[2024-01-24 13:28:19,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference
[2024-01-24 13:28:20,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,489] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8889f1f-6eab-42d9-b702-4b609a8bb0a0/GCF_021556485.1_ASM2155648v1_genomic.fna.gz | prodigal -d GCF_021556485.1_ASM2155648v1_genomic.fna/cds.fna -a GCF_021556485.1_ASM2155648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:28,830] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:28,830] [INFO] Task started: HMMsearch
[2024-01-24 13:28:28,831] [INFO] Running command: hmmsearch --tblout GCF_021556485.1_ASM2155648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/reference_markers.hmm GCF_021556485.1_ASM2155648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:29,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:29,088] [INFO] Found 6/6 markers.
[2024-01-24 13:28:29,124] [INFO] Query marker FASTA was written to GCF_021556485.1_ASM2155648v1_genomic.fna/markers.fasta
[2024-01-24 13:28:29,124] [INFO] Task started: Blastn
[2024-01-24 13:28:29,124] [INFO] Running command: blastn -query GCF_021556485.1_ASM2155648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/reference_markers.fasta -out GCF_021556485.1_ASM2155648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:29,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:29,724] [INFO] Selected 27 target genomes.
[2024-01-24 13:28:29,725] [INFO] Target genome list was writen to GCF_021556485.1_ASM2155648v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:29,736] [INFO] Task started: fastANI
[2024-01-24 13:28:29,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8889f1f-6eab-42d9-b702-4b609a8bb0a0/GCF_021556485.1_ASM2155648v1_genomic.fna.gz --refList GCF_021556485.1_ASM2155648v1_genomic.fna/target_genomes.txt --output GCF_021556485.1_ASM2155648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:51,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:51,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:51,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:51,199] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:51,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:51,200] [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 alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	100.0	1216	1217	95	conclusive
Oceanobacillus indicireducens	strain=JCM 17251	GCA_014647195.1	1004261	1004261	type	True	85.4787	855	1217	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	78.1463	82	1217	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.4195	67	1217	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.2088	104	1217	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.0023	88	1217	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.9903	83	1217	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	76.9699	93	1217	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	76.9469	103	1217	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	76.8775	116	1217	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	76.6224	90	1217	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.5909	107	1217	95	below_threshold
Lentibacillus sediminis	strain=0W14	GCA_002763455.1	1940529	1940529	type	True	76.4718	54	1217	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	76.4576	57	1217	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	76.3653	85	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:51,201] [INFO] DFAST Taxonomy check result was written to GCF_021556485.1_ASM2155648v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:51,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:51,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:51,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/checkm_data
[2024-01-24 13:28:51,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:51,244] [INFO] Task started: CheckM
[2024-01-24 13:28:51,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021556485.1_ASM2155648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021556485.1_ASM2155648v1_genomic.fna/checkm_input GCF_021556485.1_ASM2155648v1_genomic.fna/checkm_result
[2024-01-24 13:29:21,455] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:21,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:21,481] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:21,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:21,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021556485.1_ASM2155648v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:21,482] [INFO] Task started: Blastn
[2024-01-24 13:29:21,483] [INFO] Running command: blastn -query GCF_021556485.1_ASM2155648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e595ffe-3e33-4291-8e33-86a1ab1cbe5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021556485.1_ASM2155648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:22,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:22,281] [INFO] Selected 28 target genomes.
[2024-01-24 13:29:22,282] [INFO] Target genome list was writen to GCF_021556485.1_ASM2155648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:22,309] [INFO] Task started: fastANI
[2024-01-24 13:29:22,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8889f1f-6eab-42d9-b702-4b609a8bb0a0/GCF_021556485.1_ASM2155648v1_genomic.fna.gz --refList GCF_021556485.1_ASM2155648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021556485.1_ASM2155648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:41,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:41,334] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:41,335] [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_014647195.1	s__Oceanobacillus indicireducens	85.4971	854	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	97.29	97.29	0.83	0.83	2	-
GCF_000340475.1	s__Oceanobacillus kimchii	78.1198	82	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	77.4184	68	1217	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_000725285.1	s__Virgibacillus sp000725285	77.3672	72	1217	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_003352005.1	s__Oceanobacillus zhaokaii	77.2117	112	1217	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_014637405.1	s__Ornithinibacillus halotolerans	76.9916	83	1217	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_002266285.1	s__Virgibacillus_G indicus	76.9815	108	1217	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_000011245.1	s__Oceanobacillus iheyensis	76.9732	89	1217	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	76.9707	92	1217	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_002287375.1	s__Virgibacillus_G profundi	76.9014	104	1217	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_003628445.1	s__Oceanobacillus bengalensis	76.879	117	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	76.846	93	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_900162665.1	s__Oceanobacillus sojae_A	76.7396	88	1217	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	76.6572	93	1217	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	76.6134	113	1217	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	76.5336	110	1217	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_002763455.1	s__Lentibacillus_A sediminis	76.5112	53	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.4523	68	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_001307805.1	s__Lentibacillus amyloliquefaciens	76.3943	60	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991515.1	s__Oceanobacillus sojae	76.3653	85	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.95	98.95	0.93	0.93	2	-
GCF_019093865.1	s__Lentibacillus_B saliphilus	76.3374	51	1217	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,336] [INFO] GTDB search result was written to GCF_021556485.1_ASM2155648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:41,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:41,341] [INFO] DFAST_QC result json was written to GCF_021556485.1_ASM2155648v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:41,341] [INFO] DFAST_QC completed!
[2024-01-24 13:29:41,341] [INFO] Total running time: 0h1m22s