[2024-01-24 13:32:14,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:14,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:14,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference
[2024-01-24 13:32:16,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:16,233] [INFO] Task started: Prodigal
[2024-01-24 13:32:16,234] [INFO] Running command: gunzip -c /var/lib/cwl/stged78cd70-a529-405f-bc56-74f84dbf1ff3/GCF_003963515.1_ASM396351v1_genomic.fna.gz | prodigal -d GCF_003963515.1_ASM396351v1_genomic.fna/cds.fna -a GCF_003963515.1_ASM396351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:28,743] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:28,743] [INFO] Task started: HMMsearch
[2024-01-24 13:32:28,743] [INFO] Running command: hmmsearch --tblout GCF_003963515.1_ASM396351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/reference_markers.hmm GCF_003963515.1_ASM396351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:29,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:29,057] [INFO] Found 6/6 markers.
[2024-01-24 13:32:29,094] [INFO] Query marker FASTA was written to GCF_003963515.1_ASM396351v1_genomic.fna/markers.fasta
[2024-01-24 13:32:29,095] [INFO] Task started: Blastn
[2024-01-24 13:32:29,095] [INFO] Running command: blastn -query GCF_003963515.1_ASM396351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/reference_markers.fasta -out GCF_003963515.1_ASM396351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,728] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,731] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:29,732] [INFO] Target genome list was writen to GCF_003963515.1_ASM396351v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:29,740] [INFO] Task started: fastANI
[2024-01-24 13:32:29,740] [INFO] Running command: fastANI --query /var/lib/cwl/stged78cd70-a529-405f-bc56-74f84dbf1ff3/GCF_003963515.1_ASM396351v1_genomic.fna.gz --refList GCF_003963515.1_ASM396351v1_genomic.fna/target_genomes.txt --output GCF_003963515.1_ASM396351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:49,923] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:49,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:49,947] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:49,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:49,947] [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
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	100.0	1359	1359	95	conclusive
Tumebacillus avium	strain=AR23208	GCA_002162355.1	1903704	1903704	type	True	78.441	60	1359	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	78.3502	81	1359	95	below_threshold
Brevibacillus composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	78.1655	208	1359	95	below_threshold
Brevibacillus massiliensis	strain=phR	GCA_000311785.1	1118054	1118054	type	True	77.4372	217	1359	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.3111	71	1359	95	below_threshold
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	76.8327	91	1359	95	below_threshold
Brevibacillus fulvus	strain=DSM 25523	GCA_016908525.1	1125967	1125967	type	True	76.7376	101	1359	95	below_threshold
Brevibacillus migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	76.6462	116	1359	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	76.6406	124	1359	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.4191	54	1359	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	76.2313	126	1359	95	below_threshold
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	76.1333	84	1359	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	75.814	67	1359	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	75.6806	65	1359	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	75.6547	61	1359	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	75.1764	66	1359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,950] [INFO] DFAST Taxonomy check result was written to GCF_003963515.1_ASM396351v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:49,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:49,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:49,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/checkm_data
[2024-01-24 13:32:49,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:49,997] [INFO] Task started: CheckM
[2024-01-24 13:32:49,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003963515.1_ASM396351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003963515.1_ASM396351v1_genomic.fna/checkm_input GCF_003963515.1_ASM396351v1_genomic.fna/checkm_result
[2024-01-24 13:33:30,698] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:30,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:30,719] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:30,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:30,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003963515.1_ASM396351v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:30,720] [INFO] Task started: Blastn
[2024-01-24 13:33:30,720] [INFO] Running command: blastn -query GCF_003963515.1_ASM396351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf120a4a6-3a13-4f8e-9b3e-36650dc465ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003963515.1_ASM396351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:31,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:31,591] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:31,592] [INFO] Target genome list was writen to GCF_003963515.1_ASM396351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:31,638] [INFO] Task started: fastANI
[2024-01-24 13:33:31,639] [INFO] Running command: fastANI --query /var/lib/cwl/stged78cd70-a529-405f-bc56-74f84dbf1ff3/GCF_003963515.1_ASM396351v1_genomic.fna.gz --refList GCF_003963515.1_ASM396351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003963515.1_ASM396351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:47,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:47,305] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:47,305] [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_003963515.1	s__SCSIO-07484 sp003963515	100.0	1359	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__SCSIO-07484	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017656235.1	s__SCSIO-07484 sp017656235	78.6706	434	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__SCSIO-07484	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454065.1	s__Brevibacillus thermoruber	78.4959	326	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_011059135.1	s__CFH-S0501 sp011059135	78.3131	263	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__CFH-S0501	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228725.1	s__Brevibacillus sp018228725	78.2091	210	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002243345.2	s__Paenibacillus_O sp002243345	78.139	55	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCF_013096935.1	s__Brevibacillus sp003388715	77.9208	284	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	77.9043	103	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311785.1	s__Brevibacillus_C massiliensis	77.4557	215	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_C	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003710915.1	s__Brevibacillus invocatus	76.8335	91	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908525.1	s__Brevibacillus fulvus	76.7376	101	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710905.1	s__Brevibacillus parabrevis	76.724	124	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	76.3145	54	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCA_002159085.1	s__Thermobacillus sp002159085	75.9592	60	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	75.7937	66	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	75.6085	64	1359	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:47,307] [INFO] GTDB search result was written to GCF_003963515.1_ASM396351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:47,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:47,311] [INFO] DFAST_QC result json was written to GCF_003963515.1_ASM396351v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:47,311] [INFO] DFAST_QC completed!
[2024-01-24 13:33:47,311] [INFO] Total running time: 0h1m32s