[2023-06-18 21:50:41,632] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:50:41,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:50:41,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference
[2023-06-18 21:50:43,298] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:50:43,299] [INFO] Task started: Prodigal
[2023-06-18 21:50:43,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg592d0e08-1497-4185-8201-45d90aa1eeb1/GCA_018064725.1_ASM1806472v1_genomic.fna.gz | prodigal -d GCA_018064725.1_ASM1806472v1_genomic.fna/cds.fna -a GCA_018064725.1_ASM1806472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:50:54,910] [INFO] Task succeeded: Prodigal
[2023-06-18 21:50:54,910] [INFO] Task started: HMMsearch
[2023-06-18 21:50:54,910] [INFO] Running command: hmmsearch --tblout GCA_018064725.1_ASM1806472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/reference_markers.hmm GCA_018064725.1_ASM1806472v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:50:55,149] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:50:55,150] [INFO] Found 6/6 markers.
[2023-06-18 21:50:55,179] [INFO] Query marker FASTA was written to GCA_018064725.1_ASM1806472v1_genomic.fna/markers.fasta
[2023-06-18 21:50:55,179] [INFO] Task started: Blastn
[2023-06-18 21:50:55,179] [INFO] Running command: blastn -query GCA_018064725.1_ASM1806472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/reference_markers.fasta -out GCA_018064725.1_ASM1806472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:50:55,819] [INFO] Task succeeded: Blastn
[2023-06-18 21:50:55,825] [INFO] Selected 25 target genomes.
[2023-06-18 21:50:55,825] [INFO] Target genome list was writen to GCA_018064725.1_ASM1806472v1_genomic.fna/target_genomes.txt
[2023-06-18 21:50:55,850] [INFO] Task started: fastANI
[2023-06-18 21:50:55,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg592d0e08-1497-4185-8201-45d90aa1eeb1/GCA_018064725.1_ASM1806472v1_genomic.fna.gz --refList GCA_018064725.1_ASM1806472v1_genomic.fna/target_genomes.txt --output GCA_018064725.1_ASM1806472v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:51:09,243] [INFO] Task succeeded: fastANI
[2023-06-18 21:51:09,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:51:09,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:51:09,247] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:51:09,247] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:51:09,247] [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
--------------------------------------------------------------------------------
[2023-06-18 21:51:09,249] [INFO] DFAST Taxonomy check result was written to GCA_018064725.1_ASM1806472v1_genomic.fna/tc_result.tsv
[2023-06-18 21:51:09,250] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:51:09,250] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:51:09,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/checkm_data
[2023-06-18 21:51:09,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:51:09,286] [INFO] Task started: CheckM
[2023-06-18 21:51:09,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064725.1_ASM1806472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064725.1_ASM1806472v1_genomic.fna/checkm_input GCA_018064725.1_ASM1806472v1_genomic.fna/checkm_result
[2023-06-18 21:51:47,692] [INFO] Task succeeded: CheckM
[2023-06-18 21:51:47,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:51:47,723] [INFO] ===== Completeness check finished =====
[2023-06-18 21:51:47,723] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:51:47,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064725.1_ASM1806472v1_genomic.fna/markers.fasta)
[2023-06-18 21:51:47,724] [INFO] Task started: Blastn
[2023-06-18 21:51:47,724] [INFO] Running command: blastn -query GCA_018064725.1_ASM1806472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45a885e-4e49-4b70-bd9f-84e178feba27/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064725.1_ASM1806472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:51:48,834] [INFO] Task succeeded: Blastn
[2023-06-18 21:51:48,841] [INFO] Selected 19 target genomes.
[2023-06-18 21:51:48,841] [INFO] Target genome list was writen to GCA_018064725.1_ASM1806472v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:51:48,891] [INFO] Task started: fastANI
[2023-06-18 21:51:48,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg592d0e08-1497-4185-8201-45d90aa1eeb1/GCA_018064725.1_ASM1806472v1_genomic.fna.gz --refList GCA_018064725.1_ASM1806472v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064725.1_ASM1806472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:51:56,006] [INFO] Task succeeded: fastANI
[2023-06-18 21:51:56,020] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:51:56,020] [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_018064725.1	s__Cryptobacteroides sp018064725	100.0	646	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016293535.1	s__Cryptobacteroides sp016293535	78.5051	126	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554455.1	s__Cryptobacteroides sp004554455	78.4491	77	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.35	97.49	0.82	0.75	12	-
GCA_002314885.1	s__Cryptobacteroides sp002314885	78.3354	152	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938925.1	s__Cryptobacteroides sp017938925	78.0855	77	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.18	96.33	0.77	0.70	3	-
GCA_015060255.1	s__Cryptobacteroides sp015060255	77.6912	87	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.27	97.27	0.78	0.78	2	-
GCA_017415715.1	s__Cryptobacteroides sp017415715	77.426	93	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550025.1	s__Cryptobacteroides sp017550025	77.1668	71	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469845.1	s__Cryptobacteroides sp017469845	77.1591	64	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.79	96.73	0.85	0.76	5	-
GCA_017561265.1	s__Cryptobacteroides sp017561265	77.0288	66	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017560625.1	s__Cryptobacteroides sp017560625	76.8702	61	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549505.1	s__Cryptobacteroides sp017549505	76.8323	74	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399865.1	s__Cryptobacteroides sp017399865	76.7467	77	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556765.1	s__Cryptobacteroides sp017556765	76.5303	69	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:51:56,022] [INFO] GTDB search result was written to GCA_018064725.1_ASM1806472v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:51:56,025] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:51:56,028] [INFO] DFAST_QC result json was written to GCA_018064725.1_ASM1806472v1_genomic.fna/dqc_result.json
[2023-06-18 21:51:56,028] [INFO] DFAST_QC completed!
[2023-06-18 21:51:56,028] [INFO] Total running time: 0h1m14s