[2023-06-19 13:34:21,358] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:34:21,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:34:21,361] [INFO] DQC Reference Directory: /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference
[2023-06-19 13:34:22,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:34:22,565] [INFO] Task started: Prodigal
[2023-06-19 13:34:22,565] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b666f1f-2806-45e3-9ce9-557fa2e2326b/GCA_018389045.1_ASM1838904v1_genomic.fna.gz | prodigal -d GCA_018389045.1_ASM1838904v1_genomic.fna/cds.fna -a GCA_018389045.1_ASM1838904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:34:29,441] [INFO] Task succeeded: Prodigal
[2023-06-19 13:34:29,441] [INFO] Task started: HMMsearch
[2023-06-19 13:34:29,441] [INFO] Running command: hmmsearch --tblout GCA_018389045.1_ASM1838904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/reference_markers.hmm GCA_018389045.1_ASM1838904v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:34:29,682] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:34:29,683] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b666f1f-2806-45e3-9ce9-557fa2e2326b/GCA_018389045.1_ASM1838904v1_genomic.fna.gz]
[2023-06-19 13:34:29,713] [INFO] Query marker FASTA was written to GCA_018389045.1_ASM1838904v1_genomic.fna/markers.fasta
[2023-06-19 13:34:29,714] [INFO] Task started: Blastn
[2023-06-19 13:34:29,714] [INFO] Running command: blastn -query GCA_018389045.1_ASM1838904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/reference_markers.fasta -out GCA_018389045.1_ASM1838904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:34:30,333] [INFO] Task succeeded: Blastn
[2023-06-19 13:34:30,338] [INFO] Selected 11 target genomes.
[2023-06-19 13:34:30,338] [INFO] Target genome list was writen to GCA_018389045.1_ASM1838904v1_genomic.fna/target_genomes.txt
[2023-06-19 13:34:30,341] [INFO] Task started: fastANI
[2023-06-19 13:34:30,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b666f1f-2806-45e3-9ce9-557fa2e2326b/GCA_018389045.1_ASM1838904v1_genomic.fna.gz --refList GCA_018389045.1_ASM1838904v1_genomic.fna/target_genomes.txt --output GCA_018389045.1_ASM1838904v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:34:37,271] [INFO] Task succeeded: fastANI
[2023-06-19 13:34:37,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:34:37,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:34:37,278] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:34:37,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:34:37,279] [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
Thermoflexus hugenholtzii	strain=JAD2	GCA_900187885.1	1495650	1495650	type	True	80.5001	504	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:34:37,280] [INFO] DFAST Taxonomy check result was written to GCA_018389045.1_ASM1838904v1_genomic.fna/tc_result.tsv
[2023-06-19 13:34:37,281] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:34:37,281] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:34:37,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/checkm_data
[2023-06-19 13:34:37,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:34:37,318] [INFO] Task started: CheckM
[2023-06-19 13:34:37,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018389045.1_ASM1838904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018389045.1_ASM1838904v1_genomic.fna/checkm_input GCA_018389045.1_ASM1838904v1_genomic.fna/checkm_result
[2023-06-19 13:35:02,948] [INFO] Task succeeded: CheckM
[2023-06-19 13:35:02,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:35:02,973] [INFO] ===== Completeness check finished =====
[2023-06-19 13:35:02,973] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:35:02,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018389045.1_ASM1838904v1_genomic.fna/markers.fasta)
[2023-06-19 13:35:02,974] [INFO] Task started: Blastn
[2023-06-19 13:35:02,974] [INFO] Running command: blastn -query GCA_018389045.1_ASM1838904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga80e204c-4f92-4235-8373-e96ec62ccad6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018389045.1_ASM1838904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:35:03,933] [INFO] Task succeeded: Blastn
[2023-06-19 13:35:03,938] [INFO] Selected 8 target genomes.
[2023-06-19 13:35:03,938] [INFO] Target genome list was writen to GCA_018389045.1_ASM1838904v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:35:03,942] [INFO] Task started: fastANI
[2023-06-19 13:35:03,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b666f1f-2806-45e3-9ce9-557fa2e2326b/GCA_018389045.1_ASM1838904v1_genomic.fna.gz --refList GCA_018389045.1_ASM1838904v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018389045.1_ASM1838904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:35:09,124] [INFO] Task succeeded: fastANI
[2023-06-19 13:35:09,130] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:35:09,130] [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_011373175.1	s__Thermoflexus sinensis	98.9382	575	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	98.75	98.51	0.81	0.73	5	conclusive
GCA_002898735.1	s__Thermoflexus japonica	84.5242	573	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016842085.1	s__Thermoflexus tengchongensis	84.5006	642	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048055.1	s__Thermoflexus sp011048055	83.3895	597	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	99.89	99.88	0.97	0.96	4	-
GCF_900187885.1	s__Thermoflexus hugenholtzii	80.5249	502	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	97.76	95.14	0.90	0.83	5	-
GCA_017743605.1	s__Thermoflexus sp017743605	79.2361	325	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:35:09,133] [INFO] GTDB search result was written to GCA_018389045.1_ASM1838904v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:35:09,134] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:35:09,136] [INFO] DFAST_QC result json was written to GCA_018389045.1_ASM1838904v1_genomic.fna/dqc_result.json
[2023-06-19 13:35:09,137] [INFO] DFAST_QC completed!
[2023-06-19 13:35:09,137] [INFO] Total running time: 0h0m48s