[2023-06-05 10:33:45,670] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:45,673] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:45,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference
[2023-06-05 10:33:48,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:48,542] [INFO] Task started: Prodigal
[2023-06-05 10:33:48,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg62fb0d33-e6a6-4085-b44b-f8a2a197cfb1/GCA_010022095.1_ASM1002209v1_genomic.fna.gz | prodigal -d GCA_010022095.1_ASM1002209v1_genomic.fna/cds.fna -a GCA_010022095.1_ASM1002209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:33:54,141] [INFO] Task succeeded: Prodigal
[2023-06-05 10:33:54,141] [INFO] Task started: HMMsearch
[2023-06-05 10:33:54,142] [INFO] Running command: hmmsearch --tblout GCA_010022095.1_ASM1002209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/reference_markers.hmm GCA_010022095.1_ASM1002209v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:33:54,490] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:33:54,491] [INFO] Found 6/6 markers.
[2023-06-05 10:33:54,522] [INFO] Query marker FASTA was written to GCA_010022095.1_ASM1002209v1_genomic.fna/markers.fasta
[2023-06-05 10:33:54,523] [INFO] Task started: Blastn
[2023-06-05 10:33:54,523] [INFO] Running command: blastn -query GCA_010022095.1_ASM1002209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/reference_markers.fasta -out GCA_010022095.1_ASM1002209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:33:56,345] [INFO] Task succeeded: Blastn
[2023-06-05 10:33:56,351] [INFO] Selected 31 target genomes.
[2023-06-05 10:33:56,352] [INFO] Target genome list was writen to GCA_010022095.1_ASM1002209v1_genomic.fna/target_genomes.txt
[2023-06-05 10:33:56,374] [INFO] Task started: fastANI
[2023-06-05 10:33:56,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fb0d33-e6a6-4085-b44b-f8a2a197cfb1/GCA_010022095.1_ASM1002209v1_genomic.fna.gz --refList GCA_010022095.1_ASM1002209v1_genomic.fna/target_genomes.txt --output GCA_010022095.1_ASM1002209v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:34:15,812] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:15,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:34:15,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:34:15,814] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:34:15,815] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:34:15,815] [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
--------------------------------------------------------------------------------
[2023-06-05 10:34:15,817] [INFO] DFAST Taxonomy check result was written to GCA_010022095.1_ASM1002209v1_genomic.fna/tc_result.tsv
[2023-06-05 10:34:15,818] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:34:15,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:34:15,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/checkm_data
[2023-06-05 10:34:15,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:34:15,854] [INFO] Task started: CheckM
[2023-06-05 10:34:15,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010022095.1_ASM1002209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010022095.1_ASM1002209v1_genomic.fna/checkm_input GCA_010022095.1_ASM1002209v1_genomic.fna/checkm_result
[2023-06-05 10:34:39,832] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:39,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 3.01%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:34:39,860] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:39,860] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:39,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010022095.1_ASM1002209v1_genomic.fna/markers.fasta)
[2023-06-05 10:34:39,861] [INFO] Task started: Blastn
[2023-06-05 10:34:39,861] [INFO] Running command: blastn -query GCA_010022095.1_ASM1002209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb40479c-7d15-4b57-ad4a-682c31c34b0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_010022095.1_ASM1002209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:40,738] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:40,744] [INFO] Selected 27 target genomes.
[2023-06-05 10:34:40,744] [INFO] Target genome list was writen to GCA_010022095.1_ASM1002209v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:40,783] [INFO] Task started: fastANI
[2023-06-05 10:34:40,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fb0d33-e6a6-4085-b44b-f8a2a197cfb1/GCA_010022095.1_ASM1002209v1_genomic.fna.gz --refList GCA_010022095.1_ASM1002209v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010022095.1_ASM1002209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:34:54,505] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:54,518] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:34:54,519] [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_002342365.1	s__UBA3064 sp002342365	99.4515	263	278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.81	99.60	0.94	0.90	39	conclusive
GCA_002359635.1	s__UBA3064 sp002359635	78.6471	103	278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.69	99.55	0.89	0.78	24	-
GCA_900299025.1	s__UBA3064 sp005787245	76.8328	77	278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	98.97	98.30	0.89	0.84	12	-
GCA_016868095.1	s__UBA3064 sp016868095	76.7269	58	278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:34:54,522] [INFO] GTDB search result was written to GCA_010022095.1_ASM1002209v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:34:54,523] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:34:54,528] [INFO] DFAST_QC result json was written to GCA_010022095.1_ASM1002209v1_genomic.fna/dqc_result.json
[2023-06-05 10:34:54,528] [INFO] DFAST_QC completed!
[2023-06-05 10:34:54,529] [INFO] Total running time: 0h1m9s