[2023-06-19 12:10:14,949] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:14,951] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:14,951] [INFO] DQC Reference Directory: /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference
[2023-06-19 12:10:18,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:18,203] [INFO] Task started: Prodigal
[2023-06-19 12:10:18,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg82d0ca59-e007-4b07-a201-e09dee1962de/GCA_018657295.1_ASM1865729v1_genomic.fna.gz | prodigal -d GCA_018657295.1_ASM1865729v1_genomic.fna/cds.fna -a GCA_018657295.1_ASM1865729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:20,147] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:20,147] [INFO] Task started: HMMsearch
[2023-06-19 12:10:20,148] [INFO] Running command: hmmsearch --tblout GCA_018657295.1_ASM1865729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/reference_markers.hmm GCA_018657295.1_ASM1865729v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:20,445] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:20,447] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg82d0ca59-e007-4b07-a201-e09dee1962de/GCA_018657295.1_ASM1865729v1_genomic.fna.gz]
[2023-06-19 12:10:20,465] [INFO] Query marker FASTA was written to GCA_018657295.1_ASM1865729v1_genomic.fna/markers.fasta
[2023-06-19 12:10:20,465] [INFO] Task started: Blastn
[2023-06-19 12:10:20,465] [INFO] Running command: blastn -query GCA_018657295.1_ASM1865729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/reference_markers.fasta -out GCA_018657295.1_ASM1865729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:22,587] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:22,591] [INFO] Selected 22 target genomes.
[2023-06-19 12:10:22,591] [INFO] Target genome list was writen to GCA_018657295.1_ASM1865729v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:22,602] [INFO] Task started: fastANI
[2023-06-19 12:10:22,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg82d0ca59-e007-4b07-a201-e09dee1962de/GCA_018657295.1_ASM1865729v1_genomic.fna.gz --refList GCA_018657295.1_ASM1865729v1_genomic.fna/target_genomes.txt --output GCA_018657295.1_ASM1865729v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:35,181] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:35,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:35,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:35,185] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:35,185] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:10:35,186] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	78.3953	89	227	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:10:35,188] [INFO] DFAST Taxonomy check result was written to GCA_018657295.1_ASM1865729v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:35,188] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:35,188] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:35,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/checkm_data
[2023-06-19 12:10:35,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:35,204] [INFO] Task started: CheckM
[2023-06-19 12:10:35,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018657295.1_ASM1865729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018657295.1_ASM1865729v1_genomic.fna/checkm_input GCA_018657295.1_ASM1865729v1_genomic.fna/checkm_result
[2023-06-19 12:10:49,379] [INFO] Task succeeded: CheckM
[2023-06-19 12:10:49,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 12:10:49,404] [INFO] ===== Completeness check finished =====
[2023-06-19 12:10:49,405] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:10:49,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018657295.1_ASM1865729v1_genomic.fna/markers.fasta)
[2023-06-19 12:10:49,406] [INFO] Task started: Blastn
[2023-06-19 12:10:49,406] [INFO] Running command: blastn -query GCA_018657295.1_ASM1865729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge302b20e-b140-4fc7-837a-983f075e8a60/dqc_reference/reference_markers_gtdb.fasta -out GCA_018657295.1_ASM1865729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:49,849] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:49,854] [INFO] Selected 13 target genomes.
[2023-06-19 12:10:49,854] [INFO] Target genome list was writen to GCA_018657295.1_ASM1865729v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:10:49,859] [INFO] Task started: fastANI
[2023-06-19 12:10:49,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg82d0ca59-e007-4b07-a201-e09dee1962de/GCA_018657295.1_ASM1865729v1_genomic.fna.gz --refList GCA_018657295.1_ASM1865729v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018657295.1_ASM1865729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:10:53,050] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:53,070] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:10:53,070] [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
GCA_000205985.2	s__SUP05 sp000205985	99.2651	191	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__SUP05	95.0	99.29	99.11	0.83	0.80	14	conclusive
GCA_018648985.1	s__UBA2013 sp018648985	79.7447	118	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489145.1	s__UBA2013 sp003489145	79.5408	119	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_016845205.1	s__UBA2013 sp016845205	79.391	121	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	79.131	129	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003978285.1	s__UBA2013 sp003978285	78.7964	84	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978185.1	s__UBA2013 sp003978185	78.5963	75	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963565.1	s__DTVJ01 sp012963565	78.4414	85	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293165.1	s__Thioglobus autotrophicus	78.3778	90	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002909145.1	s__Thioglobus_B perditus	78.1426	87	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384345.1	s__Thioglobus pontius	77.8816	94	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCF_001298715.1	s__Thiodubiliella sp001298715	77.7579	62	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.96	97.97	0.90	0.82	38	-
--------------------------------------------------------------------------------
[2023-06-19 12:10:53,072] [INFO] GTDB search result was written to GCA_018657295.1_ASM1865729v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:10:53,073] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:10:53,076] [INFO] DFAST_QC result json was written to GCA_018657295.1_ASM1865729v1_genomic.fna/dqc_result.json
[2023-06-19 12:10:53,077] [INFO] DFAST_QC completed!
[2023-06-19 12:10:53,077] [INFO] Total running time: 0h0m38s