[2023-06-29 09:20:14,350] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:20:14,352] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:20:14,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference
[2023-06-29 09:20:17,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:20:17,559] [INFO] Task started: Prodigal
[2023-06-29 09:20:17,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c071f0f-62cd-4447-b944-65a2d3df253a/GCA_027448145.1_ASM2744814v1_genomic.fna.gz | prodigal -d GCA_027448145.1_ASM2744814v1_genomic.fna/cds.fna -a GCA_027448145.1_ASM2744814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:20:26,765] [INFO] Task succeeded: Prodigal
[2023-06-29 09:20:26,766] [INFO] Task started: HMMsearch
[2023-06-29 09:20:26,766] [INFO] Running command: hmmsearch --tblout GCA_027448145.1_ASM2744814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/reference_markers.hmm GCA_027448145.1_ASM2744814v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:20:26,996] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:20:26,998] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2c071f0f-62cd-4447-b944-65a2d3df253a/GCA_027448145.1_ASM2744814v1_genomic.fna.gz]
[2023-06-29 09:20:27,036] [INFO] Query marker FASTA was written to GCA_027448145.1_ASM2744814v1_genomic.fna/markers.fasta
[2023-06-29 09:20:27,037] [INFO] Task started: Blastn
[2023-06-29 09:20:27,037] [INFO] Running command: blastn -query GCA_027448145.1_ASM2744814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/reference_markers.fasta -out GCA_027448145.1_ASM2744814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:20:27,539] [INFO] Task succeeded: Blastn
[2023-06-29 09:20:27,543] [INFO] Selected 10 target genomes.
[2023-06-29 09:20:27,544] [INFO] Target genome list was writen to GCA_027448145.1_ASM2744814v1_genomic.fna/target_genomes.txt
[2023-06-29 09:20:27,547] [INFO] Task started: fastANI
[2023-06-29 09:20:27,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c071f0f-62cd-4447-b944-65a2d3df253a/GCA_027448145.1_ASM2744814v1_genomic.fna.gz --refList GCA_027448145.1_ASM2744814v1_genomic.fna/target_genomes.txt --output GCA_027448145.1_ASM2744814v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:20:35,238] [INFO] Task succeeded: fastANI
[2023-06-29 09:20:35,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:20:35,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:20:35,246] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:20:35,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:20:35,246] [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
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	74.6716	63	635	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.6068	97	635	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	74.5507	64	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:20:35,248] [INFO] DFAST Taxonomy check result was written to GCA_027448145.1_ASM2744814v1_genomic.fna/tc_result.tsv
[2023-06-29 09:20:35,249] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:20:35,249] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:20:35,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/checkm_data
[2023-06-29 09:20:35,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:20:35,275] [INFO] Task started: CheckM
[2023-06-29 09:20:35,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027448145.1_ASM2744814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027448145.1_ASM2744814v1_genomic.fna/checkm_input GCA_027448145.1_ASM2744814v1_genomic.fna/checkm_result
[2023-06-29 09:21:04,988] [INFO] Task succeeded: CheckM
[2023-06-29 09:21:04,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:21:05,015] [INFO] ===== Completeness check finished =====
[2023-06-29 09:21:05,016] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:21:05,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027448145.1_ASM2744814v1_genomic.fna/markers.fasta)
[2023-06-29 09:21:05,018] [INFO] Task started: Blastn
[2023-06-29 09:21:05,018] [INFO] Running command: blastn -query GCA_027448145.1_ASM2744814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07346e4e-b235-46fa-a287-96d9b1fb40ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_027448145.1_ASM2744814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:21:05,569] [INFO] Task succeeded: Blastn
[2023-06-29 09:21:05,574] [INFO] Selected 10 target genomes.
[2023-06-29 09:21:05,574] [INFO] Target genome list was writen to GCA_027448145.1_ASM2744814v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:21:05,581] [INFO] Task started: fastANI
[2023-06-29 09:21:05,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c071f0f-62cd-4447-b944-65a2d3df253a/GCA_027448145.1_ASM2744814v1_genomic.fna.gz --refList GCA_027448145.1_ASM2744814v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027448145.1_ASM2744814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:21:10,700] [INFO] Task succeeded: fastANI
[2023-06-29 09:21:10,713] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:21:10,714] [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_002495185.1	s__UBA184 sp002495185	79.5697	226	635	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503985.1	s__UBA184 sp002503985	79.3497	253	635	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044425.1	s__UBA184 sp013044425	78.1784	125	635	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290045.1	s__UBA184 sp013290045	78.0923	168	635	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708885.1	s__Cellulomonas sp000708885	74.8751	52	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699405.1	s__JAAYLR01 sp016699405	74.5498	67	635	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:21:10,716] [INFO] GTDB search result was written to GCA_027448145.1_ASM2744814v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:21:10,716] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:21:10,719] [INFO] DFAST_QC result json was written to GCA_027448145.1_ASM2744814v1_genomic.fna/dqc_result.json
[2023-06-29 09:21:10,719] [INFO] DFAST_QC completed!
[2023-06-29 09:21:10,720] [INFO] Total running time: 0h0m56s