[2024-01-25 19:57:05,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,560] [INFO] DQC Reference Directory: /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference
[2024-01-25 19:57:06,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,807] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg77d83743-f4a3-4a8d-936b-9b052a2e3850/GCF_031954365.1_ASM3195436v1_genomic.fna.gz | prodigal -d GCF_031954365.1_ASM3195436v1_genomic.fna/cds.fna -a GCF_031954365.1_ASM3195436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:18,011] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:18,011] [INFO] Task started: HMMsearch
[2024-01-25 19:57:18,011] [INFO] Running command: hmmsearch --tblout GCF_031954365.1_ASM3195436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/reference_markers.hmm GCF_031954365.1_ASM3195436v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:18,297] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:18,298] [INFO] Found 6/6 markers.
[2024-01-25 19:57:18,338] [INFO] Query marker FASTA was written to GCF_031954365.1_ASM3195436v1_genomic.fna/markers.fasta
[2024-01-25 19:57:18,338] [INFO] Task started: Blastn
[2024-01-25 19:57:18,338] [INFO] Running command: blastn -query GCF_031954365.1_ASM3195436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/reference_markers.fasta -out GCF_031954365.1_ASM3195436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:18,907] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:18,910] [INFO] Selected 21 target genomes.
[2024-01-25 19:57:18,910] [INFO] Target genome list was writen to GCF_031954365.1_ASM3195436v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:18,923] [INFO] Task started: fastANI
[2024-01-25 19:57:18,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d83743-f4a3-4a8d-936b-9b052a2e3850/GCF_031954365.1_ASM3195436v1_genomic.fna.gz --refList GCF_031954365.1_ASM3195436v1_genomic.fna/target_genomes.txt --output GCF_031954365.1_ASM3195436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:37,862] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:37,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:37,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:37,872] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:57:37,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:57:37,873] [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 gelatini	strain=DSM 100115	GCA_003710935.1	1655277	1655277	type	True	79.1637	486	1361	95	below_threshold
Brevibacillus composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	78.6115	477	1361	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	78.3924	431	1361	95	below_threshold
Brevibacillus borstelensis	strain=NRRL NRS 818	GCA_003710865.1	45462	45462	type	True	78.3882	488	1361	95	below_threshold
Brevibacillus borstelensis	strain=NBRC 15714	GCA_006540165.1	45462	45462	type	True	78.3563	486	1361	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	78.3314	433	1361	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	78.3135	429	1361	95	below_threshold
Brevibacillus panacihumi	strain=JCM 15085	GCA_003710985.1	497735	497735	type	True	77.8926	326	1361	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	77.658	391	1361	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	77.6284	381	1361	95	below_threshold
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	77.5882	292	1361	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	77.5872	281	1361	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	77.4305	250	1361	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	77.4276	308	1361	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	75.8182	59	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:37,874] [INFO] DFAST Taxonomy check result was written to GCF_031954365.1_ASM3195436v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:37,875] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:37,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:37,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/checkm_data
[2024-01-25 19:57:37,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:37,917] [INFO] Task started: CheckM
[2024-01-25 19:57:37,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031954365.1_ASM3195436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031954365.1_ASM3195436v1_genomic.fna/checkm_input GCF_031954365.1_ASM3195436v1_genomic.fna/checkm_result
[2024-01-25 19:58:12,650] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:12,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:12,668] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:12,668] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:12,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031954365.1_ASM3195436v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:12,669] [INFO] Task started: Blastn
[2024-01-25 19:58:12,669] [INFO] Running command: blastn -query GCF_031954365.1_ASM3195436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcddf22e0-df71-45b5-9c4b-cad0e9701d3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_031954365.1_ASM3195436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:13,457] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:13,459] [INFO] Selected 13 target genomes.
[2024-01-25 19:58:13,460] [INFO] Target genome list was writen to GCF_031954365.1_ASM3195436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:13,475] [INFO] Task started: fastANI
[2024-01-25 19:58:13,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d83743-f4a3-4a8d-936b-9b052a2e3850/GCF_031954365.1_ASM3195436v1_genomic.fna.gz --refList GCF_031954365.1_ASM3195436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031954365.1_ASM3195436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:26,568] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:26,577] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:26,577] [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_013096935.1	s__Brevibacillus sp003388715	99.467	1222	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	conclusive
GCF_000454065.1	s__Brevibacillus thermoruber	92.1767	1120	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_003710935.1	s__Brevibacillus gelatini	79.1919	483	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228725.1	s__Brevibacillus sp018228725	78.6252	473	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_011059135.1	s__CFH-S0501 sp011059135	78.4333	356	1361	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_003710865.1	s__Brevibacillus borstelensis	78.4072	487	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.53	99.39	0.94	0.92	8	-
GCF_004117055.1	s__Brevibacillus agri	78.3263	433	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_003710985.1	s__Brevibacillus panacihumi	77.9168	323	1361	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	77.6758	387	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003963515.1	s__SCSIO-07484 sp003963515	77.5886	292	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__SCSIO-07484	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656235.1	s__SCSIO-07484 sp017656235	77.4143	260	1361	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_002897295.1	s__Brevibacillus reuszeri_A	77.3297	252	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_015845845.1	s__Paenibacillus_B dendritiformis_C	75.9516	64	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:26,578] [INFO] GTDB search result was written to GCF_031954365.1_ASM3195436v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:26,579] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:26,582] [INFO] DFAST_QC result json was written to GCF_031954365.1_ASM3195436v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:26,582] [INFO] DFAST_QC completed!
[2024-01-25 19:58:26,582] [INFO] Total running time: 0h1m21s