[2024-01-24 14:20:14,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,236] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,236] [INFO] DQC Reference Directory: /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference
[2024-01-24 14:20:15,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,494] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg409aa997-9a9d-4088-b3da-46cd483999f0/GCF_000021485.1_ASM2148v1_genomic.fna.gz | prodigal -d GCF_000021485.1_ASM2148v1_genomic.fna/cds.fna -a GCF_000021485.1_ASM2148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:25,724] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:25,725] [INFO] Task started: HMMsearch
[2024-01-24 14:20:25,725] [INFO] Running command: hmmsearch --tblout GCF_000021485.1_ASM2148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/reference_markers.hmm GCF_000021485.1_ASM2148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:26,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:26,005] [INFO] Found 6/6 markers.
[2024-01-24 14:20:26,034] [INFO] Query marker FASTA was written to GCF_000021485.1_ASM2148v1_genomic.fna/markers.fasta
[2024-01-24 14:20:26,034] [INFO] Task started: Blastn
[2024-01-24 14:20:26,035] [INFO] Running command: blastn -query GCF_000021485.1_ASM2148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/reference_markers.fasta -out GCF_000021485.1_ASM2148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:26,761] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:26,765] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:26,765] [INFO] Target genome list was writen to GCF_000021485.1_ASM2148v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:26,774] [INFO] Task started: fastANI
[2024-01-24 14:20:26,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg409aa997-9a9d-4088-b3da-46cd483999f0/GCF_000021485.1_ASM2148v1_genomic.fna.gz --refList GCF_000021485.1_ASM2148v1_genomic.fna/target_genomes.txt --output GCF_000021485.1_ASM2148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:36,646] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:36,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:36,659] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:36,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:36,660] [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
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	100.0	994	994	95	conclusive
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	94.5388	767	994	95	below_threshold
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	94.4189	662	994	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	84.7533	470	994	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	82.2265	486	994	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	79.2096	236	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,662] [INFO] DFAST Taxonomy check result was written to GCF_000021485.1_ASM2148v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:36,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:36,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:36,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/checkm_data
[2024-01-24 14:20:36,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,697] [INFO] Task started: CheckM
[2024-01-24 14:20:36,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021485.1_ASM2148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021485.1_ASM2148v1_genomic.fna/checkm_input GCF_000021485.1_ASM2148v1_genomic.fna/checkm_result
[2024-01-24 14:21:08,938] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:08,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,964] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:08,965] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:08,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021485.1_ASM2148v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:08,966] [INFO] Task started: Blastn
[2024-01-24 14:21:08,966] [INFO] Running command: blastn -query GCF_000021485.1_ASM2148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9db341f-3573-430b-9ca0-35d711777fc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021485.1_ASM2148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:10,211] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:10,215] [INFO] Selected 7 target genomes.
[2024-01-24 14:21:10,215] [INFO] Target genome list was writen to GCF_000021485.1_ASM2148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:10,226] [INFO] Task started: fastANI
[2024-01-24 14:21:10,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg409aa997-9a9d-4088-b3da-46cd483999f0/GCF_000021485.1_ASM2148v1_genomic.fna.gz --refList GCF_000021485.1_ASM2148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021485.1_ASM2148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:15,113] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:15,119] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:15,120] [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_000021485.1	s__Acidithiobacillus ferrooxidans	100.0	994	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	conclusive
GCF_003966655.1	s__Acidithiobacillus ferridurans	94.5596	767	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	94.4992	643	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018854775.1	s__Acidithiobacillus ferriphilus	84.7458	471	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.36	97.93	0.81	0.77	8	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	84.2682	560	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	82.1949	487	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853465.1	s__Acidithiobacillus sp018853465	78.0777	237	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:15,121] [INFO] GTDB search result was written to GCF_000021485.1_ASM2148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:15,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:15,124] [INFO] DFAST_QC result json was written to GCF_000021485.1_ASM2148v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:15,124] [INFO] DFAST_QC completed!
[2024-01-24 14:21:15,124] [INFO] Total running time: 0h1m1s