[2024-01-24 15:09:55,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,296] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference
[2024-01-24 15:09:58,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,166] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,166] [INFO] Running command: gunzip -c /var/lib/cwl/stga45f4096-ad2f-4f1d-95a8-3d865251c4c8/GCF_002217365.1_ASM221736v1_genomic.fna.gz | prodigal -d GCF_002217365.1_ASM221736v1_genomic.fna/cds.fna -a GCF_002217365.1_ASM221736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:18,394] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:18,395] [INFO] Task started: HMMsearch
[2024-01-24 15:10:18,395] [INFO] Running command: hmmsearch --tblout GCF_002217365.1_ASM221736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/reference_markers.hmm GCF_002217365.1_ASM221736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:18,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:18,784] [INFO] Found 6/6 markers.
[2024-01-24 15:10:18,836] [INFO] Query marker FASTA was written to GCF_002217365.1_ASM221736v1_genomic.fna/markers.fasta
[2024-01-24 15:10:18,836] [INFO] Task started: Blastn
[2024-01-24 15:10:18,836] [INFO] Running command: blastn -query GCF_002217365.1_ASM221736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/reference_markers.fasta -out GCF_002217365.1_ASM221736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:19,537] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:19,540] [INFO] Selected 19 target genomes.
[2024-01-24 15:10:19,541] [INFO] Target genome list was writen to GCF_002217365.1_ASM221736v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:19,548] [INFO] Task started: fastANI
[2024-01-24 15:10:19,548] [INFO] Running command: fastANI --query /var/lib/cwl/stga45f4096-ad2f-4f1d-95a8-3d865251c4c8/GCF_002217365.1_ASM221736v1_genomic.fna.gz --refList GCF_002217365.1_ASM221736v1_genomic.fna/target_genomes.txt --output GCF_002217365.1_ASM221736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:43,677] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:43,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:43,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:43,698] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:43,698] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:43,699] [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 pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	100.0	1843	1843	95	conclusive
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	99.9959	1839	1843	95	conclusive
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	84.4109	1123	1843	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	84.2634	1132	1843	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	84.1932	1165	1843	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	84.1767	1195	1843	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	84.1226	1195	1843	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	83.7498	1069	1843	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	83.6506	1080	1843	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	83.5442	1181	1843	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	83.5229	1146	1843	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.3545	1173	1843	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	82.9927	1122	1843	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	82.752	1154	1843	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	82.3438	1047	1843	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	82.0864	1063	1843	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.972	1109	1843	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.8823	1082	1843	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9966	242	1843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:43,700] [INFO] DFAST Taxonomy check result was written to GCF_002217365.1_ASM221736v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:43,701] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:43,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:43,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/checkm_data
[2024-01-24 15:10:43,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:43,756] [INFO] Task started: CheckM
[2024-01-24 15:10:43,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217365.1_ASM221736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217365.1_ASM221736v1_genomic.fna/checkm_input GCF_002217365.1_ASM221736v1_genomic.fna/checkm_result
[2024-01-24 15:11:41,822] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:41,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:41,846] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:41,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:41,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217365.1_ASM221736v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:41,847] [INFO] Task started: Blastn
[2024-01-24 15:11:41,847] [INFO] Running command: blastn -query GCF_002217365.1_ASM221736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86ca3178-2743-4a9d-ac6a-a8caf1a7d8e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217365.1_ASM221736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:42,880] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:42,884] [INFO] Selected 16 target genomes.
[2024-01-24 15:11:42,884] [INFO] Target genome list was writen to GCF_002217365.1_ASM221736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,897] [INFO] Task started: fastANI
[2024-01-24 15:11:42,897] [INFO] Running command: fastANI --query /var/lib/cwl/stga45f4096-ad2f-4f1d-95a8-3d865251c4c8/GCF_002217365.1_ASM221736v1_genomic.fna.gz --refList GCF_002217365.1_ASM221736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217365.1_ASM221736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:05,158] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:05,172] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:05,172] [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_900142715.1	s__Flavobacterium pectinovorum	99.9959	1839	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	conclusive
GCF_003688345.1	s__Flavobacterium sp003688345	89.1783	1403	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001507425.1	s__Flavobacterium sp001507425	85.3318	1297	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	85.1923	1317	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004362015.1	s__Flavobacterium sp004362015	85.1665	1248	1843	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	84.4027	1229	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351595.1	s__Flavobacterium sp015351595	84.3964	1118	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900107365.1	s__Flavobacterium aquidurense	84.3804	1125	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014844035.1	s__Flavobacterium sp014844035	84.3669	1240	1843	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	84.276	1130	1843	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	84.2448	1157	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018380615.1	s__Flavobacterium psychroterrae	84.1638	1197	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	84.1284	1222	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_001975985.1	s__Flavobacterium sp001975985	84.0561	1247	1843	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	83.9057	1226	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	83.1247	1068	1843	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:05,174] [INFO] GTDB search result was written to GCF_002217365.1_ASM221736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:05,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:05,178] [INFO] DFAST_QC result json was written to GCF_002217365.1_ASM221736v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:05,178] [INFO] DFAST_QC completed!
[2024-01-24 15:12:05,178] [INFO] Total running time: 0h2m10s