[2023-06-30 17:45:50,487] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:45:50,489] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:45:50,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference
[2023-06-30 17:45:51,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:45:51,770] [INFO] Task started: Prodigal
[2023-06-30 17:45:51,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b3049a6-88ae-4ee5-998d-50dd33673576/GCA_024331045.1_ASM2433104v1_genomic.fna.gz | prodigal -d GCA_024331045.1_ASM2433104v1_genomic.fna/cds.fna -a GCA_024331045.1_ASM2433104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:45:59,441] [INFO] Task succeeded: Prodigal
[2023-06-30 17:45:59,441] [INFO] Task started: HMMsearch
[2023-06-30 17:45:59,441] [INFO] Running command: hmmsearch --tblout GCA_024331045.1_ASM2433104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/reference_markers.hmm GCA_024331045.1_ASM2433104v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:45:59,672] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:45:59,673] [INFO] Found 6/6 markers.
[2023-06-30 17:45:59,701] [INFO] Query marker FASTA was written to GCA_024331045.1_ASM2433104v1_genomic.fna/markers.fasta
[2023-06-30 17:45:59,701] [INFO] Task started: Blastn
[2023-06-30 17:45:59,701] [INFO] Running command: blastn -query GCA_024331045.1_ASM2433104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/reference_markers.fasta -out GCA_024331045.1_ASM2433104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:46:00,312] [INFO] Task succeeded: Blastn
[2023-06-30 17:46:00,315] [INFO] Selected 10 target genomes.
[2023-06-30 17:46:00,316] [INFO] Target genome list was writen to GCA_024331045.1_ASM2433104v1_genomic.fna/target_genomes.txt
[2023-06-30 17:46:00,318] [INFO] Task started: fastANI
[2023-06-30 17:46:00,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b3049a6-88ae-4ee5-998d-50dd33673576/GCA_024331045.1_ASM2433104v1_genomic.fna.gz --refList GCA_024331045.1_ASM2433104v1_genomic.fna/target_genomes.txt --output GCA_024331045.1_ASM2433104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:46:06,045] [INFO] Task succeeded: fastANI
[2023-06-30 17:46:06,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:46:06,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:46:06,049] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:46:06,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:46:06,049] [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
Nitrospira moscoviensis	strain=NSP M-1	GCA_001273775.1	42253	42253	type	True	76.4473	109	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:46:06,051] [INFO] DFAST Taxonomy check result was written to GCA_024331045.1_ASM2433104v1_genomic.fna/tc_result.tsv
[2023-06-30 17:46:06,051] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:46:06,051] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:46:06,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/checkm_data
[2023-06-30 17:46:06,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:46:06,095] [INFO] Task started: CheckM
[2023-06-30 17:46:06,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024331045.1_ASM2433104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024331045.1_ASM2433104v1_genomic.fna/checkm_input GCA_024331045.1_ASM2433104v1_genomic.fna/checkm_result
[2023-06-30 17:46:31,986] [INFO] Task succeeded: CheckM
[2023-06-30 17:46:31,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 17:46:32,003] [INFO] ===== Completeness check finished =====
[2023-06-30 17:46:32,004] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:46:32,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024331045.1_ASM2433104v1_genomic.fna/markers.fasta)
[2023-06-30 17:46:32,004] [INFO] Task started: Blastn
[2023-06-30 17:46:32,004] [INFO] Running command: blastn -query GCA_024331045.1_ASM2433104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3768f9f0-20f6-4521-b840-3898091c6c78/dqc_reference/reference_markers_gtdb.fasta -out GCA_024331045.1_ASM2433104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:46:32,797] [INFO] Task succeeded: Blastn
[2023-06-30 17:46:32,800] [INFO] Selected 19 target genomes.
[2023-06-30 17:46:32,800] [INFO] Target genome list was writen to GCA_024331045.1_ASM2433104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:46:32,811] [INFO] Task started: fastANI
[2023-06-30 17:46:32,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b3049a6-88ae-4ee5-998d-50dd33673576/GCA_024331045.1_ASM2433104v1_genomic.fna.gz --refList GCA_024331045.1_ASM2433104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024331045.1_ASM2433104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:46:43,195] [INFO] Task succeeded: fastANI
[2023-06-30 17:46:43,203] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 17:46:43,203] [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
GCF_001458695.1	s__Nitrospira_F inopinata	85.34	613	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451055.1	s__Nitrospira_F sp002451055	76.493	102	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273775.1	s__Nitrospira_E moscoviensis	76.4304	110	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015903945.1	s__Nitrospira_F sp015903945	76.4093	90	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709715.1	s__Nitrospira_A sp001567445	76.285	51	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_A	95.0	99.74	99.55	0.97	0.95	6	-
GCA_014058405.1	s__Nitrospira_F kreftii	76.2126	60	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083565.1	s__Nitrospira_F sp002083565	76.2002	84	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	95.62	95.62	0.78	0.78	2	-
GCA_005239465.1	s__Nitrospira_F sp005239465	76.0603	87	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195505.1	s__Nitrospira_F sp016195505	76.0255	55	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458775.1	s__Nitrospira_F nitrificans	75.8003	77	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005116955.1	s__Nitrospira_F sp005116955	75.7848	64	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011090425.1	s__Nitrospira_F sp011090425	75.7787	63	900	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:46:43,205] [INFO] GTDB search result was written to GCA_024331045.1_ASM2433104v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:46:43,205] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:46:43,208] [INFO] DFAST_QC result json was written to GCA_024331045.1_ASM2433104v1_genomic.fna/dqc_result.json
[2023-06-30 17:46:43,208] [INFO] DFAST_QC completed!
[2023-06-30 17:46:43,208] [INFO] Total running time: 0h0m53s