[2024-01-24 14:19:18,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference
[2024-01-24 14:19:20,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,102] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e3b7540-92c7-4b84-bbd5-174afff5b2c0/GCF_000425445.1_ASM42544v1_genomic.fna.gz | prodigal -d GCF_000425445.1_ASM42544v1_genomic.fna/cds.fna -a GCF_000425445.1_ASM42544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:39,437] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:39,437] [INFO] Task started: HMMsearch
[2024-01-24 14:19:39,437] [INFO] Running command: hmmsearch --tblout GCF_000425445.1_ASM42544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/reference_markers.hmm GCF_000425445.1_ASM42544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:39,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:39,732] [INFO] Found 6/6 markers.
[2024-01-24 14:19:39,782] [INFO] Query marker FASTA was written to GCF_000425445.1_ASM42544v1_genomic.fna/markers.fasta
[2024-01-24 14:19:39,782] [INFO] Task started: Blastn
[2024-01-24 14:19:39,782] [INFO] Running command: blastn -query GCF_000425445.1_ASM42544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/reference_markers.fasta -out GCF_000425445.1_ASM42544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:40,518] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:40,521] [INFO] Selected 18 target genomes.
[2024-01-24 14:19:40,522] [INFO] Target genome list was writen to GCF_000425445.1_ASM42544v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:40,529] [INFO] Task started: fastANI
[2024-01-24 14:19:40,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3b7540-92c7-4b84-bbd5-174afff5b2c0/GCF_000425445.1_ASM42544v1_genomic.fna.gz --refList GCF_000425445.1_ASM42544v1_genomic.fna/target_genomes.txt --output GCF_000425445.1_ASM42544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:02,737] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:02,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:02,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:02,754] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:02,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:02,754] [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 denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	100.0	1592	1594	95	conclusive
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	88.7542	1322	1594	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	87.279	1289	1594	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	87.2674	1283	1594	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	85.9699	1175	1594	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	85.4854	1129	1594	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	83.8775	1073	1594	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	83.8537	1009	1594	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	83.734	1018	1594	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.7316	1031	1594	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	83.6865	1071	1594	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	83.6731	1044	1594	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	83.6392	1061	1594	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.5616	1021	1594	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.5012	1062	1594	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.3146	1053	1594	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	82.3812	969	1594	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.7802	233	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,756] [INFO] DFAST Taxonomy check result was written to GCF_000425445.1_ASM42544v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:02,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:02,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:02,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/checkm_data
[2024-01-24 14:20:02,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:02,812] [INFO] Task started: CheckM
[2024-01-24 14:20:02,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425445.1_ASM42544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425445.1_ASM42544v1_genomic.fna/checkm_input GCF_000425445.1_ASM42544v1_genomic.fna/checkm_result
[2024-01-24 14:20:58,666] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:58,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:58,689] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:58,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:58,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425445.1_ASM42544v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:58,690] [INFO] Task started: Blastn
[2024-01-24 14:20:58,690] [INFO] Running command: blastn -query GCF_000425445.1_ASM42544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg069320b5-de6c-4227-8cc1-4aa6b4d2a4a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425445.1_ASM42544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:59,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:59,661] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:59,662] [INFO] Target genome list was writen to GCF_000425445.1_ASM42544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:59,685] [INFO] Task started: fastANI
[2024-01-24 14:20:59,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3b7540-92c7-4b84-bbd5-174afff5b2c0/GCF_000425445.1_ASM42544v1_genomic.fna.gz --refList GCF_000425445.1_ASM42544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425445.1_ASM42544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:19,807] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:19,833] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:19,834] [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_000425445.1	s__Flavobacterium denitrificans	100.0	1592	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004352915.1	s__Flavobacterium zhairuonense	88.7647	1321	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	87.301	1303	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	87.269	1290	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	86.1149	1246	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007341385.1	s__Flavobacterium daemonense	85.9699	1175	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	85.5211	1125	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013388355.1	s__Flavobacterium sp013388355	83.9822	807	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	83.8772	1073	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	83.8662	1056	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	83.8161	1013	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129555.1	s__Flavobacterium defluvii	83.734	1018	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	83.725	1073	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	83.6711	1044	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	83.6589	1069	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_002303885.1	s__Flavobacterium sp002303885	83.5599	1083	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	83.4981	1068	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:19,836] [INFO] GTDB search result was written to GCF_000425445.1_ASM42544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:19,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:19,840] [INFO] DFAST_QC result json was written to GCF_000425445.1_ASM42544v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:19,841] [INFO] DFAST_QC completed!
[2024-01-24 14:21:19,841] [INFO] Total running time: 0h2m1s