[2024-01-24 12:31:58,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference
[2024-01-24 12:32:00,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:32:00,080] [INFO] Task started: Prodigal
[2024-01-24 12:32:00,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgd37ae3e6-526f-4650-ac3d-4d194a736bd0/GCF_007997295.1_ASM799729v1_genomic.fna.gz | prodigal -d GCF_007997295.1_ASM799729v1_genomic.fna/cds.fna -a GCF_007997295.1_ASM799729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:12,459] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:12,459] [INFO] Task started: HMMsearch
[2024-01-24 12:32:12,459] [INFO] Running command: hmmsearch --tblout GCF_007997295.1_ASM799729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/reference_markers.hmm GCF_007997295.1_ASM799729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:12,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:12,780] [INFO] Found 6/6 markers.
[2024-01-24 12:32:12,812] [INFO] Query marker FASTA was written to GCF_007997295.1_ASM799729v1_genomic.fna/markers.fasta
[2024-01-24 12:32:12,812] [INFO] Task started: Blastn
[2024-01-24 12:32:12,812] [INFO] Running command: blastn -query GCF_007997295.1_ASM799729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/reference_markers.fasta -out GCF_007997295.1_ASM799729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:13,507] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:13,511] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:13,512] [INFO] Target genome list was writen to GCF_007997295.1_ASM799729v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:13,521] [INFO] Task started: fastANI
[2024-01-24 12:32:13,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37ae3e6-526f-4650-ac3d-4d194a736bd0/GCF_007997295.1_ASM799729v1_genomic.fna.gz --refList GCF_007997295.1_ASM799729v1_genomic.fna/target_genomes.txt --output GCF_007997295.1_ASM799729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:24,690] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:24,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:24,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:24,705] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:24,705] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:24,706] [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
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	100.0	1215	1216	95	conclusive
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	84.277	828	1216	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	83.2915	698	1216	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	79.6521	380	1216	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.834	206	1216	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	77.3159	179	1216	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.992	176	1216	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.8637	149	1216	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	76.8614	208	1216	95	below_threshold
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	76.785	212	1216	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.6515	98	1216	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.6144	68	1216	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	76.5317	60	1216	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.4448	83	1216	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.4057	71	1216	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	76.1381	59	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:24,708] [INFO] DFAST Taxonomy check result was written to GCF_007997295.1_ASM799729v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:24,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:24,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:24,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/checkm_data
[2024-01-24 12:32:24,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:24,749] [INFO] Task started: CheckM
[2024-01-24 12:32:24,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997295.1_ASM799729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997295.1_ASM799729v1_genomic.fna/checkm_input GCF_007997295.1_ASM799729v1_genomic.fna/checkm_result
[2024-01-24 12:33:05,552] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:05,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:05,579] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:05,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:05,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997295.1_ASM799729v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:05,580] [INFO] Task started: Blastn
[2024-01-24 12:33:05,580] [INFO] Running command: blastn -query GCF_007997295.1_ASM799729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a8f921-f7ff-4ecc-8aad-97e7546312f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997295.1_ASM799729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:06,535] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:06,543] [INFO] Selected 6 target genomes.
[2024-01-24 12:33:06,543] [INFO] Target genome list was writen to GCF_007997295.1_ASM799729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:06,549] [INFO] Task started: fastANI
[2024-01-24 12:33:06,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37ae3e6-526f-4650-ac3d-4d194a736bd0/GCF_007997295.1_ASM799729v1_genomic.fna.gz --refList GCF_007997295.1_ASM799729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997295.1_ASM799729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:12,458] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:12,469] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:12,469] [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_007997295.1	s__Gillisia hiemivivida	100.0	1215	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	conclusive
GCF_000403785.1	s__Gillisia sp000403785	85.8173	882	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634585.1	s__Gillisia mitskevichiae	84.291	827	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	83.2733	699	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827275.1	s__Gillisia sp007827275	82.989	755	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364325.1	s__Gillisia sp002364325	82.1048	545	1216	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:12,471] [INFO] GTDB search result was written to GCF_007997295.1_ASM799729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:12,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:12,482] [INFO] DFAST_QC result json was written to GCF_007997295.1_ASM799729v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:12,483] [INFO] DFAST_QC completed!
[2024-01-24 12:33:12,483] [INFO] Total running time: 0h1m14s