[2024-01-24 13:17:45,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:45,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:45,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference
[2024-01-24 13:17:47,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:47,051] [INFO] Task started: Prodigal
[2024-01-24 13:17:47,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b76aba5-fc3b-4ffc-af3f-518423c36234/GCF_009903685.1_ASM990368v1_genomic.fna.gz | prodigal -d GCF_009903685.1_ASM990368v1_genomic.fna/cds.fna -a GCF_009903685.1_ASM990368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:07,783] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:07,783] [INFO] Task started: HMMsearch
[2024-01-24 13:18:07,783] [INFO] Running command: hmmsearch --tblout GCF_009903685.1_ASM990368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/reference_markers.hmm GCF_009903685.1_ASM990368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:08,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:08,156] [INFO] Found 6/6 markers.
[2024-01-24 13:18:08,204] [INFO] Query marker FASTA was written to GCF_009903685.1_ASM990368v1_genomic.fna/markers.fasta
[2024-01-24 13:18:08,204] [INFO] Task started: Blastn
[2024-01-24 13:18:08,204] [INFO] Running command: blastn -query GCF_009903685.1_ASM990368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/reference_markers.fasta -out GCF_009903685.1_ASM990368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,919] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,923] [INFO] Selected 25 target genomes.
[2024-01-24 13:18:08,923] [INFO] Target genome list was writen to GCF_009903685.1_ASM990368v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:08,931] [INFO] Task started: fastANI
[2024-01-24 13:18:08,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b76aba5-fc3b-4ffc-af3f-518423c36234/GCF_009903685.1_ASM990368v1_genomic.fna.gz --refList GCF_009903685.1_ASM990368v1_genomic.fna/target_genomes.txt --output GCF_009903685.1_ASM990368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:28,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:28,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:28,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:28,353] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:28,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:28,354] [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 ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	100.0	1174	1175	95	conclusive
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	78.1019	330	1175	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	78.0109	316	1175	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.9049	342	1175	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.8153	271	1175	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	77.7174	256	1175	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	77.6785	280	1175	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	77.6768	311	1175	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	77.6768	311	1175	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	77.675	356	1175	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.6463	288	1175	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.6374	256	1175	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	77.6329	271	1175	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.6291	289	1175	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	77.5944	270	1175	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	77.568	304	1175	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.5536	273	1175	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	77.5356	281	1175	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	77.5146	315	1175	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	77.5146	315	1175	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.4959	276	1175	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.4308	249	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:28,355] [INFO] DFAST Taxonomy check result was written to GCF_009903685.1_ASM990368v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:28,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:28,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:28,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/checkm_data
[2024-01-24 13:18:28,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:28,398] [INFO] Task started: CheckM
[2024-01-24 13:18:28,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009903685.1_ASM990368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009903685.1_ASM990368v1_genomic.fna/checkm_input GCF_009903685.1_ASM990368v1_genomic.fna/checkm_result
[2024-01-24 13:19:28,379] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:28,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:28,423] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:28,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:28,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009903685.1_ASM990368v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:28,424] [INFO] Task started: Blastn
[2024-01-24 13:19:28,425] [INFO] Running command: blastn -query GCF_009903685.1_ASM990368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8054cd4-e2d8-4d34-9cb7-4d6ebb1cdbf0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009903685.1_ASM990368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:29,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:29,459] [INFO] Selected 24 target genomes.
[2024-01-24 13:19:29,460] [INFO] Target genome list was writen to GCF_009903685.1_ASM990368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:29,486] [INFO] Task started: fastANI
[2024-01-24 13:19:29,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b76aba5-fc3b-4ffc-af3f-518423c36234/GCF_009903685.1_ASM990368v1_genomic.fna.gz --refList GCF_009903685.1_ASM990368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009903685.1_ASM990368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:46,559] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:46,579] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:46,579] [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_009903685.1	s__Muricauda ochracea	100.0	1174	1175	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_004916895.1	s__Muricauda alvinocaridis	78.0155	315	1175	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	77.9433	357	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003382275.1	s__Muricauda nanhaiensis	77.8945	343	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745185.1	s__Muricauda sp000745185	77.8585	367	1175	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	77.8299	272	1175	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	77.797	335	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_017313225.1	s__Muricauda sp017313225	77.7418	385	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	77.7306	269	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	77.7033	259	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	77.6964	287	1175	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	77.6828	355	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003584135.1	s__Muricauda sp003584135	77.6768	311	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.6575	287	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004804315.1	s__Muricauda sp004804315	77.6406	255	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407935.1	s__Muricauda sp013407935	77.5704	268	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_003992615.1	s__Muricauda beolgyonensis	77.568	304	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	77.5536	273	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	77.5168	314	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002813125.1	s__Muricauda sp002813125	77.5001	271	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222835.1	s__Muricauda sp018222835	77.4973	235	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	77.4594	242	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	77.4308	249	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413955.1	s__Muricauda eckloniae	77.3436	278	1175	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 13:19:46,581] [INFO] GTDB search result was written to GCF_009903685.1_ASM990368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:46,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:46,591] [INFO] DFAST_QC result json was written to GCF_009903685.1_ASM990368v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:46,592] [INFO] DFAST_QC completed!
[2024-01-24 13:19:46,592] [INFO] Total running time: 0h2m1s