[2023-06-30 15:09:16,376] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:09:16,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:09:16,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference
[2023-06-30 15:09:17,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:09:17,627] [INFO] Task started: Prodigal
[2023-06-30 15:09:17,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg77d135a3-acaa-4f72-8673-1256c83ce1aa/GCA_024331125.1_ASM2433112v1_genomic.fna.gz | prodigal -d GCA_024331125.1_ASM2433112v1_genomic.fna/cds.fna -a GCA_024331125.1_ASM2433112v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:27,509] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:27,510] [INFO] Task started: HMMsearch
[2023-06-30 15:09:27,510] [INFO] Running command: hmmsearch --tblout GCA_024331125.1_ASM2433112v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/reference_markers.hmm GCA_024331125.1_ASM2433112v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:27,754] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:27,756] [INFO] Found 6/6 markers.
[2023-06-30 15:09:27,783] [INFO] Query marker FASTA was written to GCA_024331125.1_ASM2433112v1_genomic.fna/markers.fasta
[2023-06-30 15:09:27,783] [INFO] Task started: Blastn
[2023-06-30 15:09:27,783] [INFO] Running command: blastn -query GCA_024331125.1_ASM2433112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/reference_markers.fasta -out GCA_024331125.1_ASM2433112v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:28,405] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:28,409] [INFO] Selected 14 target genomes.
[2023-06-30 15:09:28,409] [INFO] Target genome list was writen to GCA_024331125.1_ASM2433112v1_genomic.fna/target_genomes.txt
[2023-06-30 15:09:28,426] [INFO] Task started: fastANI
[2023-06-30 15:09:28,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d135a3-acaa-4f72-8673-1256c83ce1aa/GCA_024331125.1_ASM2433112v1_genomic.fna.gz --refList GCA_024331125.1_ASM2433112v1_genomic.fna/target_genomes.txt --output GCA_024331125.1_ASM2433112v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:42,561] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:42,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:42,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:42,566] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:42,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:09:42,566] [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	77.0943	179	979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:09:42,569] [INFO] DFAST Taxonomy check result was written to GCA_024331125.1_ASM2433112v1_genomic.fna/tc_result.tsv
[2023-06-30 15:09:42,569] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:42,570] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:42,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/checkm_data
[2023-06-30 15:09:42,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:42,608] [INFO] Task started: CheckM
[2023-06-30 15:09:42,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024331125.1_ASM2433112v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024331125.1_ASM2433112v1_genomic.fna/checkm_input GCA_024331125.1_ASM2433112v1_genomic.fna/checkm_result
[2023-06-30 15:10:15,005] [INFO] Task succeeded: CheckM
[2023-06-30 15:10:15,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:10:15,030] [INFO] ===== Completeness check finished =====
[2023-06-30 15:10:15,031] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:10:15,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024331125.1_ASM2433112v1_genomic.fna/markers.fasta)
[2023-06-30 15:10:15,032] [INFO] Task started: Blastn
[2023-06-30 15:10:15,032] [INFO] Running command: blastn -query GCA_024331125.1_ASM2433112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec25c9c1-169d-43ce-b082-f855238837d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_024331125.1_ASM2433112v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:10:15,993] [INFO] Task succeeded: Blastn
[2023-06-30 15:10:15,997] [INFO] Selected 17 target genomes.
[2023-06-30 15:10:15,997] [INFO] Target genome list was writen to GCA_024331125.1_ASM2433112v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:10:16,037] [INFO] Task started: fastANI
[2023-06-30 15:10:16,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d135a3-acaa-4f72-8673-1256c83ce1aa/GCA_024331125.1_ASM2433112v1_genomic.fna.gz --refList GCA_024331125.1_ASM2433112v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024331125.1_ASM2433112v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:10:26,287] [INFO] Task succeeded: fastANI
[2023-06-30 15:10:26,306] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:10:26,306] [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	92.5081	877	979	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	77.3017	223	979	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	77.0943	179	979	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_002083565.1	s__Nitrospira_F sp002083565	76.9856	176	979	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	76.8353	160	979	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_002420105.1	s__Nitrospira_C sp002420105	76.7818	158	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331925.1	s__Nitrospira_F sp011331925	76.6755	126	979	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_900299325.1	s__OMJK01 sp900299325	76.6641	136	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__OMJK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014055525.1	s__Nitrospira_C sp014055525	76.6273	106	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242765.1	s__Nitrospira_F sp018242765	76.5962	101	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	98.63	98.34	0.91	0.89	3	-
GCA_902500825.1	s__Nitrospira_F sp902500825	76.4574	126	979	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_001458735.1	s__Nitrospira_F nitrosa	76.4324	102	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	95.74	95.74	0.79	0.79	2	-
GCA_016195505.1	s__Nitrospira_F sp016195505	76.263	97	979	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_002435325.1	s__Nitrospira_D sp002435325	76.1698	101	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_D	95.0	99.94	99.94	0.95	0.95	2	-
GCA_900299245.1	s__Nitrospira_D sp900299245	76.163	105	979	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015903995.1	s__Nitrospira_F sp015903995	76.0312	118	979	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 15:10:26,308] [INFO] GTDB search result was written to GCA_024331125.1_ASM2433112v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:10:26,309] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:10:26,312] [INFO] DFAST_QC result json was written to GCA_024331125.1_ASM2433112v1_genomic.fna/dqc_result.json
[2023-06-30 15:10:26,313] [INFO] DFAST_QC completed!
[2023-06-30 15:10:26,313] [INFO] Total running time: 0h1m10s