[2024-01-24 13:27:58,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference
[2024-01-24 13:27:59,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,866] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e0fffc8-e447-4358-b87b-78b491ecc309/GCF_009184425.1_ASM918442v1_genomic.fna.gz | prodigal -d GCF_009184425.1_ASM918442v1_genomic.fna/cds.fna -a GCF_009184425.1_ASM918442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:25,720] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:25,721] [INFO] Task started: HMMsearch
[2024-01-24 13:28:25,721] [INFO] Running command: hmmsearch --tblout GCF_009184425.1_ASM918442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/reference_markers.hmm GCF_009184425.1_ASM918442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:26,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:26,108] [INFO] Found 6/6 markers.
[2024-01-24 13:28:26,150] [INFO] Query marker FASTA was written to GCF_009184425.1_ASM918442v1_genomic.fna/markers.fasta
[2024-01-24 13:28:26,151] [INFO] Task started: Blastn
[2024-01-24 13:28:26,151] [INFO] Running command: blastn -query GCF_009184425.1_ASM918442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/reference_markers.fasta -out GCF_009184425.1_ASM918442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:26,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:26,816] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:26,816] [INFO] Target genome list was writen to GCF_009184425.1_ASM918442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:26,826] [INFO] Task started: fastANI
[2024-01-24 13:28:26,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0fffc8-e447-4358-b87b-78b491ecc309/GCF_009184425.1_ASM918442v1_genomic.fna.gz --refList GCF_009184425.1_ASM918442v1_genomic.fna/target_genomes.txt --output GCF_009184425.1_ASM918442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:40,769] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:40,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:40,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:40,787] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:40,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:40,788] [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 olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	100.0	1317	1317	95	conclusive
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	86.5195	925	1317	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	79.1394	532	1317	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	79.1191	535	1317	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	79.1168	524	1317	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	79.0716	509	1317	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	79.0234	439	1317	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.0121	499	1317	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	79.0071	514	1317	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	78.9955	516	1317	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	78.9383	488	1317	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	78.904	513	1317	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	78.8265	439	1317	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	78.8142	445	1317	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	77.7851	326	1317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:40,790] [INFO] DFAST Taxonomy check result was written to GCF_009184425.1_ASM918442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:40,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:40,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:40,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/checkm_data
[2024-01-24 13:28:40,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:40,834] [INFO] Task started: CheckM
[2024-01-24 13:28:40,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009184425.1_ASM918442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009184425.1_ASM918442v1_genomic.fna/checkm_input GCF_009184425.1_ASM918442v1_genomic.fna/checkm_result
[2024-01-24 13:29:53,424] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:53,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:53,448] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:53,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:53,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009184425.1_ASM918442v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:53,449] [INFO] Task started: Blastn
[2024-01-24 13:29:53,449] [INFO] Running command: blastn -query GCF_009184425.1_ASM918442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aee13da-8b0e-4627-a249-60dc9231b813/dqc_reference/reference_markers_gtdb.fasta -out GCF_009184425.1_ASM918442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:54,279] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:54,285] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:54,285] [INFO] Target genome list was writen to GCF_009184425.1_ASM918442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:54,296] [INFO] Task started: fastANI
[2024-01-24 13:29:54,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0fffc8-e447-4358-b87b-78b491ecc309/GCF_009184425.1_ASM918442v1_genomic.fna.gz --refList GCF_009184425.1_ASM918442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009184425.1_ASM918442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:04,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:04,743] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:04,743] [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_009184425.1	s__Muricauda olearia	100.0	1317	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	conclusive
GCF_003385855.1	s__Muricauda sp003385855	91.5593	1059	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	86.5064	926	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	79.6732	602	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	79.6003	599	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_000745185.1	s__Muricauda sp000745185	79.4768	596	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	79.1174	524	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	79.0754	509	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	79.0176	440	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_007785775.2	s__Muricauda sp003973595	79.0075	499	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003584165.1	s__Muricauda sp003584165	78.9991	515	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584105.1	s__Muricauda taeanensis	78.9299	510	1317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_010468565.1	s__Muricauda sp010468565	78.7133	449	1317	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 13:30:04,747] [INFO] GTDB search result was written to GCF_009184425.1_ASM918442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:04,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:04,752] [INFO] DFAST_QC result json was written to GCF_009184425.1_ASM918442v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:04,753] [INFO] DFAST_QC completed!
[2024-01-24 13:30:04,753] [INFO] Total running time: 0h2m6s