[2024-01-25 18:00:35,358] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference
[2024-01-25 18:00:36,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,499] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg16060974-9ec6-424b-810b-f361976bcf82/GCF_021129195.1_ASM2112919v1_genomic.fna.gz | prodigal -d GCF_021129195.1_ASM2112919v1_genomic.fna/cds.fna -a GCF_021129195.1_ASM2112919v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:48,966] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:48,966] [INFO] Task started: HMMsearch
[2024-01-25 18:00:48,966] [INFO] Running command: hmmsearch --tblout GCF_021129195.1_ASM2112919v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/reference_markers.hmm GCF_021129195.1_ASM2112919v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:49,233] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:49,234] [INFO] Found 6/6 markers.
[2024-01-25 18:00:49,271] [INFO] Query marker FASTA was written to GCF_021129195.1_ASM2112919v1_genomic.fna/markers.fasta
[2024-01-25 18:00:49,271] [INFO] Task started: Blastn
[2024-01-25 18:00:49,271] [INFO] Running command: blastn -query GCF_021129195.1_ASM2112919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/reference_markers.fasta -out GCF_021129195.1_ASM2112919v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:50,208] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:50,211] [INFO] Selected 13 target genomes.
[2024-01-25 18:00:50,212] [INFO] Target genome list was writen to GCF_021129195.1_ASM2112919v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:50,232] [INFO] Task started: fastANI
[2024-01-25 18:00:50,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg16060974-9ec6-424b-810b-f361976bcf82/GCF_021129195.1_ASM2112919v1_genomic.fna.gz --refList GCF_021129195.1_ASM2112919v1_genomic.fna/target_genomes.txt --output GCF_021129195.1_ASM2112919v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:04,972] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:04,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:04,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:04,982] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:04,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:04,982] [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
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	100.0	1498	1506	95	conclusive
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	91.1772	1327	1506	95	below_threshold
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	89.7164	1240	1506	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	83.5248	916	1506	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	83.4482	928	1506	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	83.3777	889	1506	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	83.3163	837	1506	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	83.2739	934	1506	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	83.0861	837	1506	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	83.0195	839	1506	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	82.9164	852	1506	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	79.8868	477	1506	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2618	326	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:04,984] [INFO] DFAST Taxonomy check result was written to GCF_021129195.1_ASM2112919v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:04,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:04,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:04,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/checkm_data
[2024-01-25 18:01:04,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:05,047] [INFO] Task started: CheckM
[2024-01-25 18:01:05,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021129195.1_ASM2112919v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021129195.1_ASM2112919v1_genomic.fna/checkm_input GCF_021129195.1_ASM2112919v1_genomic.fna/checkm_result
[2024-01-25 18:01:42,944] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:42,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:42,961] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:42,962] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:42,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021129195.1_ASM2112919v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:42,962] [INFO] Task started: Blastn
[2024-01-25 18:01:42,962] [INFO] Running command: blastn -query GCF_021129195.1_ASM2112919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd990ce22-2bc3-4fd4-9e8b-8691004c1730/dqc_reference/reference_markers_gtdb.fasta -out GCF_021129195.1_ASM2112919v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:44,830] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:44,833] [INFO] Selected 5 target genomes.
[2024-01-25 18:01:44,833] [INFO] Target genome list was writen to GCF_021129195.1_ASM2112919v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:44,842] [INFO] Task started: fastANI
[2024-01-25 18:01:44,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg16060974-9ec6-424b-810b-f361976bcf82/GCF_021129195.1_ASM2112919v1_genomic.fna.gz --refList GCF_021129195.1_ASM2112919v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021129195.1_ASM2112919v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:52,934] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:52,938] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:52,939] [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_001043555.1	s__Chromobacterium sp001043555	98.2981	1357	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003052555.1	s__Chromobacterium sp003052555	91.7571	1314	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	91.1792	1326	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCF_002081825.1	s__Chromobacterium haemolyticum_A	90.2309	1273	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.46	97.46	0.88	0.88	2	-
GCF_000711885.1	s__Chromobacterium haemolyticum	89.6893	1243	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	96.93	96.05	0.88	0.85	14	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:52,940] [INFO] GTDB search result was written to GCF_021129195.1_ASM2112919v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:52,940] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:52,943] [INFO] DFAST_QC result json was written to GCF_021129195.1_ASM2112919v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:52,943] [INFO] DFAST_QC completed!
[2024-01-25 18:01:52,943] [INFO] Total running time: 0h1m18s