[2024-01-24 14:47:19,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference
[2024-01-24 14:47:20,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,307] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a643aae-1ab5-49f5-b5cd-b8016bc40a7b/GCF_003628445.1_ASM362844v1_genomic.fna.gz | prodigal -d GCF_003628445.1_ASM362844v1_genomic.fna/cds.fna -a GCF_003628445.1_ASM362844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:28,257] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:28,257] [INFO] Task started: HMMsearch
[2024-01-24 14:47:28,258] [INFO] Running command: hmmsearch --tblout GCF_003628445.1_ASM362844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/reference_markers.hmm GCF_003628445.1_ASM362844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:28,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:28,557] [INFO] Found 6/6 markers.
[2024-01-24 14:47:28,592] [INFO] Query marker FASTA was written to GCF_003628445.1_ASM362844v1_genomic.fna/markers.fasta
[2024-01-24 14:47:28,593] [INFO] Task started: Blastn
[2024-01-24 14:47:28,593] [INFO] Running command: blastn -query GCF_003628445.1_ASM362844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/reference_markers.fasta -out GCF_003628445.1_ASM362844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:29,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:29,221] [INFO] Selected 26 target genomes.
[2024-01-24 14:47:29,221] [INFO] Target genome list was writen to GCF_003628445.1_ASM362844v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:29,235] [INFO] Task started: fastANI
[2024-01-24 14:47:29,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a643aae-1ab5-49f5-b5cd-b8016bc40a7b/GCF_003628445.1_ASM362844v1_genomic.fna.gz --refList GCF_003628445.1_ASM362844v1_genomic.fna/target_genomes.txt --output GCF_003628445.1_ASM362844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:49,591] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:49,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:49,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:49,614] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:49,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:49,615] [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 bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	100.0	1302	1305	95	conclusive
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	78.541	131	1305	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	78.0872	308	1305	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	77.9975	249	1305	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.9232	261	1305	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.8129	211	1305	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.8061	271	1305	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.6312	227	1305	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.623	204	1305	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.4231	175	1305	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.2868	204	1305	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.1541	200	1305	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.0509	158	1305	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	76.5087	54	1305	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.4992	67	1305	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.4443	82	1305	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.4359	81	1305	95	below_threshold
Gracilibacillus dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	76.391	86	1305	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	76.0804	53	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:49,617] [INFO] DFAST Taxonomy check result was written to GCF_003628445.1_ASM362844v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:49,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:49,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:49,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/checkm_data
[2024-01-24 14:47:49,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:49,680] [INFO] Task started: CheckM
[2024-01-24 14:47:49,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628445.1_ASM362844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628445.1_ASM362844v1_genomic.fna/checkm_input GCF_003628445.1_ASM362844v1_genomic.fna/checkm_result
[2024-01-24 14:48:20,575] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:20,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:20,604] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:20,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:20,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628445.1_ASM362844v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:20,606] [INFO] Task started: Blastn
[2024-01-24 14:48:20,606] [INFO] Running command: blastn -query GCF_003628445.1_ASM362844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0d2575-42c8-4874-8710-48f050925cd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628445.1_ASM362844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:21,487] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:21,490] [INFO] Selected 24 target genomes.
[2024-01-24 14:48:21,490] [INFO] Target genome list was writen to GCF_003628445.1_ASM362844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:21,511] [INFO] Task started: fastANI
[2024-01-24 14:48:21,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a643aae-1ab5-49f5-b5cd-b8016bc40a7b/GCF_003628445.1_ASM362844v1_genomic.fna.gz --refList GCF_003628445.1_ASM362844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628445.1_ASM362844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:41,077] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:41,102] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:41,102] [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_003628445.1	s__Oceanobacillus bengalensis	100.0	1302	1305	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_001659985.1	s__Oceanobacillus sp001659985	78.3523	272	1305	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_003628505.1	s__Oceanobacillus halophilus	78.0778	307	1305	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_003665065.1	s__Oceanobacillus piezotolerans	78.0393	247	1305	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_900176885.1	s__Oceanobacillus senegalensis	77.9584	262	1305	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_009733865.1	s__Oceanobacillus salinisoli	77.7999	271	1305	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	77.7629	213	1305	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_003369565.1	s__Oceanobacillus chungangensis	77.623	204	1305	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_003352005.1	s__Oceanobacillus zhaokaii	77.6139	228	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_900111445.1	s__Ornithinibacillus limi	77.2786	159	1305	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_002287375.1	s__Virgibacillus_G profundi	77.2328	208	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.2121	165	1305	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_002153375.1	s__Oceanobacillus rekensis	77.1119	204	1305	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_900129485.1	s__Ornithinibacillus halophilus	77.1011	162	1305	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_000725285.1	s__Virgibacillus sp000725285	77.0134	154	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	76.8453	64	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_001420595.1	s__Cytobacillus solani	76.6417	68	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_006861825.1	s__Psychrobacillus vulpis	76.518	55	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003176895.1	s__Gracilibacillus dipsosauri	76.3854	85	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_001278755.1	s__Psychrobacillus sp001278755	76.0967	54	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
GCF_001591505.1	s__Neobacillus niacini	76.0804	53	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013396335.1	s__Neobacillus sp013396335	75.9882	51	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:41,105] [INFO] GTDB search result was written to GCF_003628445.1_ASM362844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:41,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:41,112] [INFO] DFAST_QC result json was written to GCF_003628445.1_ASM362844v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:41,112] [INFO] DFAST_QC completed!
[2024-01-24 14:48:41,112] [INFO] Total running time: 0h1m22s