[2024-01-25 18:51:05,829] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference
[2024-01-25 18:51:06,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,973] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c0f3ee7-facd-40de-b5a5-962b822f6335/GCF_030813355.1_ASM3081335v1_genomic.fna.gz | prodigal -d GCF_030813355.1_ASM3081335v1_genomic.fna/cds.fna -a GCF_030813355.1_ASM3081335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:15,023] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:15,023] [INFO] Task started: HMMsearch
[2024-01-25 18:51:15,024] [INFO] Running command: hmmsearch --tblout GCF_030813355.1_ASM3081335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/reference_markers.hmm GCF_030813355.1_ASM3081335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:15,337] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:15,338] [INFO] Found 6/6 markers.
[2024-01-25 18:51:15,377] [INFO] Query marker FASTA was written to GCF_030813355.1_ASM3081335v1_genomic.fna/markers.fasta
[2024-01-25 18:51:15,377] [INFO] Task started: Blastn
[2024-01-25 18:51:15,377] [INFO] Running command: blastn -query GCF_030813355.1_ASM3081335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/reference_markers.fasta -out GCF_030813355.1_ASM3081335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:15,977] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:15,981] [INFO] Selected 19 target genomes.
[2024-01-25 18:51:15,981] [INFO] Target genome list was writen to GCF_030813355.1_ASM3081335v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:15,999] [INFO] Task started: fastANI
[2024-01-25 18:51:16,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c0f3ee7-facd-40de-b5a5-962b822f6335/GCF_030813355.1_ASM3081335v1_genomic.fna.gz --refList GCF_030813355.1_ASM3081335v1_genomic.fna/target_genomes.txt --output GCF_030813355.1_ASM3081335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:30,213] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:30,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:30,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:30,223] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:51:30,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:51:30,223] [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
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	78.8856	364	1594	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	78.6488	354	1594	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	78.6349	346	1594	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	78.6303	348	1594	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	78.3805	437	1594	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	78.3586	366	1594	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	78.3315	358	1594	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	78.3133	292	1594	95	below_threshold
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	77.0203	57	1594	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	76.9219	73	1594	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.8794	97	1594	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	76.6805	54	1594	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6559	72	1594	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	75.8844	56	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:30,224] [INFO] DFAST Taxonomy check result was written to GCF_030813355.1_ASM3081335v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:30,225] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:30,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:30,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/checkm_data
[2024-01-25 18:51:30,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:30,272] [INFO] Task started: CheckM
[2024-01-25 18:51:30,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813355.1_ASM3081335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813355.1_ASM3081335v1_genomic.fna/checkm_input GCF_030813355.1_ASM3081335v1_genomic.fna/checkm_result
[2024-01-25 18:51:58,478] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:58,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:58,499] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:58,499] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:58,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813355.1_ASM3081335v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:58,500] [INFO] Task started: Blastn
[2024-01-25 18:51:58,500] [INFO] Running command: blastn -query GCF_030813355.1_ASM3081335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8382fd6e-f931-4f3d-b4e1-043ac12924fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813355.1_ASM3081335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:59,318] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:59,321] [INFO] Selected 19 target genomes.
[2024-01-25 18:51:59,321] [INFO] Target genome list was writen to GCF_030813355.1_ASM3081335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:59,344] [INFO] Task started: fastANI
[2024-01-25 18:51:59,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c0f3ee7-facd-40de-b5a5-962b822f6335/GCF_030813355.1_ASM3081335v1_genomic.fna.gz --refList GCF_030813355.1_ASM3081335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813355.1_ASM3081335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:15,145] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:15,156] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:52:15,156] [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_902829255.1	s__Metabacillus niabensis	79.2935	519	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_003667825.1	s__Metabacillus litoralis_B	78.8349	344	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002577655.1	s__Metabacillus sp002577655	78.7236	321	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217835.1	s__Metabacillus litoralis_A	78.5434	438	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_016908395.1	s__Metabacillus crassostreae	78.3767	363	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497975.1	s__Metabacillus sp017497975	78.3662	437	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	78.3609	341	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	78.3433	357	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889165.1	s__Metabacillus weihaiensis	78.3084	289	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_003259415.1	s__Metabacillus sp003259415	78.2373	317	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	78.1658	340	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710145.1	s__Bacillus_BD endozanthoxylicus	77.4531	99	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591625.1	s__Metabacillus fastidiosus	77.4216	181	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343715.1	s__Mesobacillus_A harenae	77.0203	57	1594	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_000285535.1	s__Fredinandcohnia timonensis	76.9754	125	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_008364785.1	s__Bacillus_BS sp008364785	76.6084	92	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	76.4436	59	1594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:15,158] [INFO] GTDB search result was written to GCF_030813355.1_ASM3081335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:15,158] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:15,161] [INFO] DFAST_QC result json was written to GCF_030813355.1_ASM3081335v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:15,161] [INFO] DFAST_QC completed!
[2024-01-25 18:52:15,161] [INFO] Total running time: 0h1m9s