[2024-01-24 15:02:45,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:45,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:45,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference
[2024-01-24 15:02:46,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:46,854] [INFO] Task started: Prodigal
[2024-01-24 15:02:46,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg1650b776-0784-48d3-806b-299b424ab48e/GCF_002156385.1_ASM215638v1_genomic.fna.gz | prodigal -d GCF_002156385.1_ASM215638v1_genomic.fna/cds.fna -a GCF_002156385.1_ASM215638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:56,227] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:56,227] [INFO] Task started: HMMsearch
[2024-01-24 15:02:56,227] [INFO] Running command: hmmsearch --tblout GCF_002156385.1_ASM215638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/reference_markers.hmm GCF_002156385.1_ASM215638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:56,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:56,565] [INFO] Found 6/6 markers.
[2024-01-24 15:02:56,607] [INFO] Query marker FASTA was written to GCF_002156385.1_ASM215638v1_genomic.fna/markers.fasta
[2024-01-24 15:02:56,608] [INFO] Task started: Blastn
[2024-01-24 15:02:56,608] [INFO] Running command: blastn -query GCF_002156385.1_ASM215638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/reference_markers.fasta -out GCF_002156385.1_ASM215638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:57,411] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:57,414] [INFO] Selected 26 target genomes.
[2024-01-24 15:02:57,415] [INFO] Target genome list was writen to GCF_002156385.1_ASM215638v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:57,440] [INFO] Task started: fastANI
[2024-01-24 15:02:57,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg1650b776-0784-48d3-806b-299b424ab48e/GCF_002156385.1_ASM215638v1_genomic.fna.gz --refList GCF_002156385.1_ASM215638v1_genomic.fna/target_genomes.txt --output GCF_002156385.1_ASM215638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:14,649] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:14,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:14,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:14,669] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:14,669] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:14,669] [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
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.7211	197	1512	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.4025	212	1512	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	78.3117	196	1512	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	78.2753	142	1512	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	78.1045	141	1512	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.095	218	1512	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.9169	172	1512	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.8715	225	1512	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.7557	162	1512	95	below_threshold
Halalkalibacterium ligniniphilum	strain=L1	GCA_000334155.1	1134413	1134413	type	True	77.6992	147	1512	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	77.6539	67	1512	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	77.5358	165	1512	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_000513115.1	127886	127886	type	True	77.5004	167	1512	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	77.2749	151	1512	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	76.9654	135	1512	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	76.945	63	1512	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.8147	54	1512	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.0434	59	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:14,673] [INFO] DFAST Taxonomy check result was written to GCF_002156385.1_ASM215638v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:14,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:14,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:14,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/checkm_data
[2024-01-24 15:03:14,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:14,735] [INFO] Task started: CheckM
[2024-01-24 15:03:14,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156385.1_ASM215638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156385.1_ASM215638v1_genomic.fna/checkm_input GCF_002156385.1_ASM215638v1_genomic.fna/checkm_result
[2024-01-24 15:03:49,602] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:49,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:49,619] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:49,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:49,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156385.1_ASM215638v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:49,621] [INFO] Task started: Blastn
[2024-01-24 15:03:49,621] [INFO] Running command: blastn -query GCF_002156385.1_ASM215638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb4c83f-57f5-4f3a-9e78-17dc59f8a2c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156385.1_ASM215638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:50,463] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:50,466] [INFO] Selected 22 target genomes.
[2024-01-24 15:03:50,467] [INFO] Target genome list was writen to GCF_002156385.1_ASM215638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:50,482] [INFO] Task started: fastANI
[2024-01-24 15:03:50,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg1650b776-0784-48d3-806b-299b424ab48e/GCF_002156385.1_ASM215638v1_genomic.fna.gz --refList GCF_002156385.1_ASM215638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156385.1_ASM215638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:10,862] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:10,882] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:10,883] [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_002156385.1	s__45385 sp002156385	99.9943	1509	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002797395.1	s__45385 sp002797395	79.5414	456	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	78.7874	189	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	78.7116	198	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002797325.1	s__Bacillus_S sp002797325	78.5387	169	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787375.1	s__Bacillus_L okhensis	78.4291	209	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	78.0996	138	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.0854	219	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335805.1	s__FJAT-45350 sp002335805	77.986	145	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.9248	173	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	77.9022	222	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.7532	161	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_000334155.1	s__Bacillus_AN ligniniphilus	77.6992	147	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734215.1	s__Fredinandcohnia onubensis	77.6539	67	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.2265	146	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001310555.1	s__JCM-19058 sp001310555	76.9668	90	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__JCM-19058	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007293315.1	s__Alkalihalobacillus_A sp007293315	76.9509	83	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285535.1	s__Fredinandcohnia timonensis	76.5773	71	1512	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:10,885] [INFO] GTDB search result was written to GCF_002156385.1_ASM215638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:10,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:10,894] [INFO] DFAST_QC result json was written to GCF_002156385.1_ASM215638v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:10,894] [INFO] DFAST_QC completed!
[2024-01-24 15:04:10,894] [INFO] Total running time: 0h1m26s