[2024-01-24 12:22:28,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference
[2024-01-24 12:22:29,810] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,811] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f4a07a9-b784-499e-a316-ed231b68e2b0/GCF_004104375.1_ASM410437v1_genomic.fna.gz | prodigal -d GCF_004104375.1_ASM410437v1_genomic.fna/cds.fna -a GCF_004104375.1_ASM410437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:40,519] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:40,519] [INFO] Task started: HMMsearch
[2024-01-24 12:22:40,519] [INFO] Running command: hmmsearch --tblout GCF_004104375.1_ASM410437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/reference_markers.hmm GCF_004104375.1_ASM410437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:40,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:40,809] [INFO] Found 6/6 markers.
[2024-01-24 12:22:40,841] [INFO] Query marker FASTA was written to GCF_004104375.1_ASM410437v1_genomic.fna/markers.fasta
[2024-01-24 12:22:40,841] [INFO] Task started: Blastn
[2024-01-24 12:22:40,841] [INFO] Running command: blastn -query GCF_004104375.1_ASM410437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/reference_markers.fasta -out GCF_004104375.1_ASM410437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:41,578] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:41,581] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:41,582] [INFO] Target genome list was writen to GCF_004104375.1_ASM410437v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:41,602] [INFO] Task started: fastANI
[2024-01-24 12:22:41,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4a07a9-b784-499e-a316-ed231b68e2b0/GCF_004104375.1_ASM410437v1_genomic.fna.gz --refList GCF_004104375.1_ASM410437v1_genomic.fna/target_genomes.txt --output GCF_004104375.1_ASM410437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:50,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:50,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:50,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:50,845] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:50,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:50,846] [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
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	100.0	1143	1144	95	conclusive
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	79.9225	502	1144	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	79.7546	502	1144	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	78.7721	445	1144	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.4707	393	1144	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	78.3326	371	1144	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.1813	365	1144	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.8842	91	1144	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.8665	91	1144	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.7111	91	1144	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.5564	75	1144	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.5547	75	1144	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.2654	78	1144	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.9878	80	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:50,861] [INFO] DFAST Taxonomy check result was written to GCF_004104375.1_ASM410437v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:50,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:50,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:50,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/checkm_data
[2024-01-24 12:22:50,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:50,906] [INFO] Task started: CheckM
[2024-01-24 12:22:50,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104375.1_ASM410437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104375.1_ASM410437v1_genomic.fna/checkm_input GCF_004104375.1_ASM410437v1_genomic.fna/checkm_result
[2024-01-24 12:23:26,988] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:26,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:27,010] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:27,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:27,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104375.1_ASM410437v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:27,012] [INFO] Task started: Blastn
[2024-01-24 12:23:27,012] [INFO] Running command: blastn -query GCF_004104375.1_ASM410437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c25a61a-9e13-426b-a784-fc5c6b886692/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104375.1_ASM410437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:27,979] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:27,988] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:27,988] [INFO] Target genome list was writen to GCF_004104375.1_ASM410437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:27,998] [INFO] Task started: fastANI
[2024-01-24 12:23:27,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4a07a9-b784-499e-a316-ed231b68e2b0/GCF_004104375.1_ASM410437v1_genomic.fna.gz --refList GCF_004104375.1_ASM410437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104375.1_ASM410437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:36,026] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,034] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:36,034] [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_004104375.1	s__Leeuwenhoekiella aequorea	100.0	1143	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	82.1549	758	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	79.7546	502	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.7256	474	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	78.7623	446	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	78.3309	369	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	77.9253	281	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.5564	75	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_013151975.1	s__PRS1 sp013151975	76.078	71	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,036] [INFO] GTDB search result was written to GCF_004104375.1_ASM410437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:36,038] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:36,041] [INFO] DFAST_QC result json was written to GCF_004104375.1_ASM410437v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:36,041] [INFO] DFAST_QC completed!
[2024-01-24 12:23:36,041] [INFO] Total running time: 0h1m8s