[2024-01-24 13:21:46,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,176] [INFO] DQC Reference Directory: /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference
[2024-01-24 13:21:47,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,498] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,498] [INFO] Running command: gunzip -c /var/lib/cwl/stge0f00a4d-4e45-4b71-a49c-2ccf5572fcdb/GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/cds.fna -a GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,602] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,602] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,602] [INFO] Running command: hmmsearch --tblout GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/reference_markers.hmm GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,898] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,949] [INFO] Query marker FASTA was written to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:09,950] [INFO] Task started: Blastn
[2024-01-24 13:22:09,950] [INFO] Running command: blastn -query GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/reference_markers.fasta -out GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,642] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,645] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:10,645] [INFO] Target genome list was writen to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,685] [INFO] Task started: fastANI
[2024-01-24 13:22:10,686] [INFO] Running command: fastANI --query /var/lib/cwl/stge0f00a4d-4e45-4b71-a49c-2ccf5572fcdb/GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna.gz --refList GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:21,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:21,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:21,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:21,959] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:21,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:21,959] [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 parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	100.0	1471	1472	95	conclusive
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	79.3516	565	1472	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	78.4343	383	1472	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	78.4232	448	1472	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	78.3439	349	1472	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	78.2303	374	1472	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.8588	375	1472	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.7636	317	1472	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.6912	295	1472	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.6859	320	1472	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	77.3949	236	1472	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	77.353	241	1472	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.3022	279	1472	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.4894	115	1472	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3793	71	1472	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.3645	65	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:21,961] [INFO] DFAST Taxonomy check result was written to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:21,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:21,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:21,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/checkm_data
[2024-01-24 13:22:21,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:22,004] [INFO] Task started: CheckM
[2024-01-24 13:22:22,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/checkm_input GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:23,754] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:23,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,775] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:23,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:23,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:23,776] [INFO] Task started: Blastn
[2024-01-24 13:23:23,776] [INFO] Running command: blastn -query GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga88505d9-bdd9-44e7-82f9-eeb1363d8de1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:24,622] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:24,629] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:24,629] [INFO] Target genome list was writen to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:24,672] [INFO] Task started: fastANI
[2024-01-24 13:23:24,673] [INFO] Running command: fastANI --query /var/lib/cwl/stge0f00a4d-4e45-4b71-a49c-2ccf5572fcdb/GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna.gz --refList GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:34,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:34,977] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:34,977] [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_900215465.1	s__Muricauda pacifica_A	100.0	1470	1472	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_014698935.1	s__Muricauda sp014698935	80.2841	656	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	79.3516	565	1472	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	79.2232	528	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	78.9556	496	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	78.9337	550	1472	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	78.5481	453	1472	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	78.3439	349	1472	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	78.2303	374	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.7568	317	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	77.7242	346	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_010468565.1	s__Muricauda sp010468565	77.6595	271	1472	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	77.5279	269	1472	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	77.4063	239	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:34,979] [INFO] GTDB search result was written to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:34,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:34,983] [INFO] DFAST_QC result json was written to GCF_900215465.1_IMG-taxon_2728369489_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:34,983] [INFO] DFAST_QC completed!
[2024-01-24 13:23:34,983] [INFO] Total running time: 0h1m49s