[2023-06-18 19:16:43,218] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:16:43,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:16:43,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference
[2023-06-18 19:16:46,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:16:46,133] [INFO] Task started: Prodigal
[2023-06-18 19:16:46,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ee50c27-5504-4be2-8b3e-8d8353ef6459/GCA_018400545.1_ASM1840054v1_genomic.fna.gz | prodigal -d GCA_018400545.1_ASM1840054v1_genomic.fna/cds.fna -a GCA_018400545.1_ASM1840054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:16:59,200] [INFO] Task succeeded: Prodigal
[2023-06-18 19:16:59,200] [INFO] Task started: HMMsearch
[2023-06-18 19:16:59,201] [INFO] Running command: hmmsearch --tblout GCA_018400545.1_ASM1840054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/reference_markers.hmm GCA_018400545.1_ASM1840054v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:16:59,435] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:16:59,437] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7ee50c27-5504-4be2-8b3e-8d8353ef6459/GCA_018400545.1_ASM1840054v1_genomic.fna.gz]
[2023-06-18 19:16:59,480] [INFO] Query marker FASTA was written to GCA_018400545.1_ASM1840054v1_genomic.fna/markers.fasta
[2023-06-18 19:16:59,481] [INFO] Task started: Blastn
[2023-06-18 19:16:59,481] [INFO] Running command: blastn -query GCA_018400545.1_ASM1840054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/reference_markers.fasta -out GCA_018400545.1_ASM1840054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:00,107] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:00,110] [INFO] Selected 18 target genomes.
[2023-06-18 19:17:00,111] [INFO] Target genome list was writen to GCA_018400545.1_ASM1840054v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:00,112] [INFO] Task started: fastANI
[2023-06-18 19:17:00,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee50c27-5504-4be2-8b3e-8d8353ef6459/GCA_018400545.1_ASM1840054v1_genomic.fna.gz --refList GCA_018400545.1_ASM1840054v1_genomic.fna/target_genomes.txt --output GCA_018400545.1_ASM1840054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:14,462] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:14,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:14,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:14,465] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:17:14,465] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 19:17:14,465] [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 19:17:14,467] [INFO] DFAST Taxonomy check result was written to GCA_018400545.1_ASM1840054v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:14,468] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:14,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:14,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/checkm_data
[2023-06-18 19:17:14,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:14,503] [INFO] Task started: CheckM
[2023-06-18 19:17:14,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018400545.1_ASM1840054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018400545.1_ASM1840054v1_genomic.fna/checkm_input GCA_018400545.1_ASM1840054v1_genomic.fna/checkm_result
[2023-06-18 19:17:57,181] [INFO] Task succeeded: CheckM
[2023-06-18 19:17:57,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.02%
Contamintation: 1.60%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 19:17:57,205] [INFO] ===== Completeness check finished =====
[2023-06-18 19:17:57,205] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:17:57,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018400545.1_ASM1840054v1_genomic.fna/markers.fasta)
[2023-06-18 19:17:57,206] [INFO] Task started: Blastn
[2023-06-18 19:17:57,206] [INFO] Running command: blastn -query GCA_018400545.1_ASM1840054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31eea389-c061-48c8-b27d-182675876718/dqc_reference/reference_markers_gtdb.fasta -out GCA_018400545.1_ASM1840054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:57,972] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:57,976] [INFO] Selected 17 target genomes.
[2023-06-18 19:17:57,977] [INFO] Target genome list was writen to GCA_018400545.1_ASM1840054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:17:57,984] [INFO] Task started: fastANI
[2023-06-18 19:17:57,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee50c27-5504-4be2-8b3e-8d8353ef6459/GCA_018400545.1_ASM1840054v1_genomic.fna.gz --refList GCA_018400545.1_ASM1840054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018400545.1_ASM1840054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:18:07,712] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:07,727] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:18:07,728] [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_018400545.1	s__SABY01 sp018400545	100.0	668	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__SABY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012523265.1	s__SABY01 sp012523265	75.7865	50	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__SABY01	95.0	98.83	98.83	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-18 19:18:07,731] [INFO] GTDB search result was written to GCA_018400545.1_ASM1840054v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:18:07,733] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:18:07,736] [INFO] DFAST_QC result json was written to GCA_018400545.1_ASM1840054v1_genomic.fna/dqc_result.json
[2023-06-18 19:18:07,737] [INFO] DFAST_QC completed!
[2023-06-18 19:18:07,737] [INFO] Total running time: 0h1m25s