[2024-01-25 19:59:35,509] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:35,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:35,511] [INFO] DQC Reference Directory: /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference
[2024-01-25 19:59:36,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:36,678] [INFO] Task started: Prodigal
[2024-01-25 19:59:36,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fb3b7d2-c87b-4272-996d-fc9068c2561c/GCF_025996195.1_ASM2599619v1_genomic.fna.gz | prodigal -d GCF_025996195.1_ASM2599619v1_genomic.fna/cds.fna -a GCF_025996195.1_ASM2599619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:45,016] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:45,016] [INFO] Task started: HMMsearch
[2024-01-25 19:59:45,017] [INFO] Running command: hmmsearch --tblout GCF_025996195.1_ASM2599619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/reference_markers.hmm GCF_025996195.1_ASM2599619v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:45,239] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:45,240] [INFO] Found 6/6 markers.
[2024-01-25 19:59:45,267] [INFO] Query marker FASTA was written to GCF_025996195.1_ASM2599619v1_genomic.fna/markers.fasta
[2024-01-25 19:59:45,267] [INFO] Task started: Blastn
[2024-01-25 19:59:45,267] [INFO] Running command: blastn -query GCF_025996195.1_ASM2599619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/reference_markers.fasta -out GCF_025996195.1_ASM2599619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:45,916] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:45,919] [INFO] Selected 11 target genomes.
[2024-01-25 19:59:45,920] [INFO] Target genome list was writen to GCF_025996195.1_ASM2599619v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:45,930] [INFO] Task started: fastANI
[2024-01-25 19:59:45,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb3b7d2-c87b-4272-996d-fc9068c2561c/GCF_025996195.1_ASM2599619v1_genomic.fna.gz --refList GCF_025996195.1_ASM2599619v1_genomic.fna/target_genomes.txt --output GCF_025996195.1_ASM2599619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:54,133] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:54,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:54,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:54,140] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:54,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:54,140] [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
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	99.9443	925	968	95	conclusive
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	93.2346	827	968	95	below_threshold
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	85.9069	706	968	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	85.1347	671	968	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	85.1007	690	968	95	below_threshold
Acetobacter orleanensis	strain=NBRC 13752	GCA_006539325.1	104099	104099	type	True	85.0652	695	968	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.0481	54	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:54,141] [INFO] DFAST Taxonomy check result was written to GCF_025996195.1_ASM2599619v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:54,142] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:54,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:54,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/checkm_data
[2024-01-25 19:59:54,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:54,174] [INFO] Task started: CheckM
[2024-01-25 19:59:54,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025996195.1_ASM2599619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025996195.1_ASM2599619v1_genomic.fna/checkm_input GCF_025996195.1_ASM2599619v1_genomic.fna/checkm_result
[2024-01-25 20:00:21,955] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:21,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:22,004] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:22,004] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:22,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025996195.1_ASM2599619v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:22,006] [INFO] Task started: Blastn
[2024-01-25 20:00:22,006] [INFO] Running command: blastn -query GCF_025996195.1_ASM2599619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35530cf0-4d3d-4d10-aaee-6dec90bab65b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025996195.1_ASM2599619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:22,950] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:22,953] [INFO] Selected 9 target genomes.
[2024-01-25 20:00:22,953] [INFO] Target genome list was writen to GCF_025996195.1_ASM2599619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:22,959] [INFO] Task started: fastANI
[2024-01-25 20:00:22,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb3b7d2-c87b-4272-996d-fc9068c2561c/GCF_025996195.1_ASM2599619v1_genomic.fna.gz --refList GCF_025996195.1_ASM2599619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025996195.1_ASM2599619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:29,218] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:29,223] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:29,223] [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_001580535.1	s__Acetobacter cerevisiae	99.9443	925	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	conclusive
GCF_001580615.1	s__Acetobacter malorum	93.2346	827	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_002153605.1	s__Acetobacter malorum_A	91.1861	786	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_000613905.1	s__Acetobacter persici	85.9066	706	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001581005.1	s__Acetobacter orleanensis	85.1007	690	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_011516935.1	s__Acetobacter farinalis	84.1035	670	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:29,225] [INFO] GTDB search result was written to GCF_025996195.1_ASM2599619v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:29,226] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:29,228] [INFO] DFAST_QC result json was written to GCF_025996195.1_ASM2599619v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:29,229] [INFO] DFAST_QC completed!
[2024-01-25 20:00:29,229] [INFO] Total running time: 0h0m54s