[2023-06-13 18:25:31,670] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:25:31,676] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:25:31,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference
[2023-06-13 18:25:32,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:25:32,748] [INFO] Task started: Prodigal
[2023-06-13 18:25:32,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg30200a6c-fef8-44f0-9198-e5ab5c6a11d4/GCA_022827645.1_ASM2282764v1_genomic.fna.gz | prodigal -d GCA_022827645.1_ASM2282764v1_genomic.fna/cds.fna -a GCA_022827645.1_ASM2282764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:25:44,950] [INFO] Task succeeded: Prodigal
[2023-06-13 18:25:44,951] [INFO] Task started: HMMsearch
[2023-06-13 18:25:44,951] [INFO] Running command: hmmsearch --tblout GCA_022827645.1_ASM2282764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/reference_markers.hmm GCA_022827645.1_ASM2282764v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:25:45,195] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:25:45,196] [INFO] Found 6/6 markers.
[2023-06-13 18:25:45,238] [INFO] Query marker FASTA was written to GCA_022827645.1_ASM2282764v1_genomic.fna/markers.fasta
[2023-06-13 18:25:45,238] [INFO] Task started: Blastn
[2023-06-13 18:25:45,238] [INFO] Running command: blastn -query GCA_022827645.1_ASM2282764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/reference_markers.fasta -out GCA_022827645.1_ASM2282764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:25:45,774] [INFO] Task succeeded: Blastn
[2023-06-13 18:25:45,777] [INFO] Selected 22 target genomes.
[2023-06-13 18:25:45,778] [INFO] Target genome list was writen to GCA_022827645.1_ASM2282764v1_genomic.fna/target_genomes.txt
[2023-06-13 18:25:45,780] [INFO] Task started: fastANI
[2023-06-13 18:25:45,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg30200a6c-fef8-44f0-9198-e5ab5c6a11d4/GCA_022827645.1_ASM2282764v1_genomic.fna.gz --refList GCA_022827645.1_ASM2282764v1_genomic.fna/target_genomes.txt --output GCA_022827645.1_ASM2282764v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:26:02,684] [INFO] Task succeeded: fastANI
[2023-06-13 18:26:02,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:26:02,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:26:02,687] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:26:02,687] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 18:26:02,688] [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
--------------------------------------------------------------------------------
[2023-06-13 18:26:02,689] [INFO] DFAST Taxonomy check result was written to GCA_022827645.1_ASM2282764v1_genomic.fna/tc_result.tsv
[2023-06-13 18:26:02,690] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:26:02,690] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:26:02,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/checkm_data
[2023-06-13 18:26:02,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:26:02,740] [INFO] Task started: CheckM
[2023-06-13 18:26:02,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022827645.1_ASM2282764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022827645.1_ASM2282764v1_genomic.fna/checkm_input GCA_022827645.1_ASM2282764v1_genomic.fna/checkm_result
[2023-06-13 18:26:39,718] [INFO] Task succeeded: CheckM
[2023-06-13 18:26:39,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:26:39,741] [INFO] ===== Completeness check finished =====
[2023-06-13 18:26:39,741] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:26:39,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022827645.1_ASM2282764v1_genomic.fna/markers.fasta)
[2023-06-13 18:26:39,742] [INFO] Task started: Blastn
[2023-06-13 18:26:39,742] [INFO] Running command: blastn -query GCA_022827645.1_ASM2282764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba2f1c1a-5bad-4007-9496-7fe6ced2d4fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022827645.1_ASM2282764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:26:40,454] [INFO] Task succeeded: Blastn
[2023-06-13 18:26:40,459] [INFO] Selected 19 target genomes.
[2023-06-13 18:26:40,459] [INFO] Target genome list was writen to GCA_022827645.1_ASM2282764v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:26:40,460] [INFO] Task started: fastANI
[2023-06-13 18:26:40,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg30200a6c-fef8-44f0-9198-e5ab5c6a11d4/GCA_022827645.1_ASM2282764v1_genomic.fna.gz --refList GCA_022827645.1_ASM2282764v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022827645.1_ASM2282764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:26:55,029] [INFO] Task succeeded: fastANI
[2023-06-13 18:26:55,034] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:26:55,034] [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_011523265.1	s__Bin18 sp011523265	90.5783	1068	1518	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Bin18;f__Bin18;g__Bin18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238415.1	s__Bin18 sp002238415	88.432	1287	1518	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Bin18;f__Bin18;g__Bin18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523315.1	s__JAAXHF01 sp011523315	77.5266	216	1518	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Bin18;f__Bin18;g__JAAXHF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:26:55,036] [INFO] GTDB search result was written to GCA_022827645.1_ASM2282764v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:26:55,037] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:26:55,039] [INFO] DFAST_QC result json was written to GCA_022827645.1_ASM2282764v1_genomic.fna/dqc_result.json
[2023-06-13 18:26:55,039] [INFO] DFAST_QC completed!
[2023-06-13 18:26:55,039] [INFO] Total running time: 0h1m23s