[2024-01-25 19:52:50,796] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:50,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:50,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference
[2024-01-25 19:52:51,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:51,939] [INFO] Task started: Prodigal
[2024-01-25 19:52:51,939] [INFO] Running command: gunzip -c /var/lib/cwl/stga2137b11-ca89-485a-b313-312cdefe665c/GCF_009733865.1_ASM973386v1_genomic.fna.gz | prodigal -d GCF_009733865.1_ASM973386v1_genomic.fna/cds.fna -a GCF_009733865.1_ASM973386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:59,816] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:59,816] [INFO] Task started: HMMsearch
[2024-01-25 19:52:59,816] [INFO] Running command: hmmsearch --tblout GCF_009733865.1_ASM973386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/reference_markers.hmm GCF_009733865.1_ASM973386v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:00,068] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:00,070] [INFO] Found 6/6 markers.
[2024-01-25 19:53:00,101] [INFO] Query marker FASTA was written to GCF_009733865.1_ASM973386v1_genomic.fna/markers.fasta
[2024-01-25 19:53:00,102] [INFO] Task started: Blastn
[2024-01-25 19:53:00,102] [INFO] Running command: blastn -query GCF_009733865.1_ASM973386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/reference_markers.fasta -out GCF_009733865.1_ASM973386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:00,667] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:00,669] [INFO] Selected 22 target genomes.
[2024-01-25 19:53:00,670] [INFO] Target genome list was writen to GCF_009733865.1_ASM973386v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:00,679] [INFO] Task started: fastANI
[2024-01-25 19:53:00,679] [INFO] Running command: fastANI --query /var/lib/cwl/stga2137b11-ca89-485a-b313-312cdefe665c/GCF_009733865.1_ASM973386v1_genomic.fna.gz --refList GCF_009733865.1_ASM973386v1_genomic.fna/target_genomes.txt --output GCF_009733865.1_ASM973386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:17,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:17,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:17,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:17,238] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:17,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:17,238] [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 salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	100.0	1403	1407	95	conclusive
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	78.7043	456	1407	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	78.3327	395	1407	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.8295	201	1407	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.645	288	1407	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.3425	196	1407	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.3272	197	1407	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.253	200	1407	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.2426	135	1407	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.165	138	1407	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.165	172	1407	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.1367	54	1407	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.1168	126	1407	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.0698	133	1407	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	76.9124	162	1407	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.8198	139	1407	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.6727	98	1407	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.6513	72	1407	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.6461	89	1407	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.5092	87	1407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:17,239] [INFO] DFAST Taxonomy check result was written to GCF_009733865.1_ASM973386v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:17,240] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:17,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:17,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/checkm_data
[2024-01-25 19:53:17,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:17,283] [INFO] Task started: CheckM
[2024-01-25 19:53:17,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733865.1_ASM973386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733865.1_ASM973386v1_genomic.fna/checkm_input GCF_009733865.1_ASM973386v1_genomic.fna/checkm_result
[2024-01-25 19:53:44,273] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:44,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:44,291] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:44,291] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:44,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733865.1_ASM973386v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:44,292] [INFO] Task started: Blastn
[2024-01-25 19:53:44,292] [INFO] Running command: blastn -query GCF_009733865.1_ASM973386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52016466-a3fc-4cb0-bb79-35ec468fe517/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733865.1_ASM973386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:45,019] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:45,022] [INFO] Selected 21 target genomes.
[2024-01-25 19:53:45,022] [INFO] Target genome list was writen to GCF_009733865.1_ASM973386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:45,038] [INFO] Task started: fastANI
[2024-01-25 19:53:45,038] [INFO] Running command: fastANI --query /var/lib/cwl/stga2137b11-ca89-485a-b313-312cdefe665c/GCF_009733865.1_ASM973386v1_genomic.fna.gz --refList GCF_009733865.1_ASM973386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733865.1_ASM973386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:01,702] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:01,714] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:01,715] [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_009733865.1	s__Oceanobacillus salinisoli	100.0	1403	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003628505.1	s__Oceanobacillus halophilus	78.7242	453	1407	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_001659985.1	s__Oceanobacillus sp001659985	78.5033	346	1407	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_016908155.1	s__Oceanobacillus caeni	78.4579	322	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_900176885.1	s__Oceanobacillus senegalensis	78.3602	393	1407	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	77.8199	202	1407	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_003628445.1	s__Oceanobacillus bengalensis	77.6873	285	1407	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_003515705.1	s__Oceanobacillus profundus	77.3159	197	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_002153375.1	s__Oceanobacillus rekensis	77.2794	198	1407	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_009728145.1	s__Ornithinibacillus caprae	77.2571	177	1407	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_014905415.1	s__Virgibacillus salexigens	77.207	134	1407	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_003337485.1	s__Saliterribacillus persicus	77.1841	53	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369575.1	s__Oceanobacillus arenosus	77.1386	170	1407	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_000011245.1	s__Oceanobacillus iheyensis	77.1168	126	1407	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_001310895.1	s__Virgibacillus halodenitrificans	77.033	135	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	-
GCF_900187325.1	s__Virgibacillus_E ndiopensis	76.8674	165	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612345.1	s__Virgibacillus sp003612345	76.7576	112	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
GCF_016908325.1	s__Aquibacillus albus	76.6005	92	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.5126	146	1407	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:01,718] [INFO] GTDB search result was written to GCF_009733865.1_ASM973386v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:01,720] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:01,723] [INFO] DFAST_QC result json was written to GCF_009733865.1_ASM973386v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:01,723] [INFO] DFAST_QC completed!
[2024-01-25 19:54:01,723] [INFO] Total running time: 0h1m11s