[2024-01-24 13:57:32,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference
[2024-01-24 13:57:33,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,336] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,337] [INFO] Running command: gunzip -c /var/lib/cwl/stgb29606cf-5186-4d67-80b9-f84d00a2c80c/GCF_007995155.1_ASM799515v1_genomic.fna.gz | prodigal -d GCF_007995155.1_ASM799515v1_genomic.fna/cds.fna -a GCF_007995155.1_ASM799515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:43,851] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:43,851] [INFO] Task started: HMMsearch
[2024-01-24 13:57:43,852] [INFO] Running command: hmmsearch --tblout GCF_007995155.1_ASM799515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/reference_markers.hmm GCF_007995155.1_ASM799515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:44,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:44,229] [INFO] Found 6/6 markers.
[2024-01-24 13:57:44,296] [INFO] Query marker FASTA was written to GCF_007995155.1_ASM799515v1_genomic.fna/markers.fasta
[2024-01-24 13:57:44,296] [INFO] Task started: Blastn
[2024-01-24 13:57:44,296] [INFO] Running command: blastn -query GCF_007995155.1_ASM799515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/reference_markers.fasta -out GCF_007995155.1_ASM799515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:44,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:44,956] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:44,956] [INFO] Target genome list was writen to GCF_007995155.1_ASM799515v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:44,963] [INFO] Task started: fastANI
[2024-01-24 13:57:44,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgb29606cf-5186-4d67-80b9-f84d00a2c80c/GCF_007995155.1_ASM799515v1_genomic.fna.gz --refList GCF_007995155.1_ASM799515v1_genomic.fna/target_genomes.txt --output GCF_007995155.1_ASM799515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:07,153] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:07,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:07,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:07,170] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:07,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:07,170] [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
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	100.0	1633	1638	95	conclusive
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	79.6079	586	1638	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	79.3386	565	1638	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	78.8155	549	1638	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	78.8135	105	1638	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	78.6979	267	1638	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	78.358	426	1638	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.303	171	1638	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	78.1373	139	1638	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	78.0115	188	1638	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.9754	239	1638	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.8176	165	1638	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	77.6481	234	1638	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	77.5244	165	1638	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	77.3051	133	1638	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	77.2893	181	1638	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.2628	175	1638	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	77.0394	163	1638	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	77.0119	133	1638	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6494	141	1638	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.3466	105	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:07,172] [INFO] DFAST Taxonomy check result was written to GCF_007995155.1_ASM799515v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:07,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:07,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:07,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/checkm_data
[2024-01-24 13:58:07,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:07,220] [INFO] Task started: CheckM
[2024-01-24 13:58:07,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995155.1_ASM799515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995155.1_ASM799515v1_genomic.fna/checkm_input GCF_007995155.1_ASM799515v1_genomic.fna/checkm_result
[2024-01-24 13:58:44,347] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:44,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:44,377] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:44,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:44,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995155.1_ASM799515v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:44,378] [INFO] Task started: Blastn
[2024-01-24 13:58:44,378] [INFO] Running command: blastn -query GCF_007995155.1_ASM799515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21adb6da-1123-4418-bfae-b86fdf2020c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995155.1_ASM799515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:45,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:45,182] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:45,182] [INFO] Target genome list was writen to GCF_007995155.1_ASM799515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:45,200] [INFO] Task started: fastANI
[2024-01-24 13:58:45,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgb29606cf-5186-4d67-80b9-f84d00a2c80c/GCF_007995155.1_ASM799515v1_genomic.fna.gz --refList GCF_007995155.1_ASM799515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995155.1_ASM799515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:06,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,082] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:06,082] [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_007995155.1	s__Cytobacillus dafuensis	100.0	1636	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_018343665.1	s__Cytobacillus sp018343665	93.119	1306	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274725.1	s__Cytobacillus globisporus	80.2361	317	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923245.1	s__Cytobacillus depressus	79.6161	585	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	79.3658	569	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_001509555.1	s__Cytobacillus sp001509555	79.2062	600	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	79.0218	507	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039215.1	s__Cytobacillus sp019039215	78.9788	511	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	78.8159	550	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_017874625.1	s__Cytobacillus eiseniae	78.3768	423	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008855.1	s__Bacillus_BT aquiflavi	77.3051	133	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016765675.1	s__Neobacillus sp016765675	77.2574	115	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.0527	121	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836495.1	s__Cytobacillus sp014836495	77.0394	163	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,084] [INFO] GTDB search result was written to GCF_007995155.1_ASM799515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:06,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:06,090] [INFO] DFAST_QC result json was written to GCF_007995155.1_ASM799515v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:06,090] [INFO] DFAST_QC completed!
[2024-01-24 13:59:06,091] [INFO] Total running time: 0h1m34s