[2023-06-29 19:44:53,480] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:44:53,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:44:53,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference
[2023-06-29 19:44:54,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:44:54,895] [INFO] Task started: Prodigal
[2023-06-29 19:44:54,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a1566fd-9b16-4320-b9f3-396589ac5ef1/GCA_023261175.1_ASM2326117v1_genomic.fna.gz | prodigal -d GCA_023261175.1_ASM2326117v1_genomic.fna/cds.fna -a GCA_023261175.1_ASM2326117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:45:00,749] [INFO] Task succeeded: Prodigal
[2023-06-29 19:45:00,750] [INFO] Task started: HMMsearch
[2023-06-29 19:45:00,750] [INFO] Running command: hmmsearch --tblout GCA_023261175.1_ASM2326117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/reference_markers.hmm GCA_023261175.1_ASM2326117v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:45:01,035] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:45:01,036] [INFO] Found 6/6 markers.
[2023-06-29 19:45:01,067] [INFO] Query marker FASTA was written to GCA_023261175.1_ASM2326117v1_genomic.fna/markers.fasta
[2023-06-29 19:45:01,067] [INFO] Task started: Blastn
[2023-06-29 19:45:01,067] [INFO] Running command: blastn -query GCA_023261175.1_ASM2326117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/reference_markers.fasta -out GCA_023261175.1_ASM2326117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:01,861] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:01,865] [INFO] Selected 20 target genomes.
[2023-06-29 19:45:01,865] [INFO] Target genome list was writen to GCA_023261175.1_ASM2326117v1_genomic.fna/target_genomes.txt
[2023-06-29 19:45:01,870] [INFO] Task started: fastANI
[2023-06-29 19:45:01,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1566fd-9b16-4320-b9f3-396589ac5ef1/GCA_023261175.1_ASM2326117v1_genomic.fna.gz --refList GCA_023261175.1_ASM2326117v1_genomic.fna/target_genomes.txt --output GCA_023261175.1_ASM2326117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:45:18,005] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:18,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:45:18,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:45:18,007] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:45:18,007] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:45:18,008] [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
--------------------------------------------------------------------------------
[2023-06-29 19:45:18,010] [INFO] DFAST Taxonomy check result was written to GCA_023261175.1_ASM2326117v1_genomic.fna/tc_result.tsv
[2023-06-29 19:45:18,011] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:45:18,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:45:18,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/checkm_data
[2023-06-29 19:45:18,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:45:18,040] [INFO] Task started: CheckM
[2023-06-29 19:45:18,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023261175.1_ASM2326117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023261175.1_ASM2326117v1_genomic.fna/checkm_input GCA_023261175.1_ASM2326117v1_genomic.fna/checkm_result
[2023-06-29 19:45:41,926] [INFO] Task succeeded: CheckM
[2023-06-29 19:45:41,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:45:41,950] [INFO] ===== Completeness check finished =====
[2023-06-29 19:45:41,950] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:45:41,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023261175.1_ASM2326117v1_genomic.fna/markers.fasta)
[2023-06-29 19:45:41,951] [INFO] Task started: Blastn
[2023-06-29 19:45:41,951] [INFO] Running command: blastn -query GCA_023261175.1_ASM2326117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaaff38f-2734-4959-94a1-2a897a13fd61/dqc_reference/reference_markers_gtdb.fasta -out GCA_023261175.1_ASM2326117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:42,812] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:42,816] [INFO] Selected 19 target genomes.
[2023-06-29 19:45:42,816] [INFO] Target genome list was writen to GCA_023261175.1_ASM2326117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:45:42,852] [INFO] Task started: fastANI
[2023-06-29 19:45:42,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1566fd-9b16-4320-b9f3-396589ac5ef1/GCA_023261175.1_ASM2326117v1_genomic.fna.gz --refList GCA_023261175.1_ASM2326117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023261175.1_ASM2326117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:45:49,797] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:49,808] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:45:49,808] [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_002501485.1	s__Casp-actino5 sp002501485	79.2574	144	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.77	99.74	0.92	0.90	3	-
GCA_012269985.1	s__Casp-actino5 sp012269985	79.2463	162	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.07	98.07	0.92	0.92	2	-
GCA_002727235.1	s__Casp-actino5 sp002727235	78.9967	151	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	97.22	95.99	0.84	0.77	5	-
GCA_001510385.1	s__Casp-actino5 sp001510385	78.9514	178	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.68	99.68	0.96	0.96	2	-
GCA_017859785.1	s__Casp-actino5 sp017859785	76.8727	55	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.23	98.27	0.91	0.86	15	-
--------------------------------------------------------------------------------
[2023-06-29 19:45:49,810] [INFO] GTDB search result was written to GCA_023261175.1_ASM2326117v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:45:49,810] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:45:49,814] [INFO] DFAST_QC result json was written to GCA_023261175.1_ASM2326117v1_genomic.fna/dqc_result.json
[2023-06-29 19:45:49,814] [INFO] DFAST_QC completed!
[2023-06-29 19:45:49,814] [INFO] Total running time: 0h0m56s