[2023-06-18 13:19:10,406] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:19:10,409] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:19:10,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference
[2023-06-18 13:19:11,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:19:11,592] [INFO] Task started: Prodigal
[2023-06-18 13:19:11,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgea2bd0a3-b9d1-4dce-bea5-7a1abbacf3fd/GCA_018362945.1_ASM1836294v1_genomic.fna.gz | prodigal -d GCA_018362945.1_ASM1836294v1_genomic.fna/cds.fna -a GCA_018362945.1_ASM1836294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:19:16,157] [INFO] Task succeeded: Prodigal
[2023-06-18 13:19:16,158] [INFO] Task started: HMMsearch
[2023-06-18 13:19:16,158] [INFO] Running command: hmmsearch --tblout GCA_018362945.1_ASM1836294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/reference_markers.hmm GCA_018362945.1_ASM1836294v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:19:16,331] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:19:16,332] [INFO] Found 6/6 markers.
[2023-06-18 13:19:16,356] [INFO] Query marker FASTA was written to GCA_018362945.1_ASM1836294v1_genomic.fna/markers.fasta
[2023-06-18 13:19:16,357] [INFO] Task started: Blastn
[2023-06-18 13:19:16,357] [INFO] Running command: blastn -query GCA_018362945.1_ASM1836294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/reference_markers.fasta -out GCA_018362945.1_ASM1836294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:17,682] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:17,688] [INFO] Selected 25 target genomes.
[2023-06-18 13:19:17,688] [INFO] Target genome list was writen to GCA_018362945.1_ASM1836294v1_genomic.fna/target_genomes.txt
[2023-06-18 13:19:17,693] [INFO] Task started: fastANI
[2023-06-18 13:19:17,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgea2bd0a3-b9d1-4dce-bea5-7a1abbacf3fd/GCA_018362945.1_ASM1836294v1_genomic.fna.gz --refList GCA_018362945.1_ASM1836294v1_genomic.fna/target_genomes.txt --output GCA_018362945.1_ASM1836294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:19:31,153] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:31,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:19:31,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:19:31,155] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:19:31,156] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:19:31,156] [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 13:19:31,158] [INFO] DFAST Taxonomy check result was written to GCA_018362945.1_ASM1836294v1_genomic.fna/tc_result.tsv
[2023-06-18 13:19:31,161] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:19:31,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:19:31,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/checkm_data
[2023-06-18 13:19:31,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:19:31,186] [INFO] Task started: CheckM
[2023-06-18 13:19:31,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018362945.1_ASM1836294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018362945.1_ASM1836294v1_genomic.fna/checkm_input GCA_018362945.1_ASM1836294v1_genomic.fna/checkm_result
[2023-06-18 13:19:50,292] [INFO] Task succeeded: CheckM
[2023-06-18 13:19:50,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:19:50,359] [INFO] ===== Completeness check finished =====
[2023-06-18 13:19:50,359] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:19:50,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018362945.1_ASM1836294v1_genomic.fna/markers.fasta)
[2023-06-18 13:19:50,360] [INFO] Task started: Blastn
[2023-06-18 13:19:50,360] [INFO] Running command: blastn -query GCA_018362945.1_ASM1836294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8798d07f-b3ad-4260-8e53-816f2124e91d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018362945.1_ASM1836294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:51,483] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:51,488] [INFO] Selected 16 target genomes.
[2023-06-18 13:19:51,488] [INFO] Target genome list was writen to GCA_018362945.1_ASM1836294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:19:51,495] [INFO] Task started: fastANI
[2023-06-18 13:19:51,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgea2bd0a3-b9d1-4dce-bea5-7a1abbacf3fd/GCA_018362945.1_ASM1836294v1_genomic.fna.gz --refList GCA_018362945.1_ASM1836294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018362945.1_ASM1836294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:19:55,938] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:55,950] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:19:55,950] [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_000432275.1	s__CAZU01 sp000432275	98.8788	501	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.86	98.76	0.93	0.90	5	conclusive
GCA_018362935.1	s__CAZU01 sp018362935	78.1063	156	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935485.1	s__MGBC133411 sp017935485	78.0519	97	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	98.32	98.32	0.87	0.87	2	-
GCA_000436375.1	s__Scatacola_A faecigallinarum	77.8985	135	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatacola_A	95.0	97.40	96.59	0.91	0.88	10	-
GCA_905210515.1	s__CAJLXD01 sp905210515	77.8944	79	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585375.1	s__MGBC133411 sp910585375	77.8735	120	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480995.1	s__CAZU01 sp017480995	77.7878	143	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917125.1	s__Scatocola faecipullorum	77.7216	142	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_900551585.1	s__CAJLXD01 sp900551585	77.6342	112	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626035.1	s__JAGAJR01 sp017626035	77.5566	116	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917175.1	s__51-20 sp001917175	77.5135	83	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	99.01	98.90	0.93	0.93	4	-
GCA_900538765.1	s__HGM16780 sp900538765	77.2049	109	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	98.94	98.77	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-18 13:19:55,952] [INFO] GTDB search result was written to GCA_018362945.1_ASM1836294v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:19:55,952] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:19:55,957] [INFO] DFAST_QC result json was written to GCA_018362945.1_ASM1836294v1_genomic.fna/dqc_result.json
[2023-06-18 13:19:55,957] [INFO] DFAST_QC completed!
[2023-06-18 13:19:55,957] [INFO] Total running time: 0h0m46s