[2024-01-24 13:40:00,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:00,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:00,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference
[2024-01-24 13:40:01,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,456] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ab33d72-fbe0-4f3b-a7d6-0a99c5268937/GCF_000340475.1_ASM34047v1_genomic.fna.gz | prodigal -d GCF_000340475.1_ASM34047v1_genomic.fna/cds.fna -a GCF_000340475.1_ASM34047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:08,958] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:08,959] [INFO] Task started: HMMsearch
[2024-01-24 13:40:08,959] [INFO] Running command: hmmsearch --tblout GCF_000340475.1_ASM34047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/reference_markers.hmm GCF_000340475.1_ASM34047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:09,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:09,243] [INFO] Found 6/6 markers.
[2024-01-24 13:40:09,276] [INFO] Query marker FASTA was written to GCF_000340475.1_ASM34047v1_genomic.fna/markers.fasta
[2024-01-24 13:40:09,276] [INFO] Task started: Blastn
[2024-01-24 13:40:09,276] [INFO] Running command: blastn -query GCF_000340475.1_ASM34047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/reference_markers.fasta -out GCF_000340475.1_ASM34047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:09,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:09,877] [INFO] Selected 24 target genomes.
[2024-01-24 13:40:09,877] [INFO] Target genome list was writen to GCF_000340475.1_ASM34047v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:09,893] [INFO] Task started: fastANI
[2024-01-24 13:40:09,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab33d72-fbe0-4f3b-a7d6-0a99c5268937/GCF_000340475.1_ASM34047v1_genomic.fna.gz --refList GCF_000340475.1_ASM34047v1_genomic.fna/target_genomes.txt --output GCF_000340475.1_ASM34047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:24,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:24,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:24,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:24,633] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:24,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:24,633] [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
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	100.0	1276	1276	95	conclusive
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	88.6926	1056	1276	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	78.7406	187	1276	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.5502	206	1276	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	78.2957	58	1276	95	below_threshold
Oceanobacillus jeddahense	strain=S5	GCA_000750635.1	1462527	1462527	type	True	77.8946	230	1276	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.618	141	1276	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.5446	183	1276	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	77.5367	199	1276	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	77.3919	188	1276	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.2861	121	1276	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.1683	132	1276	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.7292	76	1276	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	76.1335	68	1276	95	below_threshold
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	76.0613	67	1276	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	75.7608	63	1276	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	75.7409	63	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:24,635] [INFO] DFAST Taxonomy check result was written to GCF_000340475.1_ASM34047v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:24,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:24,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:24,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/checkm_data
[2024-01-24 13:40:24,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:24,679] [INFO] Task started: CheckM
[2024-01-24 13:40:24,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340475.1_ASM34047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340475.1_ASM34047v1_genomic.fna/checkm_input GCF_000340475.1_ASM34047v1_genomic.fna/checkm_result
[2024-01-24 13:40:53,460] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:53,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,484] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:53,485] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:53,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340475.1_ASM34047v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:53,485] [INFO] Task started: Blastn
[2024-01-24 13:40:53,486] [INFO] Running command: blastn -query GCF_000340475.1_ASM34047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623dc5f5-62ec-4141-b63c-542a3668d3cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340475.1_ASM34047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:54,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:54,304] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:54,304] [INFO] Target genome list was writen to GCF_000340475.1_ASM34047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:54,314] [INFO] Task started: fastANI
[2024-01-24 13:40:54,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab33d72-fbe0-4f3b-a7d6-0a99c5268937/GCF_000340475.1_ASM34047v1_genomic.fna.gz --refList GCF_000340475.1_ASM34047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000340475.1_ASM34047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:10,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,509] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:10,510] [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_000340475.1	s__Oceanobacillus kimchii	100.0	1276	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	conclusive
GCF_000011245.1	s__Oceanobacillus iheyensis	88.6926	1056	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008304605.1	s__Oceanobacillus polygoni	78.5069	207	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900166625.1	s__Halobacillus_A massiliensis	78.4289	58	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162665.1	s__Oceanobacillus sojae_A	77.9562	191	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000750635.1	s__Oceanobacillus jeddahense	77.9109	226	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018333215.1	s__Oceanobacillus sp018333215	77.7494	231	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618145.1	s__Oceanobacillus damuensis	77.6393	142	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	77.6111	129	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153375.1	s__Oceanobacillus rekensis	77.5572	184	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645515.1	s__Oceanobacillus neutriphilus	77.5067	201	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009389585.1	s__Oceanobacillus sp009389585	77.4465	202	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905415.1	s__Virgibacillus salexigens	77.4452	163	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_018333235.1	s__Ornithinibacillus bavariensis	77.3007	101	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.1683	132	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.1495	147	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	76.7592	117	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	76.7292	76	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202495.1	s__Cerasibacillus quisquiliarum	76.1335	68	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908835.1	s__Bacillus_AD endoradicis	75.9515	65	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254155.1	s__Psychrobacillus insolitus	75.6747	55	1276	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,512] [INFO] GTDB search result was written to GCF_000340475.1_ASM34047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:10,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:10,517] [INFO] DFAST_QC result json was written to GCF_000340475.1_ASM34047v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:10,518] [INFO] DFAST_QC completed!
[2024-01-24 13:41:10,518] [INFO] Total running time: 0h1m10s