[2023-06-28 23:05:49,993] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:05:49,995] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:05:49,995] [INFO] DQC Reference Directory: /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference
[2023-06-28 23:05:51,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:05:51,273] [INFO] Task started: Prodigal
[2023-06-28 23:05:51,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgcba9fbc7-9aef-42c9-8381-504e6a5f17e9/GCA_020052435.1_ASM2005243v1_genomic.fna.gz | prodigal -d GCA_020052435.1_ASM2005243v1_genomic.fna/cds.fna -a GCA_020052435.1_ASM2005243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:05:53,877] [INFO] Task succeeded: Prodigal
[2023-06-28 23:05:53,877] [INFO] Task started: HMMsearch
[2023-06-28 23:05:53,877] [INFO] Running command: hmmsearch --tblout GCA_020052435.1_ASM2005243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/reference_markers.hmm GCA_020052435.1_ASM2005243v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:05:54,015] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:05:54,017] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcba9fbc7-9aef-42c9-8381-504e6a5f17e9/GCA_020052435.1_ASM2005243v1_genomic.fna.gz]
[2023-06-28 23:05:54,032] [INFO] Query marker FASTA was written to GCA_020052435.1_ASM2005243v1_genomic.fna/markers.fasta
[2023-06-28 23:05:54,032] [INFO] Task started: Blastn
[2023-06-28 23:05:54,033] [INFO] Running command: blastn -query GCA_020052435.1_ASM2005243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/reference_markers.fasta -out GCA_020052435.1_ASM2005243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:05:54,656] [INFO] Task succeeded: Blastn
[2023-06-28 23:05:54,660] [INFO] Selected 23 target genomes.
[2023-06-28 23:05:54,660] [INFO] Target genome list was writen to GCA_020052435.1_ASM2005243v1_genomic.fna/target_genomes.txt
[2023-06-28 23:05:54,664] [INFO] Task started: fastANI
[2023-06-28 23:05:54,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba9fbc7-9aef-42c9-8381-504e6a5f17e9/GCA_020052435.1_ASM2005243v1_genomic.fna.gz --refList GCA_020052435.1_ASM2005243v1_genomic.fna/target_genomes.txt --output GCA_020052435.1_ASM2005243v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:06:11,299] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:11,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:06:11,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:06:11,302] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:06:11,302] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:06:11,302] [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
--------------------------------------------------------------------------------
[2023-06-28 23:06:11,304] [INFO] DFAST Taxonomy check result was written to GCA_020052435.1_ASM2005243v1_genomic.fna/tc_result.tsv
[2023-06-28 23:06:11,305] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:06:11,305] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:06:11,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/checkm_data
[2023-06-28 23:06:11,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:06:11,324] [INFO] Task started: CheckM
[2023-06-28 23:06:11,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020052435.1_ASM2005243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020052435.1_ASM2005243v1_genomic.fna/checkm_input GCA_020052435.1_ASM2005243v1_genomic.fna/checkm_result
[2023-06-28 23:06:25,855] [INFO] Task succeeded: CheckM
[2023-06-28 23:06:25,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.52%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:06:25,887] [INFO] ===== Completeness check finished =====
[2023-06-28 23:06:25,887] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:06:25,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020052435.1_ASM2005243v1_genomic.fna/markers.fasta)
[2023-06-28 23:06:25,888] [INFO] Task started: Blastn
[2023-06-28 23:06:25,888] [INFO] Running command: blastn -query GCA_020052435.1_ASM2005243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0b48fa-e757-4e30-b9b7-3ca5e4afb605/dqc_reference/reference_markers_gtdb.fasta -out GCA_020052435.1_ASM2005243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:06:26,822] [INFO] Task succeeded: Blastn
[2023-06-28 23:06:26,826] [INFO] Selected 19 target genomes.
[2023-06-28 23:06:26,826] [INFO] Target genome list was writen to GCA_020052435.1_ASM2005243v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:06:26,879] [INFO] Task started: fastANI
[2023-06-28 23:06:26,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba9fbc7-9aef-42c9-8381-504e6a5f17e9/GCA_020052435.1_ASM2005243v1_genomic.fna.gz --refList GCA_020052435.1_ASM2005243v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020052435.1_ASM2005243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:06:35,423] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:35,428] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:06:35,429] [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_003599345.1	s__SURF-36 sp003599345	78.2965	70	284	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__SURF-36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541445.1	s__UBA9673 sp003541445	77.9424	79	284	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__UBA9673	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003530255.1	s__UBA9673 sp003530255	77.8833	86	284	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__UBA9673	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:06:35,431] [INFO] GTDB search result was written to GCA_020052435.1_ASM2005243v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:06:35,432] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:06:35,434] [INFO] DFAST_QC result json was written to GCA_020052435.1_ASM2005243v1_genomic.fna/dqc_result.json
[2023-06-28 23:06:35,435] [INFO] DFAST_QC completed!
[2023-06-28 23:06:35,435] [INFO] Total running time: 0h0m45s