[2024-01-24 12:46:34,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:34,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:34,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference
[2024-01-24 12:46:36,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,153] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6502e40-0cf5-44ad-ad8a-625c750d7cb7/GCF_005502275.1_ASM550227v1_genomic.fna.gz | prodigal -d GCF_005502275.1_ASM550227v1_genomic.fna/cds.fna -a GCF_005502275.1_ASM550227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:46,321] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:46,322] [INFO] Task started: HMMsearch
[2024-01-24 12:46:46,322] [INFO] Running command: hmmsearch --tblout GCF_005502275.1_ASM550227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/reference_markers.hmm GCF_005502275.1_ASM550227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:46,587] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:46,588] [INFO] Found 6/6 markers.
[2024-01-24 12:46:46,632] [INFO] Query marker FASTA was written to GCF_005502275.1_ASM550227v1_genomic.fna/markers.fasta
[2024-01-24 12:46:46,632] [INFO] Task started: Blastn
[2024-01-24 12:46:46,632] [INFO] Running command: blastn -query GCF_005502275.1_ASM550227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/reference_markers.fasta -out GCF_005502275.1_ASM550227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:47,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:47,209] [INFO] Selected 23 target genomes.
[2024-01-24 12:46:47,209] [INFO] Target genome list was writen to GCF_005502275.1_ASM550227v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:47,220] [INFO] Task started: fastANI
[2024-01-24 12:46:47,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6502e40-0cf5-44ad-ad8a-625c750d7cb7/GCF_005502275.1_ASM550227v1_genomic.fna.gz --refList GCF_005502275.1_ASM550227v1_genomic.fna/target_genomes.txt --output GCF_005502275.1_ASM550227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:04,172] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:04,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:04,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:04,189] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:04,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:04,189] [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
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	100.0	1629	1636	95	conclusive
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	81.2581	871	1636	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	79.1527	413	1636	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	79.1304	415	1636	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	78.0793	238	1636	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.6487	165	1636	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.5762	153	1636	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	77.227	51	1636	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.201	127	1636	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1294	92	1636	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.028	122	1636	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	76.9384	108	1636	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.8955	83	1636	95	below_threshold
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	76.8889	110	1636	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.8436	89	1636	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.8237	84	1636	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	76.7876	67	1636	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	76.6899	118	1636	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6258	115	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:04,191] [INFO] DFAST Taxonomy check result was written to GCF_005502275.1_ASM550227v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:04,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:04,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:04,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/checkm_data
[2024-01-24 12:47:04,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:04,246] [INFO] Task started: CheckM
[2024-01-24 12:47:04,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005502275.1_ASM550227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005502275.1_ASM550227v1_genomic.fna/checkm_input GCF_005502275.1_ASM550227v1_genomic.fna/checkm_result
[2024-01-24 12:47:39,747] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:39,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:39,770] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:39,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:39,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005502275.1_ASM550227v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:39,771] [INFO] Task started: Blastn
[2024-01-24 12:47:39,771] [INFO] Running command: blastn -query GCF_005502275.1_ASM550227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6b36a38-dd10-4521-ad2c-19183123c516/dqc_reference/reference_markers_gtdb.fasta -out GCF_005502275.1_ASM550227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,544] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,548] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:40,548] [INFO] Target genome list was writen to GCF_005502275.1_ASM550227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:40,558] [INFO] Task started: fastANI
[2024-01-24 12:47:40,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6502e40-0cf5-44ad-ad8a-625c750d7cb7/GCF_005502275.1_ASM550227v1_genomic.fna.gz --refList GCF_005502275.1_ASM550227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005502275.1_ASM550227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:55,629] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:55,643] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:55,643] [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_005502275.1	s__Robertmurraya siralis	100.0	1629	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	conclusive
GCF_008764295.1	s__Robertmurraya methanolica_A	93.2064	1065	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.93	99.93	0.84	0.82	3	-
GCF_000311725.1	s__Robertmurraya massiliosenegalensis	81.2521	871	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005116465.1	s__Robertmurraya kyonggiensis	79.2022	407	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280205.1	s__Robertmurraya yapensis	79.1366	415	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156875.1	s__Robertmurraya dakarensis	78.0867	240	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.6325	165	1636	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	-
GCF_003586445.1	s__Robertmurraya sp003586445	77.6216	161	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874625.1	s__Cytobacillus eiseniae	77.57	154	1636	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_018613035.1	s__Cytobacillus sp018613035	77.3773	151	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	77.371	152	1636	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_004341175.1	s__Neobacillus sp004341175	77.2489	134	1636	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_004358205.1	s__Neobacillus salipaludis	77.201	127	1636	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_900115925.1	s__CL95 sp900115925	76.9493	106	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013343715.1	s__Mesobacillus_A harenae	76.9087	109	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636315.1	s__Neobacillus mesonae	76.8887	107	1636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_014656545.1	s__Neobacillus sp014656545	76.5677	115	1636	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,645] [INFO] GTDB search result was written to GCF_005502275.1_ASM550227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:55,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:55,649] [INFO] DFAST_QC result json was written to GCF_005502275.1_ASM550227v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:55,649] [INFO] DFAST_QC completed!
[2024-01-24 12:47:55,650] [INFO] Total running time: 0h1m21s