[2024-01-25 19:10:50,692] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:50,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:50,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference
[2024-01-25 19:10:51,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:51,829] [INFO] Task started: Prodigal
[2024-01-25 19:10:51,830] [INFO] Running command: gunzip -c /var/lib/cwl/stga22fa26e-1121-4f83-ac11-682c730f3cc2/GCF_025847235.1_ASM2584723v1_genomic.fna.gz | prodigal -d GCF_025847235.1_ASM2584723v1_genomic.fna/cds.fna -a GCF_025847235.1_ASM2584723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:06,838] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:06,838] [INFO] Task started: HMMsearch
[2024-01-25 19:11:06,838] [INFO] Running command: hmmsearch --tblout GCF_025847235.1_ASM2584723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/reference_markers.hmm GCF_025847235.1_ASM2584723v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:07,155] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:07,156] [INFO] Found 6/6 markers.
[2024-01-25 19:11:07,200] [INFO] Query marker FASTA was written to GCF_025847235.1_ASM2584723v1_genomic.fna/markers.fasta
[2024-01-25 19:11:07,200] [INFO] Task started: Blastn
[2024-01-25 19:11:07,200] [INFO] Running command: blastn -query GCF_025847235.1_ASM2584723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/reference_markers.fasta -out GCF_025847235.1_ASM2584723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:07,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:07,870] [INFO] Selected 22 target genomes.
[2024-01-25 19:11:07,870] [INFO] Target genome list was writen to GCF_025847235.1_ASM2584723v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:07,887] [INFO] Task started: fastANI
[2024-01-25 19:11:07,887] [INFO] Running command: fastANI --query /var/lib/cwl/stga22fa26e-1121-4f83-ac11-682c730f3cc2/GCF_025847235.1_ASM2584723v1_genomic.fna.gz --refList GCF_025847235.1_ASM2584723v1_genomic.fna/target_genomes.txt --output GCF_025847235.1_ASM2584723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:31,262] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:31,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:31,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:31,275] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:11:31,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:11:31,276] [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
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	87.652	1259	1835	95	below_threshold
Flavobacterium hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	87.6124	1290	1835	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	80.6267	864	1835	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	80.6117	845	1835	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	80.5857	886	1835	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	80.5729	840	1835	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	80.5429	873	1835	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	80.4934	906	1835	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	80.3895	869	1835	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	80.3775	866	1835	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	80.0622	742	1835	95	below_threshold
Flavobacterium circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	79.995	739	1835	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	79.9756	718	1835	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	79.955	787	1835	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	79.9451	741	1835	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	79.8914	751	1835	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	79.5282	718	1835	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	79.461	734	1835	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	79.4515	730	1835	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	79.0599	603	1835	95	below_threshold
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	78.4928	418	1835	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9798	243	1835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:31,277] [INFO] DFAST Taxonomy check result was written to GCF_025847235.1_ASM2584723v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:31,278] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:31,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:31,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/checkm_data
[2024-01-25 19:11:31,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:31,332] [INFO] Task started: CheckM
[2024-01-25 19:11:31,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025847235.1_ASM2584723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025847235.1_ASM2584723v1_genomic.fna/checkm_input GCF_025847235.1_ASM2584723v1_genomic.fna/checkm_result
[2024-01-25 19:12:14,997] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:14,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:15,015] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:15,015] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:15,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025847235.1_ASM2584723v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:15,016] [INFO] Task started: Blastn
[2024-01-25 19:12:15,016] [INFO] Running command: blastn -query GCF_025847235.1_ASM2584723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8340bef9-39fa-4d16-ae08-c9cf7265e630/dqc_reference/reference_markers_gtdb.fasta -out GCF_025847235.1_ASM2584723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:15,989] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:15,993] [INFO] Selected 14 target genomes.
[2024-01-25 19:12:15,993] [INFO] Target genome list was writen to GCF_025847235.1_ASM2584723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:16,026] [INFO] Task started: fastANI
[2024-01-25 19:12:16,026] [INFO] Running command: fastANI --query /var/lib/cwl/stga22fa26e-1121-4f83-ac11-682c730f3cc2/GCF_025847235.1_ASM2584723v1_genomic.fna.gz --refList GCF_025847235.1_ASM2584723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025847235.1_ASM2584723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:33,108] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:33,116] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:12:33,117] [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_000737695.1	s__Flavobacterium hydatis	87.629	1262	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000813005.1	s__Flavobacterium sp000813005	87.1021	1273	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.28	97.24	0.92	0.92	3	-
GCF_015594725.1	s__Flavobacterium sp015594725	85.5088	1082	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	85.3023	1130	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	80.859	924	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222055.1	s__Flavobacterium araucananum	80.6268	864	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001686925.1	s__Flavobacterium piscis	80.6046	846	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_018380615.1	s__Flavobacterium psychroterrae	80.5455	873	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426145.1	s__Flavobacterium sp000426145	80.5378	755	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142735.1	s__Flavobacterium saccharophilum	80.3323	781	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427905.1	s__Flavobacterium sp001427905	80.279	838	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	80.2241	846	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004345565.1	s__Flavobacterium circumlabens	79.9493	740	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	-
GCF_009674775.1	s__Flavobacterium sp009674775	79.7	711	1835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:33,118] [INFO] GTDB search result was written to GCF_025847235.1_ASM2584723v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:33,119] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:33,124] [INFO] DFAST_QC result json was written to GCF_025847235.1_ASM2584723v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:33,124] [INFO] DFAST_QC completed!
[2024-01-25 19:12:33,124] [INFO] Total running time: 0h1m42s