[2023-06-07 21:13:34,800] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:34,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:34,802] [INFO] DQC Reference Directory: /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference
[2023-06-07 21:13:36,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:36,207] [INFO] Task started: Prodigal
[2023-06-07 21:13:36,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg67a74a5e-1b1f-4530-8ebb-4f96d82b9d00/GCA_947486875.1_ZE-15may19-79_genomic.fna.gz | prodigal -d GCA_947486875.1_ZE-15may19-79_genomic.fna/cds.fna -a GCA_947486875.1_ZE-15may19-79_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:42,917] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:42,917] [INFO] Task started: HMMsearch
[2023-06-07 21:13:42,917] [INFO] Running command: hmmsearch --tblout GCA_947486875.1_ZE-15may19-79_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/reference_markers.hmm GCA_947486875.1_ZE-15may19-79_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:43,136] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:43,137] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg67a74a5e-1b1f-4530-8ebb-4f96d82b9d00/GCA_947486875.1_ZE-15may19-79_genomic.fna.gz]
[2023-06-07 21:13:43,154] [INFO] Query marker FASTA was written to GCA_947486875.1_ZE-15may19-79_genomic.fna/markers.fasta
[2023-06-07 21:13:43,154] [INFO] Task started: Blastn
[2023-06-07 21:13:43,154] [INFO] Running command: blastn -query GCA_947486875.1_ZE-15may19-79_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/reference_markers.fasta -out GCA_947486875.1_ZE-15may19-79_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:43,649] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:43,653] [INFO] Selected 10 target genomes.
[2023-06-07 21:13:43,653] [INFO] Target genome list was writen to GCA_947486875.1_ZE-15may19-79_genomic.fna/target_genomes.txt
[2023-06-07 21:13:43,658] [INFO] Task started: fastANI
[2023-06-07 21:13:43,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a74a5e-1b1f-4530-8ebb-4f96d82b9d00/GCA_947486875.1_ZE-15may19-79_genomic.fna.gz --refList GCA_947486875.1_ZE-15may19-79_genomic.fna/target_genomes.txt --output GCA_947486875.1_ZE-15may19-79_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:13:51,774] [INFO] Task succeeded: fastANI
[2023-06-07 21:13:51,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:13:51,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:13:51,779] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:13:51,779] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:13:51,779] [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
--------------------------------------------------------------------------------
[2023-06-07 21:13:51,781] [INFO] DFAST Taxonomy check result was written to GCA_947486875.1_ZE-15may19-79_genomic.fna/tc_result.tsv
[2023-06-07 21:13:51,781] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:13:51,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:13:51,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/checkm_data
[2023-06-07 21:13:51,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:13:51,802] [INFO] Task started: CheckM
[2023-06-07 21:13:51,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947486875.1_ZE-15may19-79_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947486875.1_ZE-15may19-79_genomic.fna/checkm_input GCA_947486875.1_ZE-15may19-79_genomic.fna/checkm_result
[2023-06-07 21:14:16,529] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:16,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:16,551] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:16,551] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:16,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947486875.1_ZE-15may19-79_genomic.fna/markers.fasta)
[2023-06-07 21:14:16,552] [INFO] Task started: Blastn
[2023-06-07 21:14:16,552] [INFO] Running command: blastn -query GCA_947486875.1_ZE-15may19-79_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cf9b45-901d-4275-9d1c-5c15ebfff0d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_947486875.1_ZE-15may19-79_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:16,989] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:16,993] [INFO] Selected 8 target genomes.
[2023-06-07 21:14:16,993] [INFO] Target genome list was writen to GCA_947486875.1_ZE-15may19-79_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:16,994] [INFO] Task started: fastANI
[2023-06-07 21:14:16,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a74a5e-1b1f-4530-8ebb-4f96d82b9d00/GCA_947486875.1_ZE-15may19-79_genomic.fna.gz --refList GCA_947486875.1_ZE-15may19-79_genomic.fna/target_genomes_gtdb.txt --output GCA_947486875.1_ZE-15may19-79_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:20,238] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:20,248] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:14:20,248] [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_903895475.1	s__UBA953 sp903895475	97.3668	274	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.79	97.63	0.79	0.78	5	conclusive
GCA_903924185.1	s__UBA953 sp903924185	93.8814	226	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.29	99.29	0.85	0.85	2	-
GCA_003569205.1	s__UBA953 sp003569205	93.2017	292	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919185.1	s__UBA953 sp903919185	91.2801	277	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.87	99.74	0.94	0.93	4	-
GCA_002293065.1	s__UBA953 sp002293065	85.8054	291	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.98	96.04	0.82	0.76	4	-
GCA_903925205.1	s__UBA953 sp903925205	85.5755	270	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924965.1	s__UBA953 sp009924965	82.6136	181	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002293125.1	s__UBA953 sp002293125	79.719	147	340	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.83	99.83	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:20,250] [INFO] GTDB search result was written to GCA_947486875.1_ZE-15may19-79_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:20,251] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:20,254] [INFO] DFAST_QC result json was written to GCA_947486875.1_ZE-15may19-79_genomic.fna/dqc_result.json
[2023-06-07 21:14:20,254] [INFO] DFAST_QC completed!
[2023-06-07 21:14:20,255] [INFO] Total running time: 0h0m45s