[2024-01-24 11:43:42,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,229] [INFO] DQC Reference Directory: /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference
[2024-01-24 11:43:43,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,729] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg026367d1-9451-43b6-a4b1-3a9b6f8de5fd/GCF_003337485.1_ASM333748v1_genomic.fna.gz | prodigal -d GCF_003337485.1_ASM333748v1_genomic.fna/cds.fna -a GCF_003337485.1_ASM333748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:50,829] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:50,829] [INFO] Task started: HMMsearch
[2024-01-24 11:43:50,829] [INFO] Running command: hmmsearch --tblout GCF_003337485.1_ASM333748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/reference_markers.hmm GCF_003337485.1_ASM333748v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,198] [INFO] Found 6/6 markers.
[2024-01-24 11:43:51,232] [INFO] Query marker FASTA was written to GCF_003337485.1_ASM333748v1_genomic.fna/markers.fasta
[2024-01-24 11:43:51,232] [INFO] Task started: Blastn
[2024-01-24 11:43:51,232] [INFO] Running command: blastn -query GCF_003337485.1_ASM333748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/reference_markers.fasta -out GCF_003337485.1_ASM333748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:51,910] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:51,916] [INFO] Selected 26 target genomes.
[2024-01-24 11:43:51,916] [INFO] Target genome list was writen to GCF_003337485.1_ASM333748v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:51,935] [INFO] Task started: fastANI
[2024-01-24 11:43:51,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg026367d1-9451-43b6-a4b1-3a9b6f8de5fd/GCF_003337485.1_ASM333748v1_genomic.fna.gz --refList GCF_003337485.1_ASM333748v1_genomic.fna/target_genomes.txt --output GCF_003337485.1_ASM333748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:11,289] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:11,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:11,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:11,303] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:11,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:11,304] [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
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	100.0	1232	1234	95	conclusive
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.5579	95	1234	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.3818	99	1234	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.3047	143	1234	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.3037	207	1234	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.2757	142	1234	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	77.2618	183	1234	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	77.1325	186	1234	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	77.0648	203	1234	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	77.0564	189	1234	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.0537	213	1234	95	below_threshold
Amphibacillus sediminis	strain=NBRC 103570	GCA_001552275.1	360185	360185	type	True	77.0512	56	1234	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.9719	120	1234	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	76.9244	57	1234	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.7351	125	1234	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.5461	55	1234	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.5055	79	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:11,306] [INFO] DFAST Taxonomy check result was written to GCF_003337485.1_ASM333748v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:11,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:11,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:11,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/checkm_data
[2024-01-24 11:44:11,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:11,353] [INFO] Task started: CheckM
[2024-01-24 11:44:11,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337485.1_ASM333748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337485.1_ASM333748v1_genomic.fna/checkm_input GCF_003337485.1_ASM333748v1_genomic.fna/checkm_result
[2024-01-24 11:44:40,626] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:40,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:40,651] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:40,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:40,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337485.1_ASM333748v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:40,653] [INFO] Task started: Blastn
[2024-01-24 11:44:40,653] [INFO] Running command: blastn -query GCF_003337485.1_ASM333748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg866bf392-bd75-4568-ad53-ac10e9941de5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337485.1_ASM333748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:41,667] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:41,672] [INFO] Selected 26 target genomes.
[2024-01-24 11:44:41,672] [INFO] Target genome list was writen to GCF_003337485.1_ASM333748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:41,691] [INFO] Task started: fastANI
[2024-01-24 11:44:41,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg026367d1-9451-43b6-a4b1-3a9b6f8de5fd/GCF_003337485.1_ASM333748v1_genomic.fna.gz --refList GCF_003337485.1_ASM333748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337485.1_ASM333748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:57,831] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:57,853] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:57,853] [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_003337485.1	s__Saliterribacillus persicus	100.0	1232	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001458115.1	s__Gracilibacillus massiliensis	77.55	212	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.441	104	1234	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_014083865.1	s__Paraliobacillus salinarum	77.3731	101	1234	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_009650095.1	s__Gracilibacillus sp002797295	77.3037	207	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_014280935.1	s__HU2P27 sp014280935	77.2589	142	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599345.1	s__Gracilibacillus sp017599345	77.2328	186	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007301515.1	s__Radiobacillus deserti	77.1997	84	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821065.1	s__Oceanobacillus oncorhynchi	77.1839	52	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.79	98.49	0.90	0.88	3	-
GCF_900114645.1	s__Gracilibacillus orientalis	77.1581	197	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.1221	82	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	77.0529	213	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_001552275.1	s__Amphibacillus_B sediminis	77.0512	56	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908325.1	s__Aquibacillus albus	76.9719	120	1234	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_003665065.1	s__Oceanobacillus piezotolerans	76.9244	57	1234	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_001038485.1	s__Ornithinibacillus californiensis	76.9059	67	1234	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_014207435.1	s__Salirhabdus euzebyi	76.7597	67	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005870085.1	s__BH258 sp005870085	76.7351	125	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.6657	70	1234	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_010993955.1	s__YIM-98839 sp010993955	76.5327	78	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515705.1	s__Oceanobacillus profundus	76.5107	80	1234	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_009183415.1	s__Niallia sp009183415	75.8588	66	1234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:57,855] [INFO] GTDB search result was written to GCF_003337485.1_ASM333748v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:57,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:57,862] [INFO] DFAST_QC result json was written to GCF_003337485.1_ASM333748v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:57,863] [INFO] DFAST_QC completed!
[2024-01-24 11:44:57,863] [INFO] Total running time: 0h1m16s