[2024-01-24 13:49:39,900] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:39,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:39,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference
[2024-01-24 13:49:41,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,206] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg14e3b3be-7373-477b-a761-15cec2902226/GCF_003710915.1_ASM371091v1_genomic.fna.gz | prodigal -d GCF_003710915.1_ASM371091v1_genomic.fna/cds.fna -a GCF_003710915.1_ASM371091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,091] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,091] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,091] [INFO] Running command: hmmsearch --tblout GCF_003710915.1_ASM371091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/reference_markers.hmm GCF_003710915.1_ASM371091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:55,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:55,458] [INFO] Found 6/6 markers.
[2024-01-24 13:49:55,506] [INFO] Query marker FASTA was written to GCF_003710915.1_ASM371091v1_genomic.fna/markers.fasta
[2024-01-24 13:49:55,506] [INFO] Task started: Blastn
[2024-01-24 13:49:55,506] [INFO] Running command: blastn -query GCF_003710915.1_ASM371091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/reference_markers.fasta -out GCF_003710915.1_ASM371091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,184] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:56,185] [INFO] Target genome list was writen to GCF_003710915.1_ASM371091v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:56,193] [INFO] Task started: fastANI
[2024-01-24 13:49:56,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e3b3be-7373-477b-a761-15cec2902226/GCF_003710915.1_ASM371091v1_genomic.fna.gz --refList GCF_003710915.1_ASM371091v1_genomic.fna/target_genomes.txt --output GCF_003710915.1_ASM371091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:15,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:15,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:15,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:15,580] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:15,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:15,581] [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 invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	100.0	1537	1539	95	conclusive
Brevibacillus panacihumi	strain=JCM 15085	GCA_003710985.1	497735	497735	type	True	80.8455	835	1539	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	79.2171	509	1539	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	79.0174	508	1539	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	78.9666	414	1539	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	78.9461	412	1539	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	78.9036	447	1539	95	below_threshold
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	78.8956	472	1539	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	78.8667	444	1539	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	78.8124	485	1539	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	78.7809	496	1539	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	78.7803	478	1539	95	below_threshold
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	78.7602	436	1539	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	78.7327	481	1539	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	78.6837	465	1539	95	below_threshold
Brevibacillus reuszeri	strain=NBRC 15719	GCA_006540225.1	54915	54915	type	True	78.6668	465	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,582] [INFO] DFAST Taxonomy check result was written to GCF_003710915.1_ASM371091v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:15,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:15,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:15,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/checkm_data
[2024-01-24 13:50:15,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:15,630] [INFO] Task started: CheckM
[2024-01-24 13:50:15,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710915.1_ASM371091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710915.1_ASM371091v1_genomic.fna/checkm_input GCF_003710915.1_ASM371091v1_genomic.fna/checkm_result
[2024-01-24 13:50:59,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:59,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:59,441] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:59,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:59,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710915.1_ASM371091v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:59,442] [INFO] Task started: Blastn
[2024-01-24 13:50:59,442] [INFO] Running command: blastn -query GCF_003710915.1_ASM371091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg058f3d50-835f-48a6-8423-7e2a122a633f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710915.1_ASM371091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,374] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,378] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:00,378] [INFO] Target genome list was writen to GCF_003710915.1_ASM371091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,417] [INFO] Task started: fastANI
[2024-01-24 13:51:00,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e3b3be-7373-477b-a761-15cec2902226/GCF_003710915.1_ASM371091v1_genomic.fna.gz --refList GCF_003710915.1_ASM371091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710915.1_ASM371091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:21,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:21,686] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:21,687] [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_003710915.1	s__Brevibacillus invocatus	100.0	1537	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000503775.1	s__Brevibacillus panacihumi_A	81.123	856	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710985.1	s__Brevibacillus panacihumi	80.85	834	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.2324	494	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420695.1	s__Brevibacillus choshinensis	79.211	508	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	79.0368	500	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_003710815.1	s__Brevibacillus centrosporus	79.0176	529	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_001039275.2	s__Brevibacillus brevis_C	78.9883	448	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_005217615.1	s__Brevibacillus antibioticus	78.9666	414	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013475.1	s__Brevibacillus porteri	78.9572	411	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_900637055.1	s__Brevibacillus brevis	78.9036	447	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_001187725.1	s__Brevibacillus reuszeri	78.8956	472	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004117055.1	s__Brevibacillus agri	78.8035	486	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_013284355.1	s__Brevibacillus sp013284355	78.7856	427	1539	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	78.7505	479	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003710935.1	s__Brevibacillus gelatini	78.7394	423	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282075.1	s__Brevibacillus sp000282075	78.6589	430	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_003013405.1	s__Brevibacillus formosus	78.6331	449	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:21,688] [INFO] GTDB search result was written to GCF_003710915.1_ASM371091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:21,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:21,692] [INFO] DFAST_QC result json was written to GCF_003710915.1_ASM371091v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:21,692] [INFO] DFAST_QC completed!
[2024-01-24 13:51:21,693] [INFO] Total running time: 0h1m42s