[2024-01-24 13:40:31,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:31,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:31,830] [INFO] DQC Reference Directory: /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference
[2024-01-24 13:40:33,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:33,099] [INFO] Task started: Prodigal
[2024-01-24 13:40:33,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbbe6602-528a-43b9-b19b-0df09d284e11/GCF_004104045.1_ASM410404v1_genomic.fna.gz | prodigal -d GCF_004104045.1_ASM410404v1_genomic.fna/cds.fna -a GCF_004104045.1_ASM410404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,236] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,236] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,236] [INFO] Running command: hmmsearch --tblout GCF_004104045.1_ASM410404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/reference_markers.hmm GCF_004104045.1_ASM410404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,558] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,591] [INFO] Query marker FASTA was written to GCF_004104045.1_ASM410404v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,592] [INFO] Task started: Blastn
[2024-01-24 13:40:49,592] [INFO] Running command: blastn -query GCF_004104045.1_ASM410404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/reference_markers.fasta -out GCF_004104045.1_ASM410404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,305] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:50,306] [INFO] Target genome list was writen to GCF_004104045.1_ASM410404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,312] [INFO] Task started: fastANI
[2024-01-24 13:40:50,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbe6602-528a-43b9-b19b-0df09d284e11/GCF_004104045.1_ASM410404v1_genomic.fna.gz --refList GCF_004104045.1_ASM410404v1_genomic.fna/target_genomes.txt --output GCF_004104045.1_ASM410404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,870] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,881] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:58,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:58,881] [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=LMG 24856	GCA_004104045.1	573501	573501	type	True	100.0	1303	1303	95	conclusive
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	99.9941	1300	1303	95	conclusive
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	85.0103	934	1303	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	80.0368	724	1303	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	80.035	716	1303	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	79.86	684	1303	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0897	51	1303	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.6493	51	1303	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.1032	64	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,883] [INFO] DFAST Taxonomy check result was written to GCF_004104045.1_ASM410404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/checkm_data
[2024-01-24 13:40:58,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,931] [INFO] Task started: CheckM
[2024-01-24 13:40:58,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104045.1_ASM410404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104045.1_ASM410404v1_genomic.fna/checkm_input GCF_004104045.1_ASM410404v1_genomic.fna/checkm_result
[2024-01-24 13:41:47,659] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:47,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,682] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:47,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:47,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104045.1_ASM410404v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:47,683] [INFO] Task started: Blastn
[2024-01-24 13:41:47,683] [INFO] Running command: blastn -query GCF_004104045.1_ASM410404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7cd84bd-00b1-4d52-aa14-5dc017d71b69/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104045.1_ASM410404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:48,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:48,567] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:48,567] [INFO] Target genome list was writen to GCF_004104045.1_ASM410404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:48,572] [INFO] Task started: fastANI
[2024-01-24 13:41:48,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbe6602-528a-43b9-b19b-0df09d284e11/GCF_004104045.1_ASM410404v1_genomic.fna.gz --refList GCF_004104045.1_ASM410404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104045.1_ASM410404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:54,842] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:54,854] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:54,854] [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	99.9941	1300	1303	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	85.0285	932	1303	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	80.0273	717	1303	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	79.8564	684	1303	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	79.76	712	1303	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	79.1105	482	1303	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	76.4096	66	1303	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 13:41:54,856] [INFO] GTDB search result was written to GCF_004104045.1_ASM410404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:54,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:54,860] [INFO] DFAST_QC result json was written to GCF_004104045.1_ASM410404v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:54,861] [INFO] DFAST_QC completed!
[2024-01-24 13:41:54,861] [INFO] Total running time: 0h1m23s