[2023-06-18 10:25:30,622] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:30,625] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:30,625] [INFO] DQC Reference Directory: /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference
[2023-06-18 10:25:31,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:31,994] [INFO] Task started: Prodigal
[2023-06-18 10:25:31,994] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9ad041d-07d9-41a2-b44c-d87f2591baf9/GCA_018609965.1_ASM1860996v1_genomic.fna.gz | prodigal -d GCA_018609965.1_ASM1860996v1_genomic.fna/cds.fna -a GCA_018609965.1_ASM1860996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:45,441] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:45,441] [INFO] Task started: HMMsearch
[2023-06-18 10:25:45,441] [INFO] Running command: hmmsearch --tblout GCA_018609965.1_ASM1860996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/reference_markers.hmm GCA_018609965.1_ASM1860996v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:45,664] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:45,666] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd9ad041d-07d9-41a2-b44c-d87f2591baf9/GCA_018609965.1_ASM1860996v1_genomic.fna.gz]
[2023-06-18 10:25:45,726] [INFO] Query marker FASTA was written to GCA_018609965.1_ASM1860996v1_genomic.fna/markers.fasta
[2023-06-18 10:25:45,727] [INFO] Task started: Blastn
[2023-06-18 10:25:45,727] [INFO] Running command: blastn -query GCA_018609965.1_ASM1860996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/reference_markers.fasta -out GCA_018609965.1_ASM1860996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:46,266] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:46,271] [INFO] Selected 14 target genomes.
[2023-06-18 10:25:46,271] [INFO] Target genome list was writen to GCA_018609965.1_ASM1860996v1_genomic.fna/target_genomes.txt
[2023-06-18 10:25:46,274] [INFO] Task started: fastANI
[2023-06-18 10:25:46,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ad041d-07d9-41a2-b44c-d87f2591baf9/GCA_018609965.1_ASM1860996v1_genomic.fna.gz --refList GCA_018609965.1_ASM1860996v1_genomic.fna/target_genomes.txt --output GCA_018609965.1_ASM1860996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:25:55,458] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:55,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:25:55,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:25:55,472] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:25:55,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 10:25:55,472] [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
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	77.6931	255	713	95	below_threshold
Halobaculum roseum	strain=CGMCC 1.15501	GCA_019880245.1	2175149	2175149	type	True	77.5924	278	713	95	below_threshold
Halobaculum salinum	strain=NJ-3-1	GCA_013402875.1	2743089	2743089	type	True	77.5495	253	713	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	77.4603	284	713	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	77.3779	224	713	95	below_threshold
Halorubrum salinum	strain=GX71	GCA_024494575.1	767517	767517	type	True	77.1213	168	713	95	below_threshold
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	76.9863	196	713	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	76.8309	165	713	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	76.7899	199	713	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	76.7264	152	713	95	below_threshold
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	76.6944	139	713	95	below_threshold
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	76.6563	131	713	95	below_threshold
Halorientalis persicus	strain=IBRC-M 10043	GCA_900110215.1	1367881	1367881	type	True	76.6504	168	713	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	76.6031	178	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:25:55,477] [INFO] DFAST Taxonomy check result was written to GCA_018609965.1_ASM1860996v1_genomic.fna/tc_result.tsv
[2023-06-18 10:25:55,478] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:25:55,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:25:55,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/checkm_data
[2023-06-18 10:25:55,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:25:55,515] [INFO] Task started: CheckM
[2023-06-18 10:25:55,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018609965.1_ASM1860996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018609965.1_ASM1860996v1_genomic.fna/checkm_input GCA_018609965.1_ASM1860996v1_genomic.fna/checkm_result
[2023-06-18 10:26:36,139] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:36,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:36,170] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:36,170] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:36,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018609965.1_ASM1860996v1_genomic.fna/markers.fasta)
[2023-06-18 10:26:36,171] [INFO] Task started: Blastn
[2023-06-18 10:26:36,171] [INFO] Running command: blastn -query GCA_018609965.1_ASM1860996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0dcef71-1e57-44de-991b-b30c14411f37/dqc_reference/reference_markers_gtdb.fasta -out GCA_018609965.1_ASM1860996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:36,678] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:36,683] [INFO] Selected 11 target genomes.
[2023-06-18 10:26:36,683] [INFO] Target genome list was writen to GCA_018609965.1_ASM1860996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:36,755] [INFO] Task started: fastANI
[2023-06-18 10:26:36,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ad041d-07d9-41a2-b44c-d87f2591baf9/GCA_018609965.1_ASM1860996v1_genomic.fna.gz --refList GCA_018609965.1_ASM1860996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018609965.1_ASM1860996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:26:43,691] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:43,713] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:26:43,713] [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
GCA_018609965.1	s__Halobaculum sp018609965	100.0	699	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003020945.1	s__Halobaculum sp003020945	78.0545	268	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013402875.1	s__Halobaculum sp013402875	77.5361	254	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831625.1	s__Halobaculum sp009831625	77.4595	284	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336875.1	s__Halorubrum californiense	77.1909	221	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_001462205.1	s__Haloparvum sedimenti	77.1236	218	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloparvum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252755.1	s__Halorubrum sp002252755	76.8943	224	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.78	98.49	0.85	0.82	5	-
GCF_900102305.1	s__Halorientalis regularis	76.8602	161	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022005.1	s__QS-5-70-15 sp003022005	76.6708	145	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-5-70-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110215.1	s__Halorientalis persicus	76.6497	168	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021085.1	s__PXRE01 sp003021085	76.4088	138	713	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__PXRE01;g__PXRE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:26:43,717] [INFO] GTDB search result was written to GCA_018609965.1_ASM1860996v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:26:43,719] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:26:43,722] [INFO] DFAST_QC result json was written to GCA_018609965.1_ASM1860996v1_genomic.fna/dqc_result.json
[2023-06-18 10:26:43,723] [INFO] DFAST_QC completed!
[2023-06-18 10:26:43,723] [INFO] Total running time: 0h1m13s