[2024-01-25 20:03:05,805] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference
[2024-01-25 20:03:06,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,965] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,965] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd0ef427-3149-4226-b45f-76d88cb6365d/GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/cds.fna -a GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:15,536] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:15,537] [INFO] Task started: HMMsearch
[2024-01-25 20:03:15,537] [INFO] Running command: hmmsearch --tblout GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/reference_markers.hmm GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:15,764] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:15,765] [INFO] Found 6/6 markers.
[2024-01-25 20:03:15,793] [INFO] Query marker FASTA was written to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:03:15,794] [INFO] Task started: Blastn
[2024-01-25 20:03:15,794] [INFO] Running command: blastn -query GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/reference_markers.fasta -out GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:16,413] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:16,417] [INFO] Selected 14 target genomes.
[2024-01-25 20:03:16,418] [INFO] Target genome list was writen to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:03:16,433] [INFO] Task started: fastANI
[2024-01-25 20:03:16,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0ef427-3149-4226-b45f-76d88cb6365d/GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna.gz --refList GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:26,169] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:26,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:26,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:26,178] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:26,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:26,179] [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
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	100.0	1151	1152	95	conclusive
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	80.3728	651	1152	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	80.2977	650	1152	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	80.0699	649	1152	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	79.4499	550	1152	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.4207	573	1152	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	79.1774	521	1152	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	78.7798	484	1152	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.4103	259	1152	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.1691	242	1152	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.1415	253	1152	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.054	247	1152	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.9534	250	1152	95	below_threshold
Polaribacter gangjinensis	strain=JCM 16152	GCA_020532765.1	574710	574710	type	True	76.8807	199	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:26,180] [INFO] DFAST Taxonomy check result was written to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:03:26,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:26,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:26,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/checkm_data
[2024-01-25 20:03:26,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:26,217] [INFO] Task started: CheckM
[2024-01-25 20:03:26,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/checkm_input GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:03:54,230] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:54,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:54,247] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:54,247] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:54,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:03:54,247] [INFO] Task started: Blastn
[2024-01-25 20:03:54,247] [INFO] Running command: blastn -query GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b954aa0-1b5c-40b3-ac0e-4028d930b469/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:55,176] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:55,178] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:55,179] [INFO] Target genome list was writen to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:55,190] [INFO] Task started: fastANI
[2024-01-25 20:03:55,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0ef427-3149-4226-b45f-76d88cb6365d/GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna.gz --refList GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:04,286] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:04,295] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:04,295] [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_900116115.1	s__Lutibacter maritimus	100.0	1150	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016342705.1	s__Lutibacter sp016342705	86.4993	895	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	80.2997	648	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018054895.1	s__Lutibacter sp018054895	80.1715	488	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	80.1348	615	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188355.1	s__Lutibacter flavus	80.0781	648	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	79.6924	569	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	79.4449	571	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	79.4242	553	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	79.4087	519	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	78.7304	483	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767395.1	s__Lutibacter sp015767395	78.6473	326	1152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:04,296] [INFO] GTDB search result was written to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:04,297] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:04,303] [INFO] DFAST_QC result json was written to GCF_900116115.1_IMG-taxon_2622736611_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:04:04,304] [INFO] DFAST_QC completed!
[2024-01-25 20:04:04,304] [INFO] Total running time: 0h0m58s