[2023-06-19 12:58:50,745] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:58:50,747] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:58:50,747] [INFO] DQC Reference Directory: /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference
[2023-06-19 12:58:52,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:58:52,053] [INFO] Task started: Prodigal
[2023-06-19 12:58:52,054] [INFO] Running command: gunzip -c /var/lib/cwl/stge9e73866-d9d4-43ed-a45b-770c7aa3f0eb/GCA_013285655.1_ASM1328565v1_genomic.fna.gz | prodigal -d GCA_013285655.1_ASM1328565v1_genomic.fna/cds.fna -a GCA_013285655.1_ASM1328565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:59:02,493] [INFO] Task succeeded: Prodigal
[2023-06-19 12:59:02,494] [INFO] Task started: HMMsearch
[2023-06-19 12:59:02,494] [INFO] Running command: hmmsearch --tblout GCA_013285655.1_ASM1328565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/reference_markers.hmm GCA_013285655.1_ASM1328565v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:59:02,756] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:59:02,758] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge9e73866-d9d4-43ed-a45b-770c7aa3f0eb/GCA_013285655.1_ASM1328565v1_genomic.fna.gz]
[2023-06-19 12:59:02,788] [INFO] Query marker FASTA was written to GCA_013285655.1_ASM1328565v1_genomic.fna/markers.fasta
[2023-06-19 12:59:02,788] [INFO] Task started: Blastn
[2023-06-19 12:59:02,789] [INFO] Running command: blastn -query GCA_013285655.1_ASM1328565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/reference_markers.fasta -out GCA_013285655.1_ASM1328565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:03,366] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:03,371] [INFO] Selected 18 target genomes.
[2023-06-19 12:59:03,371] [INFO] Target genome list was writen to GCA_013285655.1_ASM1328565v1_genomic.fna/target_genomes.txt
[2023-06-19 12:59:03,375] [INFO] Task started: fastANI
[2023-06-19 12:59:03,375] [INFO] Running command: fastANI --query /var/lib/cwl/stge9e73866-d9d4-43ed-a45b-770c7aa3f0eb/GCA_013285655.1_ASM1328565v1_genomic.fna.gz --refList GCA_013285655.1_ASM1328565v1_genomic.fna/target_genomes.txt --output GCA_013285655.1_ASM1328565v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:59:15,704] [INFO] Task succeeded: fastANI
[2023-06-19 12:59:15,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:59:15,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:59:15,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:59:15,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:59:15,707] [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
--------------------------------------------------------------------------------
[2023-06-19 12:59:15,709] [INFO] DFAST Taxonomy check result was written to GCA_013285655.1_ASM1328565v1_genomic.fna/tc_result.tsv
[2023-06-19 12:59:15,710] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:59:15,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:59:15,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/checkm_data
[2023-06-19 12:59:15,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:59:15,748] [INFO] Task started: CheckM
[2023-06-19 12:59:15,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013285655.1_ASM1328565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013285655.1_ASM1328565v1_genomic.fna/checkm_input GCA_013285655.1_ASM1328565v1_genomic.fna/checkm_result
[2023-06-19 12:59:49,601] [INFO] Task succeeded: CheckM
[2023-06-19 12:59:49,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:59:49,620] [INFO] ===== Completeness check finished =====
[2023-06-19 12:59:49,620] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:59:49,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013285655.1_ASM1328565v1_genomic.fna/markers.fasta)
[2023-06-19 12:59:49,621] [INFO] Task started: Blastn
[2023-06-19 12:59:49,621] [INFO] Running command: blastn -query GCA_013285655.1_ASM1328565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1ec27a4-d6af-4f4c-b57e-4a2ac64235a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_013285655.1_ASM1328565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:50,367] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:50,372] [INFO] Selected 17 target genomes.
[2023-06-19 12:59:50,373] [INFO] Target genome list was writen to GCA_013285655.1_ASM1328565v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:59:50,431] [INFO] Task started: fastANI
[2023-06-19 12:59:50,432] [INFO] Running command: fastANI --query /var/lib/cwl/stge9e73866-d9d4-43ed-a45b-770c7aa3f0eb/GCA_013285655.1_ASM1328565v1_genomic.fna.gz --refList GCA_013285655.1_ASM1328565v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013285655.1_ASM1328565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:00:00,214] [INFO] Task succeeded: fastANI
[2023-06-19 13:00:00,225] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:00:00,225] [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_013285655.1	s__JABEUT01 sp013285655	100.0	833	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__Palsa-948_A;g__JABEUT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013288345.1	s__JABEUT01 sp013288345	79.1896	333	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__Palsa-948_A;g__JABEUT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289475.1	s__JABEUT01 sp013289475	78.378	186	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__Palsa-948_A;g__JABEUT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289395.1	s__JABEUT01 sp013289395	77.4722	107	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__Palsa-948_A;g__JABEUT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901055.1	s__JABEUT01 sp903901055	75.8922	53	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__Palsa-948_A;g__JABEUT01	95.0	99.94	99.90	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2023-06-19 13:00:00,228] [INFO] GTDB search result was written to GCA_013285655.1_ASM1328565v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:00:00,229] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:00:00,232] [INFO] DFAST_QC result json was written to GCA_013285655.1_ASM1328565v1_genomic.fna/dqc_result.json
[2023-06-19 13:00:00,232] [INFO] DFAST_QC completed!
[2023-06-19 13:00:00,232] [INFO] Total running time: 0h1m9s