[2024-01-24 13:40:55,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference
[2024-01-24 13:40:56,447] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,448] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2403274-b0f7-4064-9d91-a04d7f9a2e3e/GCF_010882125.1_ASM1088212v1_genomic.fna.gz | prodigal -d GCF_010882125.1_ASM1088212v1_genomic.fna/cds.fna -a GCF_010882125.1_ASM1088212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:04,615] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:04,615] [INFO] Task started: HMMsearch
[2024-01-24 13:41:04,615] [INFO] Running command: hmmsearch --tblout GCF_010882125.1_ASM1088212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/reference_markers.hmm GCF_010882125.1_ASM1088212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:04,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:04,957] [INFO] Found 6/6 markers.
[2024-01-24 13:41:04,991] [INFO] Query marker FASTA was written to GCF_010882125.1_ASM1088212v1_genomic.fna/markers.fasta
[2024-01-24 13:41:04,991] [INFO] Task started: Blastn
[2024-01-24 13:41:04,992] [INFO] Running command: blastn -query GCF_010882125.1_ASM1088212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/reference_markers.fasta -out GCF_010882125.1_ASM1088212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:05,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:05,545] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:05,545] [INFO] Target genome list was writen to GCF_010882125.1_ASM1088212v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:05,552] [INFO] Task started: fastANI
[2024-01-24 13:41:05,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2403274-b0f7-4064-9d91-a04d7f9a2e3e/GCF_010882125.1_ASM1088212v1_genomic.fna.gz --refList GCF_010882125.1_ASM1088212v1_genomic.fna/target_genomes.txt --output GCF_010882125.1_ASM1088212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,809] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:22,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:22,810] [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
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	100.0	1451	1454	95	conclusive
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	83.866	920	1454	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	78.8382	154	1454	95	below_threshold
Peribacillus cavernae	strain=L5	GCA_003989135.1	1674310	1674310	type	True	77.6512	103	1454	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	77.6368	68	1454	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.6285	94	1454	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	77.5788	69	1454	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	77.489	96	1454	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.4597	139	1454	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.4351	122	1454	95	below_threshold
Bacillus massiliglaciei	strain=Marseille-P2600	GCA_900098925.1	1816693	1816693	type	True	77.352	86	1454	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	77.3198	66	1454	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	77.2792	90	1454	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.1567	109	1454	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.0499	108	1454	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.9902	74	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,811] [INFO] DFAST Taxonomy check result was written to GCF_010882125.1_ASM1088212v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/checkm_data
[2024-01-24 13:41:22,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:22,857] [INFO] Task started: CheckM
[2024-01-24 13:41:22,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010882125.1_ASM1088212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010882125.1_ASM1088212v1_genomic.fna/checkm_input GCF_010882125.1_ASM1088212v1_genomic.fna/checkm_result
[2024-01-24 13:41:50,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:50,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,897] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:50,898] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:50,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010882125.1_ASM1088212v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:50,898] [INFO] Task started: Blastn
[2024-01-24 13:41:50,898] [INFO] Running command: blastn -query GCF_010882125.1_ASM1088212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e73042-f8f2-473a-bc45-f6aa0bf5d531/dqc_reference/reference_markers_gtdb.fasta -out GCF_010882125.1_ASM1088212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,656] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,659] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:51,659] [INFO] Target genome list was writen to GCF_010882125.1_ASM1088212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,671] [INFO] Task started: fastANI
[2024-01-24 13:41:51,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2403274-b0f7-4064-9d91-a04d7f9a2e3e/GCF_010882125.1_ASM1088212v1_genomic.fna.gz --refList GCF_010882125.1_ASM1088212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010882125.1_ASM1088212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:13,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,042] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:13,043] [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_010882125.1	s__Bacillus_BN alkalitolerans	100.0	1451	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003073175.1	s__Bacillus_BN acanthi	83.866	920	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343665.1	s__Cytobacillus sp018343665	80.0084	175	1454	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_007995155.1	s__Cytobacillus dafuensis	78.8653	152	1454	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_016908835.1	s__Bacillus_AD endoradicis	78.6028	129	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039215.1	s__Cytobacillus sp019039215	77.9582	123	1454	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_001866655.1	s__Neobacillus sp001866655	77.9445	132	1454	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_014217835.1	s__Metabacillus litoralis_A	77.8302	126	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_008923245.1	s__Cytobacillus depressus	77.796	145	1454	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_018613065.1	s__Neobacillus sp018613065	77.7277	140	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_001510645.1	s__Peribacillus sp001510645	77.6828	148	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003989135.1	s__Peribacillus cavernae	77.6801	102	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	77.4135	94	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940785.1	s__Neobacillus sp001940785	77.3858	93	1454	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_900098925.1	s__Peribacillus massiliglaciei	77.3519	86	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001636495.1	s__Sutcliffiella_A horikoshii_A	77.3444	78	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	77.3411	90	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_001889165.1	s__Metabacillus weihaiensis	77.2824	90	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_900156865.1	s__Fredinandcohnia sinesaloumensis	77.2623	98	1454	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_902829255.1	s__Metabacillus niabensis	77.1536	83	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_013179555.1	s__Rossellomorea haikouensis_A	77.073	64	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	77.0597	114	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_014656545.1	s__Neobacillus sp014656545	77.0499	108	1454	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_002250055.1	s__Sutcliffiella cohnii	76.7512	94	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_007679095.1	s__DE0126 sp007679095	76.6041	63	1454	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,044] [INFO] GTDB search result was written to GCF_010882125.1_ASM1088212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:13,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:13,048] [INFO] DFAST_QC result json was written to GCF_010882125.1_ASM1088212v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:13,048] [INFO] DFAST_QC completed!
[2024-01-24 13:42:13,048] [INFO] Total running time: 0h1m18s