[2024-01-24 12:16:08,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,179] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference
[2024-01-24 12:16:09,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,551] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,551] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd3f28f7-96f5-4f15-838f-e9d513e68084/GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/cds.fna -a GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:30,555] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:30,555] [INFO] Task started: HMMsearch
[2024-01-24 12:16:30,555] [INFO] Running command: hmmsearch --tblout GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/reference_markers.hmm GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:30,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:30,869] [INFO] Found 6/6 markers.
[2024-01-24 12:16:30,901] [INFO] Query marker FASTA was written to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:16:30,901] [INFO] Task started: Blastn
[2024-01-24 12:16:30,902] [INFO] Running command: blastn -query GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/reference_markers.fasta -out GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,565] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:31,565] [INFO] Target genome list was writen to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:16:31,573] [INFO] Task started: fastANI
[2024-01-24 12:16:31,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd3f28f7-96f5-4f15-838f-e9d513e68084/GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna.gz --refList GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:46,582] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:46,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:46,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:46,598] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:46,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:46,598] [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 zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	100.0	1243	1243	95	conclusive
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	99.9981	1240	1243	95	conclusive
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	80.4554	663	1243	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	80.3461	607	1243	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	80.0055	592	1243	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	79.8887	609	1243	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	79.8842	596	1243	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	79.7249	569	1243	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	79.6845	610	1243	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	79.6344	624	1243	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	79.5838	575	1243	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	79.575	576	1243	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	79.3279	428	1243	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	79.1617	460	1243	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.0257	433	1243	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.88	454	1243	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	78.8242	550	1243	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.975	331	1243	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.666	279	1243	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.4898	237	1243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:46,601] [INFO] DFAST Taxonomy check result was written to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:16:46,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:46,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:46,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/checkm_data
[2024-01-24 12:16:46,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:46,645] [INFO] Task started: CheckM
[2024-01-24 12:16:46,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/checkm_input GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:17:45,883] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:45,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:45,908] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:45,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:45,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:17:45,909] [INFO] Task started: Blastn
[2024-01-24 12:17:45,909] [INFO] Running command: blastn -query GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c613c0-36a7-4ef9-a4c4-25e55fc20771/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:46,830] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:46,834] [INFO] Selected 21 target genomes.
[2024-01-24 12:17:46,834] [INFO] Target genome list was writen to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:46,849] [INFO] Task started: fastANI
[2024-01-24 12:17:46,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd3f28f7-96f5-4f15-838f-e9d513e68084/GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna.gz --refList GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:02,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:02,625] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:02,626] [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_900102925.1	s__Muricauda zhangzhouensis	100.0	1243	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017313275.1	s__Muricauda lutimaris_A	80.4554	663	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	80.3461	607	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_011068285.1	s__Muricauda sp011068285	80.0055	592	1243	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	79.9297	635	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCA_002167435.2	s__Muricauda sp002167435	79.7447	621	1243	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	79.6859	612	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	79.6523	618	1243	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	79.6506	622	1243	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	79.6242	616	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	79.5849	612	1243	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	79.5523	519	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	79.4858	587	1243	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	79.4855	483	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	79.3279	428	1243	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	79.1754	530	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_003058265.1	s__Muricauda sp003058265	79.1617	460	1243	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	78.8869	502	1243	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	78.8554	455	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	78.8242	550	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	77.9849	330	1243	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 12:18:02,627] [INFO] GTDB search result was written to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:02,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:02,632] [INFO] DFAST_QC result json was written to GCF_900102925.1_IMG-taxon_2667527237_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:18:02,632] [INFO] DFAST_QC completed!
[2024-01-24 12:18:02,632] [INFO] Total running time: 0h1m54s