[2024-01-25 17:38:50,750] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference
[2024-01-25 17:38:51,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,939] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgc15dad68-8ec9-4fcc-97af-6ad6b4bc089c/GCF_029028005.1_ASM2902800v1_genomic.fna.gz | prodigal -d GCF_029028005.1_ASM2902800v1_genomic.fna/cds.fna -a GCF_029028005.1_ASM2902800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:00,204] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:00,205] [INFO] Task started: HMMsearch
[2024-01-25 17:39:00,205] [INFO] Running command: hmmsearch --tblout GCF_029028005.1_ASM2902800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/reference_markers.hmm GCF_029028005.1_ASM2902800v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:00,469] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:00,470] [INFO] Found 6/6 markers.
[2024-01-25 17:39:00,507] [INFO] Query marker FASTA was written to GCF_029028005.1_ASM2902800v1_genomic.fna/markers.fasta
[2024-01-25 17:39:00,508] [INFO] Task started: Blastn
[2024-01-25 17:39:00,508] [INFO] Running command: blastn -query GCF_029028005.1_ASM2902800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/reference_markers.fasta -out GCF_029028005.1_ASM2902800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:01,066] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:01,069] [INFO] Selected 26 target genomes.
[2024-01-25 17:39:01,069] [INFO] Target genome list was writen to GCF_029028005.1_ASM2902800v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:01,075] [INFO] Task started: fastANI
[2024-01-25 17:39:01,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15dad68-8ec9-4fcc-97af-6ad6b4bc089c/GCF_029028005.1_ASM2902800v1_genomic.fna.gz --refList GCF_029028005.1_ASM2902800v1_genomic.fna/target_genomes.txt --output GCF_029028005.1_ASM2902800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:19,780] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:19,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:19,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:19,793] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:19,793] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:19,794] [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
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	83.6836	1051	1605	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	80.5647	733	1605	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	77.3942	131	1605	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	77.3477	143	1605	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.3453	194	1605	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.2984	103	1605	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	77.2084	141	1605	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.197	142	1605	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.1835	120	1605	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	77.1115	70	1605	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	77.0264	78	1605	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.9094	99	1605	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.9001	134	1605	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	76.8971	167	1605	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.8798	59	1605	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.8164	128	1605	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.7876	138	1605	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	76.7769	91	1605	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.7628	72	1605	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.5953	112	1605	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.2607	86	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:19,795] [INFO] DFAST Taxonomy check result was written to GCF_029028005.1_ASM2902800v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:19,796] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:19,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:19,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/checkm_data
[2024-01-25 17:39:19,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:19,847] [INFO] Task started: CheckM
[2024-01-25 17:39:19,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029028005.1_ASM2902800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029028005.1_ASM2902800v1_genomic.fna/checkm_input GCF_029028005.1_ASM2902800v1_genomic.fna/checkm_result
[2024-01-25 17:39:48,466] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:48,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:48,487] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:48,487] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:48,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029028005.1_ASM2902800v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:48,488] [INFO] Task started: Blastn
[2024-01-25 17:39:48,488] [INFO] Running command: blastn -query GCF_029028005.1_ASM2902800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b0c138-2bbc-4448-9f26-59b9ff2d68b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_029028005.1_ASM2902800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:49,383] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:49,386] [INFO] Selected 19 target genomes.
[2024-01-25 17:39:49,386] [INFO] Target genome list was writen to GCF_029028005.1_ASM2902800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:49,413] [INFO] Task started: fastANI
[2024-01-25 17:39:49,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15dad68-8ec9-4fcc-97af-6ad6b4bc089c/GCF_029028005.1_ASM2902800v1_genomic.fna.gz --refList GCF_029028005.1_ASM2902800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029028005.1_ASM2902800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:04,856] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:04,868] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:40:04,868] [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_019024285.1	s__Bacillus_BH sp019024285	83.6746	1052	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	80.5586	735	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_017745675.1	s__Bacillus_BH sp017745675	80.4819	687	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	77.4883	136	1605	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_002797325.1	s__Bacillus_S sp002797325	77.4874	115	1605	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_002109385.1	s__Bacillus_L krulwichiae	77.3776	143	1605	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_000787375.1	s__Bacillus_L okhensis	77.3619	130	1605	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_000621445.1	s__Bacillus_AO bogoriensis	77.3481	189	1605	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_002156385.1	s__45385 sp002156385	77.3034	134	1605	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_003184905.1	s__Priestia sp003184905	77.2805	81	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.2743	103	1605	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_001866075.3	s__Anaerobacillus isosaccharinicus	77.2194	141	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262935.1	s__Lottiidibacillus patelloidae	77.0607	75	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_E;f__SA5d-4;g__Lottiidibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	76.9303	134	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	76.8971	167	1605	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.804	138	1605	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_016908835.1	s__Bacillus_AD endoradicis	76.1581	76	1605	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:04,870] [INFO] GTDB search result was written to GCF_029028005.1_ASM2902800v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:04,870] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:04,874] [INFO] DFAST_QC result json was written to GCF_029028005.1_ASM2902800v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:04,874] [INFO] DFAST_QC completed!
[2024-01-25 17:40:04,874] [INFO] Total running time: 0h1m14s