[2023-06-29 08:24:17,717] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:24:17,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:24:17,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference
[2023-06-29 08:24:20,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:24:20,046] [INFO] Task started: Prodigal
[2023-06-29 08:24:20,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg452ae10b-2498-417a-956f-9d18a96774a7/GCA_020048595.1_ASM2004859v1_genomic.fna.gz | prodigal -d GCA_020048595.1_ASM2004859v1_genomic.fna/cds.fna -a GCA_020048595.1_ASM2004859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:24:36,287] [INFO] Task succeeded: Prodigal
[2023-06-29 08:24:36,288] [INFO] Task started: HMMsearch
[2023-06-29 08:24:36,288] [INFO] Running command: hmmsearch --tblout GCA_020048595.1_ASM2004859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/reference_markers.hmm GCA_020048595.1_ASM2004859v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:24:36,563] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:24:36,565] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg452ae10b-2498-417a-956f-9d18a96774a7/GCA_020048595.1_ASM2004859v1_genomic.fna.gz]
[2023-06-29 08:24:36,613] [INFO] Query marker FASTA was written to GCA_020048595.1_ASM2004859v1_genomic.fna/markers.fasta
[2023-06-29 08:24:36,614] [INFO] Task started: Blastn
[2023-06-29 08:24:36,614] [INFO] Running command: blastn -query GCA_020048595.1_ASM2004859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/reference_markers.fasta -out GCA_020048595.1_ASM2004859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:37,294] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:37,297] [INFO] Selected 15 target genomes.
[2023-06-29 08:24:37,298] [INFO] Target genome list was writen to GCA_020048595.1_ASM2004859v1_genomic.fna/target_genomes.txt
[2023-06-29 08:24:37,302] [INFO] Task started: fastANI
[2023-06-29 08:24:37,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg452ae10b-2498-417a-956f-9d18a96774a7/GCA_020048595.1_ASM2004859v1_genomic.fna.gz --refList GCA_020048595.1_ASM2004859v1_genomic.fna/target_genomes.txt --output GCA_020048595.1_ASM2004859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:24:46,567] [INFO] Task succeeded: fastANI
[2023-06-29 08:24:46,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:24:46,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:24:46,571] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:24:46,571] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 08:24:46,571] [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 08:24:46,587] [INFO] DFAST Taxonomy check result was written to GCA_020048595.1_ASM2004859v1_genomic.fna/tc_result.tsv
[2023-06-29 08:24:46,588] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:24:46,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:24:46,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/checkm_data
[2023-06-29 08:24:46,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:24:46,640] [INFO] Task started: CheckM
[2023-06-29 08:24:46,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020048595.1_ASM2004859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020048595.1_ASM2004859v1_genomic.fna/checkm_input GCA_020048595.1_ASM2004859v1_genomic.fna/checkm_result
[2023-06-29 08:25:36,225] [INFO] Task succeeded: CheckM
[2023-06-29 08:25:36,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.68%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 08:25:36,262] [INFO] ===== Completeness check finished =====
[2023-06-29 08:25:36,262] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:25:36,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020048595.1_ASM2004859v1_genomic.fna/markers.fasta)
[2023-06-29 08:25:36,263] [INFO] Task started: Blastn
[2023-06-29 08:25:36,264] [INFO] Running command: blastn -query GCA_020048595.1_ASM2004859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ebbb1c2-970e-498b-b99a-edcdad97be25/dqc_reference/reference_markers_gtdb.fasta -out GCA_020048595.1_ASM2004859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:25:36,902] [INFO] Task succeeded: Blastn
[2023-06-29 08:25:36,908] [INFO] Selected 13 target genomes.
[2023-06-29 08:25:36,908] [INFO] Target genome list was writen to GCA_020048595.1_ASM2004859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:25:36,921] [INFO] Task started: fastANI
[2023-06-29 08:25:36,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg452ae10b-2498-417a-956f-9d18a96774a7/GCA_020048595.1_ASM2004859v1_genomic.fna.gz --refList GCA_020048595.1_ASM2004859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020048595.1_ASM2004859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:25:46,474] [INFO] Task succeeded: fastANI
[2023-06-29 08:25:46,482] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:25:46,482] [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_903879715.1	s__UBA4417 sp903879715	80.5346	572	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.96	99.96	0.96	0.96	2	-
GCA_903913645.1	s__UBA4417 sp903913645	79.5069	503	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917425.1	s__UBA4417 sp903917425	77.9943	216	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887815.1	s__UBA4417 sp903887815	77.3684	167	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.90	99.90	0.90	0.90	2	-
GCA_903878265.1	s__UBA4417 sp903878265	77.1813	181	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.16	98.69	0.84	0.83	4	-
GCA_903946925.1	s__UBA4417 sp903946925	76.9119	190	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.75	99.75	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-29 08:25:46,484] [INFO] GTDB search result was written to GCA_020048595.1_ASM2004859v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:25:46,485] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:25:46,487] [INFO] DFAST_QC result json was written to GCA_020048595.1_ASM2004859v1_genomic.fna/dqc_result.json
[2023-06-29 08:25:46,488] [INFO] DFAST_QC completed!
[2023-06-29 08:25:46,488] [INFO] Total running time: 0h1m29s