[2023-06-27 06:55:22,034] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:55:22,037] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:55:22,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference
[2023-06-27 06:55:23,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:55:23,415] [INFO] Task started: Prodigal
[2023-06-27 06:55:23,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg92c3b611-acb2-4076-a9b4-41e2a770afbb/GCA_026985495.1_ASM2698549v1_genomic.fna.gz | prodigal -d GCA_026985495.1_ASM2698549v1_genomic.fna/cds.fna -a GCA_026985495.1_ASM2698549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:55:25,771] [INFO] Task succeeded: Prodigal
[2023-06-27 06:55:25,771] [INFO] Task started: HMMsearch
[2023-06-27 06:55:25,771] [INFO] Running command: hmmsearch --tblout GCA_026985495.1_ASM2698549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/reference_markers.hmm GCA_026985495.1_ASM2698549v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:55:25,989] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:55:25,991] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg92c3b611-acb2-4076-a9b4-41e2a770afbb/GCA_026985495.1_ASM2698549v1_genomic.fna.gz]
[2023-06-27 06:55:26,015] [INFO] Query marker FASTA was written to GCA_026985495.1_ASM2698549v1_genomic.fna/markers.fasta
[2023-06-27 06:55:26,015] [INFO] Task started: Blastn
[2023-06-27 06:55:26,016] [INFO] Running command: blastn -query GCA_026985495.1_ASM2698549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/reference_markers.fasta -out GCA_026985495.1_ASM2698549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:55:28,085] [INFO] Task succeeded: Blastn
[2023-06-27 06:55:28,089] [INFO] Selected 21 target genomes.
[2023-06-27 06:55:28,090] [INFO] Target genome list was writen to GCA_026985495.1_ASM2698549v1_genomic.fna/target_genomes.txt
[2023-06-27 06:55:28,117] [INFO] Task started: fastANI
[2023-06-27 06:55:28,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c3b611-acb2-4076-a9b4-41e2a770afbb/GCA_026985495.1_ASM2698549v1_genomic.fna.gz --refList GCA_026985495.1_ASM2698549v1_genomic.fna/target_genomes.txt --output GCA_026985495.1_ASM2698549v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:55:35,155] [INFO] Task succeeded: fastANI
[2023-06-27 06:55:35,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:55:35,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:55:35,157] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:55:35,157] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:55:35,157] [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
--------------------------------------------------------------------------------
[2023-06-27 06:55:35,159] [INFO] DFAST Taxonomy check result was written to GCA_026985495.1_ASM2698549v1_genomic.fna/tc_result.tsv
[2023-06-27 06:55:35,160] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:55:35,160] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:55:35,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/checkm_data
[2023-06-27 06:55:35,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:55:35,187] [INFO] Task started: CheckM
[2023-06-27 06:55:35,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026985495.1_ASM2698549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026985495.1_ASM2698549v1_genomic.fna/checkm_input GCA_026985495.1_ASM2698549v1_genomic.fna/checkm_result
[2023-06-27 06:55:50,928] [INFO] Task succeeded: CheckM
[2023-06-27 06:55:50,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:55:50,950] [INFO] ===== Completeness check finished =====
[2023-06-27 06:55:50,951] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:55:50,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026985495.1_ASM2698549v1_genomic.fna/markers.fasta)
[2023-06-27 06:55:50,951] [INFO] Task started: Blastn
[2023-06-27 06:55:50,951] [INFO] Running command: blastn -query GCA_026985495.1_ASM2698549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050f39ab-7158-4b11-8099-a43ed6bb8ecc/dqc_reference/reference_markers_gtdb.fasta -out GCA_026985495.1_ASM2698549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:55:51,790] [INFO] Task succeeded: Blastn
[2023-06-27 06:55:51,794] [INFO] Selected 11 target genomes.
[2023-06-27 06:55:51,794] [INFO] Target genome list was writen to GCA_026985495.1_ASM2698549v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:55:51,797] [INFO] Task started: fastANI
[2023-06-27 06:55:51,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c3b611-acb2-4076-a9b4-41e2a770afbb/GCA_026985495.1_ASM2698549v1_genomic.fna.gz --refList GCA_026985495.1_ASM2698549v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026985495.1_ASM2698549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:55:56,195] [INFO] Task succeeded: fastANI
[2023-06-27 06:55:56,255] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:55:56,256] [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_003978395.1	s__UBA1140 sp003978395	78.6296	167	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727935.1	s__UBA1140 sp902727935	78.4112	144	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727905.1	s__UBA1140 sp902727905	78.2738	134	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727895.1	s__UBA1140 sp902727895	78.1786	168	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727915.1	s__UBA1140 sp902727915	78.1377	147	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727995.1	s__UBA1140 sp902727995	78.1352	150	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822805.1	s__UBA1140 sp018822805	77.9991	149	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	99.99	99.99	0.97	0.97	2	-
GCF_010892395.1	s__UBA1140 sp010892395	77.3592	85	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153055.1	s__UBA1140 sp013153055	77.2429	99	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494795.1	s__UBA1140 sp015494795	77.1597	102	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727855.1	s__Sulfurovum sp902727855	76.6264	63	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:55:56,258] [INFO] GTDB search result was written to GCA_026985495.1_ASM2698549v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:55:56,259] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:55:56,262] [INFO] DFAST_QC result json was written to GCA_026985495.1_ASM2698549v1_genomic.fna/dqc_result.json
[2023-06-27 06:55:56,262] [INFO] DFAST_QC completed!
[2023-06-27 06:55:56,263] [INFO] Total running time: 0h0m34s