[2024-01-24 13:49:30,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,229] [INFO] DQC Reference Directory: /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference
[2024-01-24 13:49:31,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,631] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6ed2f8b-70f6-480a-9bc6-46a8a509623e/GCF_006718285.1_ASM671828v1_genomic.fna.gz | prodigal -d GCF_006718285.1_ASM671828v1_genomic.fna/cds.fna -a GCF_006718285.1_ASM671828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,627] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,627] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,627] [INFO] Running command: hmmsearch --tblout GCF_006718285.1_ASM671828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/reference_markers.hmm GCF_006718285.1_ASM671828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,934] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,968] [INFO] Query marker FASTA was written to GCF_006718285.1_ASM671828v1_genomic.fna/markers.fasta
[2024-01-24 13:49:42,968] [INFO] Task started: Blastn
[2024-01-24 13:49:42,968] [INFO] Running command: blastn -query GCF_006718285.1_ASM671828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/reference_markers.fasta -out GCF_006718285.1_ASM671828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,699] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:43,700] [INFO] Target genome list was writen to GCF_006718285.1_ASM671828v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,766] [INFO] Task started: fastANI
[2024-01-24 13:49:43,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ed2f8b-70f6-480a-9bc6-46a8a509623e/GCF_006718285.1_ASM671828v1_genomic.fna.gz --refList GCF_006718285.1_ASM671828v1_genomic.fna/target_genomes.txt --output GCF_006718285.1_ASM671828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:51,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:51,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:51,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:51,940] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:51,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:51,940] [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 thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	100.0	1128	1132	95	conclusive
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	97.1355	755	1132	95	conclusive
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	96.9454	868	1132	95	conclusive
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	79.3322	232	1132	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	78.8263	246	1132	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	77.6994	205	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:51,942] [INFO] DFAST Taxonomy check result was written to GCF_006718285.1_ASM671828v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:51,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:51,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:51,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/checkm_data
[2024-01-24 13:49:51,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:51,982] [INFO] Task started: CheckM
[2024-01-24 13:49:51,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006718285.1_ASM671828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006718285.1_ASM671828v1_genomic.fna/checkm_input GCF_006718285.1_ASM671828v1_genomic.fna/checkm_result
[2024-01-24 13:50:27,970] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:27,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,991] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:27,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:27,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006718285.1_ASM671828v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:27,992] [INFO] Task started: Blastn
[2024-01-24 13:50:27,992] [INFO] Running command: blastn -query GCF_006718285.1_ASM671828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga648a6fc-f4b6-45c0-ac97-742552f2a7be/dqc_reference/reference_markers_gtdb.fasta -out GCF_006718285.1_ASM671828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:29,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:29,138] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:29,138] [INFO] Target genome list was writen to GCF_006718285.1_ASM671828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:29,143] [INFO] Task started: fastANI
[2024-01-24 13:50:29,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ed2f8b-70f6-480a-9bc6-46a8a509623e/GCF_006718285.1_ASM671828v1_genomic.fna.gz --refList GCF_006718285.1_ASM671828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006718285.1_ASM671828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:34,240] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:34,250] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:34,250] [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_009662475.1	s__Acidithiobacillus thiooxidans	96.9567	867	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	conclusive
GCF_015100155.1	s__Acidithiobacillus sp015100155	94.5153	788	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_018853815.1	s__Acidithiobacillus sp018853815	92.8502	759	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853445.1	s__Acidithiobacillus sp018853445	91.6666	691	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847505.1	s__Acidithiobacillus sp002847505	81.2229	533	1132	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	80.9306	516	1132	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 13:50:34,252] [INFO] GTDB search result was written to GCF_006718285.1_ASM671828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:34,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:34,255] [INFO] DFAST_QC result json was written to GCF_006718285.1_ASM671828v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:34,255] [INFO] DFAST_QC completed!
[2024-01-24 13:50:34,255] [INFO] Total running time: 0h1m4s