[2024-01-24 15:02:23,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference
[2024-01-24 15:02:24,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,865] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,866] [INFO] Running command: gunzip -c /var/lib/cwl/stga289f410-b340-4707-a6b0-1420ef7f4ae2/GCF_003316845.1_ASM331684v1_genomic.fna.gz | prodigal -d GCF_003316845.1_ASM331684v1_genomic.fna/cds.fna -a GCF_003316845.1_ASM331684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:52,383] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:52,383] [INFO] Task started: HMMsearch
[2024-01-24 15:02:52,383] [INFO] Running command: hmmsearch --tblout GCF_003316845.1_ASM331684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/reference_markers.hmm GCF_003316845.1_ASM331684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:52,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:52,716] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,764] [INFO] Query marker FASTA was written to GCF_003316845.1_ASM331684v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,764] [INFO] Task started: Blastn
[2024-01-24 15:02:52,764] [INFO] Running command: blastn -query GCF_003316845.1_ASM331684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/reference_markers.fasta -out GCF_003316845.1_ASM331684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:53,470] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:53,474] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:53,474] [INFO] Target genome list was writen to GCF_003316845.1_ASM331684v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:53,484] [INFO] Task started: fastANI
[2024-01-24 15:02:53,484] [INFO] Running command: fastANI --query /var/lib/cwl/stga289f410-b340-4707-a6b0-1420ef7f4ae2/GCF_003316845.1_ASM331684v1_genomic.fna.gz --refList GCF_003316845.1_ASM331684v1_genomic.fna/target_genomes.txt --output GCF_003316845.1_ASM331684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:12,843] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:12,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:12,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:12,860] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:12,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:12,861] [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
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	100.0	1705	1706	95	conclusive
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	77.9657	448	1706	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.5907	440	1706	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.9618	162	1706	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	76.9444	156	1706	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.8147	256	1706	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	76.7625	242	1706	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.7558	151	1706	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.7213	228	1706	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.6565	185	1706	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.6287	238	1706	95	below_threshold
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	76.5579	228	1706	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.547	138	1706	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	76.5438	180	1706	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.2764	91	1706	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.1651	114	1706	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	76.1235	117	1706	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.1134	122	1706	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.0312	98	1706	95	below_threshold
Echinicola rosea	strain=JL3085	GCA_005281475.1	1807691	1807691	type	True	75.8328	94	1706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:12,862] [INFO] DFAST Taxonomy check result was written to GCF_003316845.1_ASM331684v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:12,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:12,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:12,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/checkm_data
[2024-01-24 15:03:12,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:12,922] [INFO] Task started: CheckM
[2024-01-24 15:03:12,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003316845.1_ASM331684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003316845.1_ASM331684v1_genomic.fna/checkm_input GCF_003316845.1_ASM331684v1_genomic.fna/checkm_result
[2024-01-24 15:04:33,347] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:33,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:33,365] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:33,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:33,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003316845.1_ASM331684v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:33,366] [INFO] Task started: Blastn
[2024-01-24 15:04:33,366] [INFO] Running command: blastn -query GCF_003316845.1_ASM331684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg144fe3c5-a04c-41ef-9e74-914164e8a4e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003316845.1_ASM331684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:34,275] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:34,279] [INFO] Selected 19 target genomes.
[2024-01-24 15:04:34,280] [INFO] Target genome list was writen to GCF_003316845.1_ASM331684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:34,295] [INFO] Task started: fastANI
[2024-01-24 15:04:34,296] [INFO] Running command: fastANI --query /var/lib/cwl/stga289f410-b340-4707-a6b0-1420ef7f4ae2/GCF_003316845.1_ASM331684v1_genomic.fna.gz --refList GCF_003316845.1_ASM331684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003316845.1_ASM331684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:50,676] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:50,696] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:50,696] [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_003316845.1	s__Aquiflexum_A aquatile	100.0	1705	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176595.1	s__Aquiflexum balticum	77.9582	447	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	77.574	441	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	77.3978	299	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	76.9444	156	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	76.8704	193	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_004216715.1	s__Cecembia calidifontis	76.8162	257	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.7607	223	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.7531	150	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.7446	244	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.7213	228	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.6287	238	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_014637795.1	s__Belliella aquatica	76.5325	181	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	76.3811	115	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.2865	92	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.1705	115	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017254845.1	s__Algoriphagus sp017254845	76.1138	122	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281475.1	s__Echinicola rosea	75.8328	94	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010993705.1	s__Cyclobacterium sp010993705	75.7682	73	1706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:50,698] [INFO] GTDB search result was written to GCF_003316845.1_ASM331684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:50,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:50,703] [INFO] DFAST_QC result json was written to GCF_003316845.1_ASM331684v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:50,703] [INFO] DFAST_QC completed!
[2024-01-24 15:04:50,703] [INFO] Total running time: 0h2m27s