[2024-01-24 14:12:03,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:03,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:03,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference
[2024-01-24 14:12:04,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:04,759] [INFO] Task started: Prodigal
[2024-01-24 14:12:04,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgefc2e3b9-f7cc-4b79-ace8-2e1ebc4dc3ec/GCF_002196895.1_ASM219689v1_genomic.fna.gz | prodigal -d GCF_002196895.1_ASM219689v1_genomic.fna/cds.fna -a GCF_002196895.1_ASM219689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:17,581] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:17,582] [INFO] Task started: HMMsearch
[2024-01-24 14:12:17,582] [INFO] Running command: hmmsearch --tblout GCF_002196895.1_ASM219689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/reference_markers.hmm GCF_002196895.1_ASM219689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:17,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:17,937] [INFO] Found 6/6 markers.
[2024-01-24 14:12:17,989] [INFO] Query marker FASTA was written to GCF_002196895.1_ASM219689v1_genomic.fna/markers.fasta
[2024-01-24 14:12:17,989] [INFO] Task started: Blastn
[2024-01-24 14:12:17,989] [INFO] Running command: blastn -query GCF_002196895.1_ASM219689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/reference_markers.fasta -out GCF_002196895.1_ASM219689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:19,081] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:19,084] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:19,085] [INFO] Target genome list was writen to GCF_002196895.1_ASM219689v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:19,092] [INFO] Task started: fastANI
[2024-01-24 14:12:19,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc2e3b9-f7cc-4b79-ace8-2e1ebc4dc3ec/GCF_002196895.1_ASM219689v1_genomic.fna.gz --refList GCF_002196895.1_ASM219689v1_genomic.fna/target_genomes.txt --output GCF_002196895.1_ASM219689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:32,141] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:32,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:32,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:32,161] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:32,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:32,161] [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
Haematobacter missouriensis	strain=H1892	GCA_002196895.1	366616	366616	type	True	100.0	1373	1382	95	conclusive
Haematobacter missouriensis	strain=CCUG 52307	GCA_000740775.1	366616	366616	type	True	99.9596	1235	1382	95	conclusive
Haematobacter massiliensis	strain=CCUG 47968	GCA_000740795.1	195105	195105	type	True	88.4085	1062	1382	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4839	323	1382	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	78.1789	285	1382	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.09	303	1382	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.0659	282	1382	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	78.0349	343	1382	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.0018	326	1382	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.966	291	1382	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	77.7148	303	1382	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.6458	274	1382	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	77.5443	248	1382	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4698	279	1382	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.4304	248	1382	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	77.3559	263	1382	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.1714	226	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:32,163] [INFO] DFAST Taxonomy check result was written to GCF_002196895.1_ASM219689v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:32,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:32,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:32,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/checkm_data
[2024-01-24 14:12:32,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:32,205] [INFO] Task started: CheckM
[2024-01-24 14:12:32,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002196895.1_ASM219689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002196895.1_ASM219689v1_genomic.fna/checkm_input GCF_002196895.1_ASM219689v1_genomic.fna/checkm_result
[2024-01-24 14:13:12,176] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:12,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:12,195] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:12,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:12,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002196895.1_ASM219689v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:12,197] [INFO] Task started: Blastn
[2024-01-24 14:13:12,197] [INFO] Running command: blastn -query GCF_002196895.1_ASM219689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e0e3b5-8b80-443c-af61-c0a5a31c3ca3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002196895.1_ASM219689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:13,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:13,980] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:13,980] [INFO] Target genome list was writen to GCF_002196895.1_ASM219689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:14,002] [INFO] Task started: fastANI
[2024-01-24 14:13:14,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc2e3b9-f7cc-4b79-ace8-2e1ebc4dc3ec/GCF_002196895.1_ASM219689v1_genomic.fna.gz --refList GCF_002196895.1_ASM219689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002196895.1_ASM219689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:25,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:25,292] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:25,292] [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_000740775.1	s__Haematobacter missouriensis	99.9596	1235	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Haematobacter	95.0	99.82	99.68	0.96	0.95	3	conclusive
GCF_002196855.1	s__Haematobacter sp002196855	93.0584	1137	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Haematobacter	95.0	98.61	98.61	0.86	0.86	2	-
GCF_000740795.1	s__Haematobacter massiliensis	88.4087	1063	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Haematobacter	95.0	99.83	99.63	0.96	0.93	4	-
GCF_001620265.1	s__Frigidibacter mobilis	78.4532	376	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017599285.1	s__Cereibacter_A azotoformans	78.2005	263	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_003993775.1	s__Frigidibacter sp003993775	78.1777	362	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	78.0159	348	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	77.996	306	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCA_008933605.1	s__Albidovulum sp008933605	77.7848	240	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871005.1	s__Acidimangrovimonas sediminis	77.595	299	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	77.5443	248	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	77.5248	287	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	77.5126	268	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	77.4352	199	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249215.1	s__SZUA-611 sp003249215	77.268	254	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551745.1	s__Rhodobaculum sp003551745	76.8858	152	1382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,294] [INFO] GTDB search result was written to GCF_002196895.1_ASM219689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:25,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:25,299] [INFO] DFAST_QC result json was written to GCF_002196895.1_ASM219689v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:25,299] [INFO] DFAST_QC completed!
[2024-01-24 14:13:25,299] [INFO] Total running time: 0h1m22s