[2024-01-24 13:01:26,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference
[2024-01-24 13:01:27,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,774] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg4194a483-6b11-44f7-bbfe-509c1b49c3b0/GCF_020523925.1_ASM2052392v1_genomic.fna.gz | prodigal -d GCF_020523925.1_ASM2052392v1_genomic.fna/cds.fna -a GCF_020523925.1_ASM2052392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:38,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:38,537] [INFO] Task started: HMMsearch
[2024-01-24 13:01:38,537] [INFO] Running command: hmmsearch --tblout GCF_020523925.1_ASM2052392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/reference_markers.hmm GCF_020523925.1_ASM2052392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:38,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:38,858] [INFO] Found 6/6 markers.
[2024-01-24 13:01:38,899] [INFO] Query marker FASTA was written to GCF_020523925.1_ASM2052392v1_genomic.fna/markers.fasta
[2024-01-24 13:01:38,900] [INFO] Task started: Blastn
[2024-01-24 13:01:38,900] [INFO] Running command: blastn -query GCF_020523925.1_ASM2052392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/reference_markers.fasta -out GCF_020523925.1_ASM2052392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:39,677] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:39,681] [INFO] Selected 18 target genomes.
[2024-01-24 13:01:39,681] [INFO] Target genome list was writen to GCF_020523925.1_ASM2052392v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:39,688] [INFO] Task started: fastANI
[2024-01-24 13:01:39,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg4194a483-6b11-44f7-bbfe-509c1b49c3b0/GCF_020523925.1_ASM2052392v1_genomic.fna.gz --refList GCF_020523925.1_ASM2052392v1_genomic.fna/target_genomes.txt --output GCF_020523925.1_ASM2052392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:52,563] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:52,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:52,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:52,578] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:52,578] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:52,579] [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
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	88.5995	850	1186	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	81.7419	705	1186	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	79.0778	491	1186	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.7286	413	1186	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.4791	494	1186	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.4777	499	1186	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.4748	500	1186	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.0076	449	1186	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.9968	341	1186	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.9309	352	1186	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.9228	452	1186	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.92	318	1186	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8068	359	1186	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.6931	346	1186	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5248	243	1186	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.4435	284	1186	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.3649	293	1186	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.3345	226	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:52,580] [INFO] DFAST Taxonomy check result was written to GCF_020523925.1_ASM2052392v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:52,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:52,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:52,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/checkm_data
[2024-01-24 13:01:52,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:52,623] [INFO] Task started: CheckM
[2024-01-24 13:01:52,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020523925.1_ASM2052392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020523925.1_ASM2052392v1_genomic.fna/checkm_input GCF_020523925.1_ASM2052392v1_genomic.fna/checkm_result
[2024-01-24 13:02:26,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:26,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:26,498] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:26,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:26,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020523925.1_ASM2052392v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:26,499] [INFO] Task started: Blastn
[2024-01-24 13:02:26,499] [INFO] Running command: blastn -query GCF_020523925.1_ASM2052392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfd2e7fa-ac62-44ea-9452-c8e05cd3eee7/dqc_reference/reference_markers_gtdb.fasta -out GCF_020523925.1_ASM2052392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:27,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:27,438] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:27,438] [INFO] Target genome list was writen to GCF_020523925.1_ASM2052392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:27,456] [INFO] Task started: fastANI
[2024-01-24 13:02:27,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg4194a483-6b11-44f7-bbfe-509c1b49c3b0/GCF_020523925.1_ASM2052392v1_genomic.fna.gz --refList GCF_020523925.1_ASM2052392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020523925.1_ASM2052392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:40,766] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:40,786] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:40,786] [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_000943565.1	s__Tamlana_B sedimentorum	88.6157	849	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	81.7534	704	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	79.079	491	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.7618	446	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	78.5119	437	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.4929	490	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.4869	493	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.445	363	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.3718	382	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.2755	431	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.1785	389	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	78.1706	451	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	78.1531	463	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_009796805.1	s__Algibacter sp009796805	78.1232	472	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.005	448	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001642835.1	s__Tamlana_A agarivorans	77.9218	353	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.8282	303	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_007827365.1	s__Olleya sp002323495	77.4385	269	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,787] [INFO] GTDB search result was written to GCF_020523925.1_ASM2052392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:40,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:40,794] [INFO] DFAST_QC result json was written to GCF_020523925.1_ASM2052392v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:40,794] [INFO] DFAST_QC completed!
[2024-01-24 13:02:40,794] [INFO] Total running time: 0h1m14s