[2024-01-24 13:49:33,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference
[2024-01-24 13:49:35,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:35,087] [INFO] Task started: Prodigal
[2024-01-24 13:49:35,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg28bd8f56-ba53-4ed7-b3ef-7061403f3044/GCF_004919095.1_ASM491909v1_genomic.fna.gz | prodigal -d GCF_004919095.1_ASM491909v1_genomic.fna/cds.fna -a GCF_004919095.1_ASM491909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,815] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,816] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,816] [INFO] Running command: hmmsearch --tblout GCF_004919095.1_ASM491909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/reference_markers.hmm GCF_004919095.1_ASM491909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:46,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:46,095] [INFO] Found 6/6 markers.
[2024-01-24 13:49:46,135] [INFO] Query marker FASTA was written to GCF_004919095.1_ASM491909v1_genomic.fna/markers.fasta
[2024-01-24 13:49:46,136] [INFO] Task started: Blastn
[2024-01-24 13:49:46,136] [INFO] Running command: blastn -query GCF_004919095.1_ASM491909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/reference_markers.fasta -out GCF_004919095.1_ASM491909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,338] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:47,338] [INFO] Target genome list was writen to GCF_004919095.1_ASM491909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:47,344] [INFO] Task started: fastANI
[2024-01-24 13:49:47,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bd8f56-ba53-4ed7-b3ef-7061403f3044/GCF_004919095.1_ASM491909v1_genomic.fna.gz --refList GCF_004919095.1_ASM491909v1_genomic.fna/target_genomes.txt --output GCF_004919095.1_ASM491909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,343] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,356] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,357] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,357] [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
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	100.0	1114	1117	95	conclusive
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	93.9072	950	1117	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	82.3089	555	1117	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	81.7228	525	1117	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	81.0709	562	1117	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	80.5299	546	1117	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	80.3703	487	1117	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	80.301	521	1117	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	80.2567	521	1117	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	80.2057	469	1117	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	80.0687	557	1117	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	80.0189	474	1117	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.8105	491	1117	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	78.9018	354	1117	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.0667	380	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,358] [INFO] DFAST Taxonomy check result was written to GCF_004919095.1_ASM491909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,359] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/checkm_data
[2024-01-24 13:50:00,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,403] [INFO] Task started: CheckM
[2024-01-24 13:50:00,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004919095.1_ASM491909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004919095.1_ASM491909v1_genomic.fna/checkm_input GCF_004919095.1_ASM491909v1_genomic.fna/checkm_result
[2024-01-24 13:50:34,302] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:34,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,321] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:34,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:34,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004919095.1_ASM491909v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:34,322] [INFO] Task started: Blastn
[2024-01-24 13:50:34,323] [INFO] Running command: blastn -query GCF_004919095.1_ASM491909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc18cfc5b-126c-463e-bc88-53db750a75e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004919095.1_ASM491909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:36,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:36,323] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:36,323] [INFO] Target genome list was writen to GCF_004919095.1_ASM491909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:36,331] [INFO] Task started: fastANI
[2024-01-24 13:50:36,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bd8f56-ba53-4ed7-b3ef-7061403f3044/GCF_004919095.1_ASM491909v1_genomic.fna.gz --refList GCF_004919095.1_ASM491909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004919095.1_ASM491909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:44,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,708] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:44,709] [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_004919095.1	s__STGJ01 sp004919095	100.0	1114	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010435965.1	s__STGJ01 sp010435965	93.9072	950	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	82.3494	551	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_003355495.1	s__Crenobacter cavernae	81.7187	527	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	81.0291	547	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	80.7968	514	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	80.6316	406	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003856275.1	s__STGJ01 sp003856275	80.4991	564	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	97.91	97.91	0.91	0.91	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	80.4732	521	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	80.0516	558	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:44,711] [INFO] GTDB search result was written to GCF_004919095.1_ASM491909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:44,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:44,716] [INFO] DFAST_QC result json was written to GCF_004919095.1_ASM491909v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:44,716] [INFO] DFAST_QC completed!
[2024-01-24 13:50:44,717] [INFO] Total running time: 0h1m11s