[2023-06-13 06:11:32,851] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:32,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:32,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference
[2023-06-13 06:11:34,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:34,239] [INFO] Task started: Prodigal
[2023-06-13 06:11:34,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg2376005f-ce5f-4179-aa30-a26c11e89fad/GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna.gz | prodigal -d GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/cds.fna -a GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:47,534] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:47,534] [INFO] Task started: HMMsearch
[2023-06-13 06:11:47,535] [INFO] Running command: hmmsearch --tblout GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/reference_markers.hmm GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:47,811] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:47,813] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2376005f-ce5f-4179-aa30-a26c11e89fad/GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna.gz]
[2023-06-13 06:11:47,864] [INFO] Query marker FASTA was written to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/markers.fasta
[2023-06-13 06:11:47,864] [INFO] Task started: Blastn
[2023-06-13 06:11:47,865] [INFO] Running command: blastn -query GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/reference_markers.fasta -out GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:48,441] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:48,445] [INFO] Selected 11 target genomes.
[2023-06-13 06:11:48,445] [INFO] Target genome list was writen to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/target_genomes.txt
[2023-06-13 06:11:48,451] [INFO] Task started: fastANI
[2023-06-13 06:11:48,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg2376005f-ce5f-4179-aa30-a26c11e89fad/GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna.gz --refList GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/target_genomes.txt --output GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:58,783] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:58,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:58,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:58,790] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:11:58,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 06:11:58,791] [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
Roseiflexus castenholzii	strain=DSM 13941	GCA_000017805.1	120962	120962	type	True	84.5979	1260	1430	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	74.739	50	1430	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	74.5871	50	1430	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	74.5489	63	1430	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:11:58,793] [INFO] DFAST Taxonomy check result was written to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/tc_result.tsv
[2023-06-13 06:11:58,794] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:58,794] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:58,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/checkm_data
[2023-06-13 06:11:58,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:58,846] [INFO] Task started: CheckM
[2023-06-13 06:11:58,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/checkm_input GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/checkm_result
[2023-06-13 06:12:41,137] [INFO] Task succeeded: CheckM
[2023-06-13 06:12:41,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:12:41,161] [INFO] ===== Completeness check finished =====
[2023-06-13 06:12:41,162] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:12:41,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/markers.fasta)
[2023-06-13 06:12:41,163] [INFO] Task started: Blastn
[2023-06-13 06:12:41,163] [INFO] Running command: blastn -query GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949dd5c3-dd46-4e8e-9f79-9f90fcc47bc7/dqc_reference/reference_markers_gtdb.fasta -out GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:12:41,886] [INFO] Task succeeded: Blastn
[2023-06-13 06:12:41,891] [INFO] Selected 11 target genomes.
[2023-06-13 06:12:41,891] [INFO] Target genome list was writen to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:12:41,927] [INFO] Task started: fastANI
[2023-06-13 06:12:41,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg2376005f-ce5f-4179-aa30-a26c11e89fad/GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna.gz --refList GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:12:52,049] [INFO] Task succeeded: fastANI
[2023-06-13 06:12:52,060] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 06:12:52,060] [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_000017805.1	s__Roseiflexus castenholzii	84.6328	1255	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016665.1	s__Roseiflexus sp000016665	80.2399	999	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	98.43	98.43	0.97	0.97	2	-
GCA_017743475.1	s__Roseiflexus sp017743475	78.9822	771	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	98.84	95.62	0.92	0.85	6	-
GCA_013388755.1	s__JACAEQ01 sp013388755	77.3207	413	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JACAEQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722075.1	s__Kouleothrix sp016722075	75.9979	168	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.966	202	1430	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:12:52,062] [INFO] GTDB search result was written to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:12:52,063] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:12:52,065] [INFO] DFAST_QC result json was written to GCA_938083345.1_S1_Bin_METABAT_321_1_genomic.fna/dqc_result.json
[2023-06-13 06:12:52,066] [INFO] DFAST_QC completed!
[2023-06-13 06:12:52,066] [INFO] Total running time: 0h1m19s