[2024-01-24 14:14:06,102] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference
[2024-01-24 14:14:07,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,548] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ff0a844-65bf-45d2-bb98-15160a96e4d2/GCF_003992615.1_ASM399261v1_genomic.fna.gz | prodigal -d GCF_003992615.1_ASM399261v1_genomic.fna/cds.fna -a GCF_003992615.1_ASM399261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:33,003] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:33,004] [INFO] Task started: HMMsearch
[2024-01-24 14:14:33,004] [INFO] Running command: hmmsearch --tblout GCF_003992615.1_ASM399261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/reference_markers.hmm GCF_003992615.1_ASM399261v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,277] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,311] [INFO] Query marker FASTA was written to GCF_003992615.1_ASM399261v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,312] [INFO] Task started: Blastn
[2024-01-24 14:14:33,312] [INFO] Running command: blastn -query GCF_003992615.1_ASM399261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/reference_markers.fasta -out GCF_003992615.1_ASM399261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:33,963] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:33,968] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:33,969] [INFO] Target genome list was writen to GCF_003992615.1_ASM399261v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:33,996] [INFO] Task started: fastANI
[2024-01-24 14:14:33,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff0a844-65bf-45d2-bb98-15160a96e4d2/GCF_003992615.1_ASM399261v1_genomic.fna.gz --refList GCF_003992615.1_ASM399261v1_genomic.fna/target_genomes.txt --output GCF_003992615.1_ASM399261v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:48,695] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:48,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:48,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:48,714] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:48,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:48,715] [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
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	100.0	1246	1248	95	conclusive
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	80.5336	671	1248	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	80.1439	654	1248	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	80.1431	654	1248	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	80.0566	680	1248	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	80.0466	679	1248	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	79.5064	560	1248	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	79.2331	570	1248	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.0626	559	1248	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	78.9543	507	1248	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	78.928	503	1248	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	78.9002	546	1248	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.8584	501	1248	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	78.7935	555	1248	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	78.6622	437	1248	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.599	69	1248	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.4124	53	1248	95	below_threshold
Subsaximicrobium wynnwilliamsii	strain=G#7(T)	GCA_007997225.1	291179	291179	type	True	76.3165	55	1248	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	76.2953	85	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:48,717] [INFO] DFAST Taxonomy check result was written to GCF_003992615.1_ASM399261v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:48,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:48,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:48,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/checkm_data
[2024-01-24 14:14:48,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:48,761] [INFO] Task started: CheckM
[2024-01-24 14:14:48,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992615.1_ASM399261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992615.1_ASM399261v1_genomic.fna/checkm_input GCF_003992615.1_ASM399261v1_genomic.fna/checkm_result
[2024-01-24 14:15:58,613] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:58,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:58,633] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:58,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:58,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992615.1_ASM399261v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:58,634] [INFO] Task started: Blastn
[2024-01-24 14:15:58,634] [INFO] Running command: blastn -query GCF_003992615.1_ASM399261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb3f2d5-b490-478f-863d-a582147debcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992615.1_ASM399261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:59,683] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:59,686] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:59,687] [INFO] Target genome list was writen to GCF_003992615.1_ASM399261v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:59,703] [INFO] Task started: fastANI
[2024-01-24 14:15:59,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff0a844-65bf-45d2-bb98-15160a96e4d2/GCF_003992615.1_ASM399261v1_genomic.fna.gz --refList GCF_003992615.1_ASM399261v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992615.1_ASM399261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:15,214] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:15,232] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:15,232] [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_003992615.1	s__Muricauda beolgyonensis	100.0	1245	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010500845.1	s__Muricauda sediminis	80.5248	672	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	80.1492	653	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003584165.1	s__Muricauda sp003584165	80.0642	679	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003058265.1	s__Muricauda sp003058265	79.5104	560	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	79.2459	568	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_001683915.1	s__Muricauda sp001683915	79.0892	495	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_007785775.2	s__Muricauda sp003973595	79.0626	559	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003581615.1	s__Muricauda lutimaris	78.9802	509	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	78.928	503	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	78.9083	545	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	78.8578	501	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCA_002167435.2	s__Muricauda sp002167435	78.7725	492	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	78.6825	492	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_000745185.1	s__Muricauda sp000745185	78.6697	532	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	78.6622	437	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:15,233] [INFO] GTDB search result was written to GCF_003992615.1_ASM399261v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:15,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:15,238] [INFO] DFAST_QC result json was written to GCF_003992615.1_ASM399261v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:15,238] [INFO] DFAST_QC completed!
[2024-01-24 14:16:15,238] [INFO] Total running time: 0h2m9s