[2024-01-25 18:57:05,646] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:05,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:05,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference
[2024-01-25 18:57:06,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:06,773] [INFO] Task started: Prodigal
[2024-01-25 18:57:06,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg86e77568-b674-41e6-b0a6-9462f632833d/GCF_014836615.1_ASM1483661v1_genomic.fna.gz | prodigal -d GCF_014836615.1_ASM1483661v1_genomic.fna/cds.fna -a GCF_014836615.1_ASM1483661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:14,552] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:14,553] [INFO] Task started: HMMsearch
[2024-01-25 18:57:14,553] [INFO] Running command: hmmsearch --tblout GCF_014836615.1_ASM1483661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/reference_markers.hmm GCF_014836615.1_ASM1483661v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:14,782] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:14,783] [INFO] Found 6/6 markers.
[2024-01-25 18:57:14,813] [INFO] Query marker FASTA was written to GCF_014836615.1_ASM1483661v1_genomic.fna/markers.fasta
[2024-01-25 18:57:14,813] [INFO] Task started: Blastn
[2024-01-25 18:57:14,813] [INFO] Running command: blastn -query GCF_014836615.1_ASM1483661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/reference_markers.fasta -out GCF_014836615.1_ASM1483661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:15,423] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:15,426] [INFO] Selected 32 target genomes.
[2024-01-25 18:57:15,427] [INFO] Target genome list was writen to GCF_014836615.1_ASM1483661v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:15,441] [INFO] Task started: fastANI
[2024-01-25 18:57:15,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e77568-b674-41e6-b0a6-9462f632833d/GCF_014836615.1_ASM1483661v1_genomic.fna.gz --refList GCF_014836615.1_ASM1483661v1_genomic.fna/target_genomes.txt --output GCF_014836615.1_ASM1483661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:34,725] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:34,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:34,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:34,735] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:34,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:34,736] [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
Sporosarcina quadrami	strain=Sa2YVA2	GCA_014836615.1	2762234	2762234	type	True	100.0	1167	1171	95	conclusive
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	78.9741	368	1171	95	below_threshold
Savagea serpentis	strain=SN6	GCA_015351395.1	2785297	2785297	type	True	77.5889	59	1171	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.5139	163	1171	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	77.4362	161	1171	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	76.9893	59	1171	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.7371	57	1171	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	76.6944	116	1171	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	76.6221	72	1171	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	76.6068	51	1171	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	76.6028	60	1171	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	76.5823	62	1171	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	76.5292	72	1171	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	76.381	52	1171	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	76.3683	50	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:34,737] [INFO] DFAST Taxonomy check result was written to GCF_014836615.1_ASM1483661v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:34,737] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:34,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:34,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/checkm_data
[2024-01-25 18:57:34,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:34,776] [INFO] Task started: CheckM
[2024-01-25 18:57:34,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836615.1_ASM1483661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836615.1_ASM1483661v1_genomic.fna/checkm_input GCF_014836615.1_ASM1483661v1_genomic.fna/checkm_result
[2024-01-25 18:58:01,989] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:01,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:02,013] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:02,013] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:02,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836615.1_ASM1483661v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:02,014] [INFO] Task started: Blastn
[2024-01-25 18:58:02,014] [INFO] Running command: blastn -query GCF_014836615.1_ASM1483661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg767aeb1f-993d-4e76-b14a-6165729ebb4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836615.1_ASM1483661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:02,770] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:02,772] [INFO] Selected 29 target genomes.
[2024-01-25 18:58:02,773] [INFO] Target genome list was writen to GCF_014836615.1_ASM1483661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:02,791] [INFO] Task started: fastANI
[2024-01-25 18:58:02,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e77568-b674-41e6-b0a6-9462f632833d/GCF_014836615.1_ASM1483661v1_genomic.fna.gz --refList GCF_014836615.1_ASM1483661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836615.1_ASM1483661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:21,379] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:21,390] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:21,390] [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_014836615.1	s__Sporosarcina sp014836615	100.0	1167	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007991495.1	s__Sporosarcina luteola	78.986	367	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001531445.1	s__Sporosarcina koreensis_C	78.6782	374	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204635.1	s__Sporosarcina luteola_A	77.7864	206	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498505.1	s__Sporosarcina sp017498505	77.7724	209	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820585.1	s__Sporosarcina sp016820585	77.7535	162	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563475.1	s__Sporosarcina sp001563475	77.5964	121	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351395.1	s__Savagea serpentis	77.5889	59	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Savagea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000586555.1	s__Sporosarcina sp000586555	77.5142	131	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609045.1	s__Sporosarcina tadaridae	77.5139	163	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650995.1	s__Sporosarcina sp009650995	77.4945	113	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002743055.1	s__Sporosarcina sp002743055	77.3345	126	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220335.1	s__Sporosarcina newyorkensis	77.2521	134	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	97.56	97.56	0.86	0.86	2	-
GCF_002109325.1	s__Sporosarcina ureae_C	77.153	118	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.86	98.81	0.92	0.91	3	-
GCF_014282005.1	s__Sporosarcina sp014282005	77.125	177	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	96.23	96.23	0.81	0.81	2	-
GCF_000829195.1	s__Sporosarcina sp000829195	77.0838	135	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017921835.1	s__Sporosarcina sp017921835	76.9368	112	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278755.1	s__Psychrobacillus sp001278755	76.5193	62	1171	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:21,392] [INFO] GTDB search result was written to GCF_014836615.1_ASM1483661v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:21,393] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:21,396] [INFO] DFAST_QC result json was written to GCF_014836615.1_ASM1483661v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:21,396] [INFO] DFAST_QC completed!
[2024-01-25 18:58:21,396] [INFO] Total running time: 0h1m16s