[2023-06-18 18:10:31,155] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:31,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:31,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference
[2023-06-18 18:10:32,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:32,466] [INFO] Task started: Prodigal
[2023-06-18 18:10:32,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg00655197-5e02-44de-9753-e23f0ff5a5db/GCA_018657125.1_ASM1865712v1_genomic.fna.gz | prodigal -d GCA_018657125.1_ASM1865712v1_genomic.fna/cds.fna -a GCA_018657125.1_ASM1865712v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:39,904] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:39,904] [INFO] Task started: HMMsearch
[2023-06-18 18:10:39,904] [INFO] Running command: hmmsearch --tblout GCA_018657125.1_ASM1865712v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/reference_markers.hmm GCA_018657125.1_ASM1865712v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:40,212] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:40,216] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00655197-5e02-44de-9753-e23f0ff5a5db/GCA_018657125.1_ASM1865712v1_genomic.fna.gz]
[2023-06-18 18:10:40,253] [INFO] Query marker FASTA was written to GCA_018657125.1_ASM1865712v1_genomic.fna/markers.fasta
[2023-06-18 18:10:40,253] [INFO] Task started: Blastn
[2023-06-18 18:10:40,254] [INFO] Running command: blastn -query GCA_018657125.1_ASM1865712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/reference_markers.fasta -out GCA_018657125.1_ASM1865712v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:40,877] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:40,882] [INFO] Selected 28 target genomes.
[2023-06-18 18:10:40,882] [INFO] Target genome list was writen to GCA_018657125.1_ASM1865712v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:40,883] [INFO] Task started: fastANI
[2023-06-18 18:10:40,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg00655197-5e02-44de-9753-e23f0ff5a5db/GCA_018657125.1_ASM1865712v1_genomic.fna.gz --refList GCA_018657125.1_ASM1865712v1_genomic.fna/target_genomes.txt --output GCA_018657125.1_ASM1865712v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:56,048] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:56,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:56,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:56,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:56,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:56,052] [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
--------------------------------------------------------------------------------
[2023-06-18 18:10:56,055] [INFO] DFAST Taxonomy check result was written to GCA_018657125.1_ASM1865712v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:56,059] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:56,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:56,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/checkm_data
[2023-06-18 18:10:56,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:56,110] [INFO] Task started: CheckM
[2023-06-18 18:10:56,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018657125.1_ASM1865712v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018657125.1_ASM1865712v1_genomic.fna/checkm_input GCA_018657125.1_ASM1865712v1_genomic.fna/checkm_result
[2023-06-18 18:11:25,023] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:25,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:25,052] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:25,053] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:25,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018657125.1_ASM1865712v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:25,054] [INFO] Task started: Blastn
[2023-06-18 18:11:25,054] [INFO] Running command: blastn -query GCA_018657125.1_ASM1865712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4bc058-8d55-4dcd-9b23-6d6100593291/dqc_reference/reference_markers_gtdb.fasta -out GCA_018657125.1_ASM1865712v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:25,897] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:25,901] [INFO] Selected 18 target genomes.
[2023-06-18 18:11:25,901] [INFO] Target genome list was writen to GCA_018657125.1_ASM1865712v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:25,903] [INFO] Task started: fastANI
[2023-06-18 18:11:25,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg00655197-5e02-44de-9753-e23f0ff5a5db/GCA_018657125.1_ASM1865712v1_genomic.fna.gz --refList GCA_018657125.1_ASM1865712v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018657125.1_ASM1865712v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:34,033] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:34,043] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:34,043] [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_018648825.1	s__Thiopontia sp018648825	99.8327	652	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.74	99.68	0.85	0.80	15	conclusive
GCA_013349825.1	s__Thiopontia sp013349825	79.4317	218	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.78	99.58	0.88	0.82	21	-
GCA_018671205.1	s__Thiopontia sp018671205	77.6133	162	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384675.1	s__Thiopontia autotrophica	77.2986	98	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.91	99.91	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:34,057] [INFO] GTDB search result was written to GCA_018657125.1_ASM1865712v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:34,064] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:34,067] [INFO] DFAST_QC result json was written to GCA_018657125.1_ASM1865712v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:34,067] [INFO] DFAST_QC completed!
[2023-06-18 18:11:34,068] [INFO] Total running time: 0h1m3s