[2023-06-27 13:28:57,374] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:28:57,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:28:57,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference
[2023-06-27 13:28:58,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:28:58,953] [INFO] Task started: Prodigal
[2023-06-27 13:28:58,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg4eb690cb-3bd3-4e17-84e5-bda2ebb75c67/GCA_027445305.1_ASM2744530v1_genomic.fna.gz | prodigal -d GCA_027445305.1_ASM2744530v1_genomic.fna/cds.fna -a GCA_027445305.1_ASM2744530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:29:04,005] [INFO] Task succeeded: Prodigal
[2023-06-27 13:29:04,005] [INFO] Task started: HMMsearch
[2023-06-27 13:29:04,005] [INFO] Running command: hmmsearch --tblout GCA_027445305.1_ASM2744530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/reference_markers.hmm GCA_027445305.1_ASM2744530v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:29:04,199] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:29:04,201] [INFO] Found 6/6 markers.
[2023-06-27 13:29:04,223] [INFO] Query marker FASTA was written to GCA_027445305.1_ASM2744530v1_genomic.fna/markers.fasta
[2023-06-27 13:29:04,223] [INFO] Task started: Blastn
[2023-06-27 13:29:04,223] [INFO] Running command: blastn -query GCA_027445305.1_ASM2744530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/reference_markers.fasta -out GCA_027445305.1_ASM2744530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:04,885] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:04,889] [INFO] Selected 11 target genomes.
[2023-06-27 13:29:04,889] [INFO] Target genome list was writen to GCA_027445305.1_ASM2744530v1_genomic.fna/target_genomes.txt
[2023-06-27 13:29:04,893] [INFO] Task started: fastANI
[2023-06-27 13:29:04,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eb690cb-3bd3-4e17-84e5-bda2ebb75c67/GCA_027445305.1_ASM2744530v1_genomic.fna.gz --refList GCA_027445305.1_ASM2744530v1_genomic.fna/target_genomes.txt --output GCA_027445305.1_ASM2744530v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:29:12,830] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:12,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:29:12,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:29:12,838] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 13:29:12,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 13:29:12,839] [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 ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	97.8078	361	516	95	conclusive
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	84.2499	340	516	95	below_threshold
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	84.0488	304	516	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	83.9718	331	516	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	80.9008	282	516	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:29:12,841] [INFO] DFAST Taxonomy check result was written to GCA_027445305.1_ASM2744530v1_genomic.fna/tc_result.tsv
[2023-06-27 13:29:12,841] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:29:12,842] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:29:12,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/checkm_data
[2023-06-27 13:29:12,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:29:12,865] [INFO] Task started: CheckM
[2023-06-27 13:29:12,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027445305.1_ASM2744530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027445305.1_ASM2744530v1_genomic.fna/checkm_input GCA_027445305.1_ASM2744530v1_genomic.fna/checkm_result
[2023-06-27 13:29:33,543] [INFO] Task succeeded: CheckM
[2023-06-27 13:29:33,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:29:33,560] [INFO] ===== Completeness check finished =====
[2023-06-27 13:29:33,561] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:29:33,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027445305.1_ASM2744530v1_genomic.fna/markers.fasta)
[2023-06-27 13:29:33,561] [INFO] Task started: Blastn
[2023-06-27 13:29:33,561] [INFO] Running command: blastn -query GCA_027445305.1_ASM2744530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00d73c1e-f987-4b67-821e-56abb71051bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_027445305.1_ASM2744530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:34,773] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:34,776] [INFO] Selected 6 target genomes.
[2023-06-27 13:29:34,776] [INFO] Target genome list was writen to GCA_027445305.1_ASM2744530v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:29:34,782] [INFO] Task started: fastANI
[2023-06-27 13:29:34,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eb690cb-3bd3-4e17-84e5-bda2ebb75c67/GCA_027445305.1_ASM2744530v1_genomic.fna.gz --refList GCA_027445305.1_ASM2744530v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027445305.1_ASM2744530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:29:38,172] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:38,178] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:29:38,178] [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_018854775.1	s__Acidithiobacillus ferriphilus	97.7998	362	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.36	97.93	0.81	0.77	8	conclusive
GCF_018853935.1	s__Acidithiobacillus ferrivorans	92.1256	375	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	84.2499	340	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	83.9743	312	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	83.9718	331	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	80.9008	282	516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:29:38,180] [INFO] GTDB search result was written to GCA_027445305.1_ASM2744530v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:29:38,181] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:29:38,184] [INFO] DFAST_QC result json was written to GCA_027445305.1_ASM2744530v1_genomic.fna/dqc_result.json
[2023-06-27 13:29:38,184] [INFO] DFAST_QC completed!
[2023-06-27 13:29:38,184] [INFO] Total running time: 0h0m41s