomic.fna.gz | prodigal -d GCF_000259075.1_ASM25907v1_genomic.fna/cds.fna -a GCF_000259075.1_ASM25907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:57,078] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:57,078] [INFO] Task started: HMMsearch
[2024-01-25 19:06:57,079] [INFO] Running command: hmmsearch --tblout GCF_000259075.1_ASM25907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/reference_markers.hmm GCF_000259075.1_ASM25907v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:57,327] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:57,329] [INFO] Found 6/6 markers.
[2024-01-25 19:06:57,370] [INFO] Query marker FASTA was written to GCF_000259075.1_ASM25907v1_genomic.fna/markers.fasta
[2024-01-25 19:06:57,371] [INFO] Task started: Blastn
[2024-01-25 19:06:57,371] [INFO] Running command: blastn -query GCF_000259075.1_ASM25907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/reference_markers.fasta -out GCF_000259075.1_ASM25907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:57,926] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:57,929] [INFO] Selected 17 target genomes.
[2024-01-25 19:06:57,929] [INFO] Target genome list was writen to GCF_000259075.1_ASM25907v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:57,975] [INFO] Task started: fastANI
[2024-01-25 19:06:57,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caabca0-145f-4fd7-8912-9fd631ab682f/GCF_000259075.1_ASM25907v1_genomic.fna.gz --refList GCF_000259075.1_ASM25907v1_genomic.fna/target_genomes.txt --output GCF_000259075.1_ASM25907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:14,022] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:14,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:14,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:14,030] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:07:14,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:14,030] [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
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000259075.1	989	989	type	True	100.0	1625	1627	95	conclusive
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000614895.1	989	989	type	True	99.9553	1578	1627	95	conclusive
Marinilabilia rubra	strain=WTE16	GCA_003121985.1	2162893	2162893	type	True	78.7679	377	1627	95	below_threshold
Anaerophaga thermohalophila	strain=DSM 12881	GCA_000191885.2	177400	177400	type	True	77.2733	266	1627	95	below_threshold
Thermophagus xiamenensis	strain=DSM 19012	GCA_900112795.1	385682	385682	type	True	76.8405	137	1627	95	below_threshold
Thermophagus xiamenensis	strain=HS1	GCA_000220155.2	385682	385682	type	True	76.7208	136	1627	95	below_threshold
Geofilum rhodophaeum	strain=HF401	GCA_002210225.1	1965019	1965019	type	True	76.4902	68	1627	95	below_threshold
Carboxylicivirga sediminis	strain=JR1	GCA_018156225.1	2006564	2006564	type	True	75.8648	58	1627	95	below_threshold
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	75.5419	64	1627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:14,032] [INFO] DFAST Taxonomy check result was written to GCF_000259075.1_ASM25907v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:14,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:14,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:14,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/checkm_data
[2024-01-25 19:07:14,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:14,084] [INFO] Task started: CheckM
[2024-01-25 19:07:14,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000259075.1_ASM25907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000259075.1_ASM25907v1_genomic.fna/checkm_input GCF_000259075.1_ASM25907v1_genomic.fna/checkm_result
[2024-01-25 19:08:13,718] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:13,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:13,776] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:13,776] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:13,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000259075.1_ASM25907v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:13,778] [INFO] Task started: Blastn
[2024-01-25 19:08:13,778] [INFO] Running command: blastn -query GCF_000259075.1_ASM25907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c21d96c-8126-42dc-9f53-c3fa093139c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000259075.1_ASM25907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:14,656] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:14,659] [INFO] Selected 9 target genomes.
[2024-01-25 19:08:14,659] [INFO] Target genome list was writen to GCF_000259075.1_ASM25907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:14,687] [INFO] Task started: fastANI
[2024-01-25 19:08:14,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caabca0-145f-4fd7-8912-9fd631ab682f/GCF_000259075.1_ASM25907v1_genomic.fna.gz --refList GCF_000259075.1_ASM25907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000259075.1_ASM25907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:25,105] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:25,110] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:25,111] [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_000259075.1	s__Marinilabilia salmonicolor	100.0	1625	1627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCF_003003035.1	s__Marinilabilia salmonicolor_A	86.544	1225	1627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	98.82	98.82	0.92	0.92	2	-
GCA_002411085.1	s__Marinilabilia sp002411085	82.1159	645	1627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278715.1	s__Marinilabilia sp016278715	80.1272	710	1627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121985.1	s__Marinilabilia rubra	78.7436	376	1627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:25,112] [INFO] GTDB search result was written to GCF_000259075.1_ASM25907v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:25,113] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:25,115] [INFO] DFAST_QC result json was written to GCF_000259075.1_ASM25907v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:25,116] [INFO] DFAST_QC completed!
[2024-01-25 19:08:25,116] [INFO] Total running time: 0h1m49s