[2023-06-04 20:54:52,746] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:54:52,749] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:54:52,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference
[2023-06-04 20:54:54,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:54:54,244] [INFO] Task started: Prodigal
[2023-06-04 20:54:54,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg016af342-545d-4659-8c05-5654f4823260/GCA_001439005.1_ASM143900v1_genomic.fna.gz | prodigal -d GCA_001439005.1_ASM143900v1_genomic.fna/cds.fna -a GCA_001439005.1_ASM143900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:54:58,722] [INFO] Task succeeded: Prodigal
[2023-06-04 20:54:58,723] [INFO] Task started: HMMsearch
[2023-06-04 20:54:58,723] [INFO] Running command: hmmsearch --tblout GCA_001439005.1_ASM143900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/reference_markers.hmm GCA_001439005.1_ASM143900v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:54:58,931] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:54:58,934] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg016af342-545d-4659-8c05-5654f4823260/GCA_001439005.1_ASM143900v1_genomic.fna.gz]
[2023-06-04 20:54:58,957] [INFO] Query marker FASTA was written to GCA_001439005.1_ASM143900v1_genomic.fna/markers.fasta
[2023-06-04 20:54:58,957] [INFO] Task started: Blastn
[2023-06-04 20:54:58,957] [INFO] Running command: blastn -query GCA_001439005.1_ASM143900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/reference_markers.fasta -out GCA_001439005.1_ASM143900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:54:59,509] [INFO] Task succeeded: Blastn
[2023-06-04 20:54:59,519] [INFO] Selected 10 target genomes.
[2023-06-04 20:54:59,520] [INFO] Target genome list was writen to GCA_001439005.1_ASM143900v1_genomic.fna/target_genomes.txt
[2023-06-04 20:54:59,571] [INFO] Task started: fastANI
[2023-06-04 20:54:59,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg016af342-545d-4659-8c05-5654f4823260/GCA_001439005.1_ASM143900v1_genomic.fna.gz --refList GCA_001439005.1_ASM143900v1_genomic.fna/target_genomes.txt --output GCA_001439005.1_ASM143900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:55:02,974] [INFO] Task succeeded: fastANI
[2023-06-04 20:55:02,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:55:02,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:55:02,991] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:55:02,991] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:55:02,992] [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
--------------------------------------------------------------------------------
[2023-06-04 20:55:03,006] [INFO] DFAST Taxonomy check result was written to GCA_001439005.1_ASM143900v1_genomic.fna/tc_result.tsv
[2023-06-04 20:55:03,007] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:55:03,007] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:55:03,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/checkm_data
[2023-06-04 20:55:03,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:55:03,040] [INFO] Task started: CheckM
[2023-06-04 20:55:03,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001439005.1_ASM143900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001439005.1_ASM143900v1_genomic.fna/checkm_input GCA_001439005.1_ASM143900v1_genomic.fna/checkm_result
[2023-06-04 20:55:24,715] [INFO] Task succeeded: CheckM
[2023-06-04 20:55:24,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 2.08%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-04 20:55:24,745] [INFO] ===== Completeness check finished =====
[2023-06-04 20:55:24,745] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:55:24,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001439005.1_ASM143900v1_genomic.fna/markers.fasta)
[2023-06-04 20:55:24,746] [INFO] Task started: Blastn
[2023-06-04 20:55:24,746] [INFO] Running command: blastn -query GCA_001439005.1_ASM143900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf48ba79-d2fc-4b54-9f39-c0bec1366866/dqc_reference/reference_markers_gtdb.fasta -out GCA_001439005.1_ASM143900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:55:25,494] [INFO] Task succeeded: Blastn
[2023-06-04 20:55:25,501] [INFO] Selected 12 target genomes.
[2023-06-04 20:55:25,501] [INFO] Target genome list was writen to GCA_001439005.1_ASM143900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:55:25,559] [INFO] Task started: fastANI
[2023-06-04 20:55:25,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg016af342-545d-4659-8c05-5654f4823260/GCA_001439005.1_ASM143900v1_genomic.fna.gz --refList GCA_001439005.1_ASM143900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001439005.1_ASM143900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:55:28,670] [INFO] Task succeeded: fastANI
[2023-06-04 20:55:28,681] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:55:28,681] [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_001438985.1	s__UBA3006 sp001438985	98.9245	213	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.19	98.19	0.91	0.91	2	conclusive
GCA_014190095.1	s__UBA3006 sp014190095	81.6414	163	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903895515.1	s__UBA3006 sp903895515	80.719	136	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.23	97.46	0.84	0.83	3	-
GCA_017853385.1	s__UBA3006 sp017853385	79.2897	151	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903850275.1	s__UBA3006 sp903850275	78.2507	55	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	96.61	96.61	0.70	0.70	2	-
GCA_007279905.1	s__UBA3006 sp007279905	76.8317	52	274	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:55:28,684] [INFO] GTDB search result was written to GCA_001439005.1_ASM143900v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:55:28,684] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:55:28,688] [INFO] DFAST_QC result json was written to GCA_001439005.1_ASM143900v1_genomic.fna/dqc_result.json
[2023-06-04 20:55:28,688] [INFO] DFAST_QC completed!
[2023-06-04 20:55:28,688] [INFO] Total running time: 0h0m36s