[2024-01-24 14:06:30,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,107] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference
[2024-01-24 14:06:31,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,597] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg8956ad30-805c-47a9-8902-f473ed740adb/GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/cds.fna -a GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:48,562] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:48,563] [INFO] Task started: HMMsearch
[2024-01-24 14:06:48,563] [INFO] Running command: hmmsearch --tblout GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/reference_markers.hmm GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:48,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:48,909] [INFO] Found 6/6 markers.
[2024-01-24 14:06:48,946] [INFO] Query marker FASTA was written to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:48,947] [INFO] Task started: Blastn
[2024-01-24 14:06:48,947] [INFO] Running command: blastn -query GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/reference_markers.fasta -out GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:49,598] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:49,601] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:49,602] [INFO] Target genome list was writen to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:49,626] [INFO] Task started: fastANI
[2024-01-24 14:06:49,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg8956ad30-805c-47a9-8902-f473ed740adb/GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna.gz --refList GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:58,227] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:58,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:58,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:58,237] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:58,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:58,237] [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
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	100.0	1333	1336	95	conclusive
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	99.9866	1298	1336	95	conclusive
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	85.0801	942	1336	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	80.1455	727	1336	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	80.1406	718	1336	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	79.9416	678	1336	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6397	71	1336	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.5298	51	1336	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.9294	68	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,239] [INFO] DFAST Taxonomy check result was written to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:58,239] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:58,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:58,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/checkm_data
[2024-01-24 14:06:58,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:58,294] [INFO] Task started: CheckM
[2024-01-24 14:06:58,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/checkm_input GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:46,523] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:46,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:46,545] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:46,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:46,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:46,547] [INFO] Task started: Blastn
[2024-01-24 14:07:46,547] [INFO] Running command: blastn -query GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ffc1c1-ef44-451f-bf6b-b564be202c9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:47,410] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:47,413] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:47,414] [INFO] Target genome list was writen to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:47,424] [INFO] Task started: fastANI
[2024-01-24 14:07:47,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg8956ad30-805c-47a9-8902-f473ed740adb/GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna.gz --refList GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:53,665] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:53,674] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:53,675] [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_900130045.1	s__Leeuwenhoekiella palythoae	100.0	1333	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	conclusive
GCF_000152985.1	s__Leeuwenhoekiella blandensis	85.0801	942	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	80.1585	716	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	79.9226	681	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.8898	702	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	79.5152	497	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.4356	67	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:53,676] [INFO] GTDB search result was written to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:53,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:53,680] [INFO] DFAST_QC result json was written to GCF_900130045.1_IMG-taxon_2622736499_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:53,680] [INFO] DFAST_QC completed!
[2024-01-24 14:07:53,680] [INFO] Total running time: 0h1m24s