[2024-01-24 14:06:05,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference
[2024-01-24 14:06:07,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,330] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg831c4159-b1ca-45a1-8583-9cb2a501691e/GCF_017377355.1_ASM1737735v1_genomic.fna.gz | prodigal -d GCF_017377355.1_ASM1737735v1_genomic.fna/cds.fna -a GCF_017377355.1_ASM1737735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:23,733] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:23,733] [INFO] Task started: HMMsearch
[2024-01-24 14:06:23,733] [INFO] Running command: hmmsearch --tblout GCF_017377355.1_ASM1737735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/reference_markers.hmm GCF_017377355.1_ASM1737735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:24,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:24,171] [INFO] Found 6/6 markers.
[2024-01-24 14:06:24,226] [INFO] Query marker FASTA was written to GCF_017377355.1_ASM1737735v1_genomic.fna/markers.fasta
[2024-01-24 14:06:24,227] [INFO] Task started: Blastn
[2024-01-24 14:06:24,227] [INFO] Running command: blastn -query GCF_017377355.1_ASM1737735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/reference_markers.fasta -out GCF_017377355.1_ASM1737735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:24,887] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:24,890] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:24,890] [INFO] Target genome list was writen to GCF_017377355.1_ASM1737735v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:24,905] [INFO] Task started: fastANI
[2024-01-24 14:06:24,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg831c4159-b1ca-45a1-8583-9cb2a501691e/GCF_017377355.1_ASM1737735v1_genomic.fna.gz --refList GCF_017377355.1_ASM1737735v1_genomic.fna/target_genomes.txt --output GCF_017377355.1_ASM1737735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:43,959] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:43,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:43,966] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:43,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:43,967] [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
Desulfonema limicola	strain=5ac10	GCA_017377355.1	45656	45656	type	True	100.0	2298	2302	95	conclusive
Desulfobacula toluolica	strain=Tol2	GCA_000307105.1	28223	28223	type	True	75.9813	69	2302	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	75.544	50	2302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,970] [INFO] DFAST Taxonomy check result was written to GCF_017377355.1_ASM1737735v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:43,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:43,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:43,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/checkm_data
[2024-01-24 14:06:43,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:44,053] [INFO] Task started: CheckM
[2024-01-24 14:06:44,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017377355.1_ASM1737735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017377355.1_ASM1737735v1_genomic.fna/checkm_input GCF_017377355.1_ASM1737735v1_genomic.fna/checkm_result
[2024-01-24 14:07:33,829] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:33,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,853] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:33,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:33,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017377355.1_ASM1737735v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:33,855] [INFO] Task started: Blastn
[2024-01-24 14:07:33,855] [INFO] Running command: blastn -query GCF_017377355.1_ASM1737735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e25b3b0-a78f-4378-a0d1-93967802d41e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017377355.1_ASM1737735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:34,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:34,721] [INFO] Selected 26 target genomes.
[2024-01-24 14:07:34,722] [INFO] Target genome list was writen to GCF_017377355.1_ASM1737735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:34,796] [INFO] Task started: fastANI
[2024-01-24 14:07:34,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg831c4159-b1ca-45a1-8583-9cb2a501691e/GCF_017377355.1_ASM1737735v1_genomic.fna.gz --refList GCF_017377355.1_ASM1737735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017377355.1_ASM1737735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:54,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:54,189] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:54,189] [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_017377355.1	s__Desulfonema limicola	100.0	2297	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfonema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011390755.1	s__JAABRU01 sp011390755	77.0453	225	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307105.1	s__Desulfobacula toluolica	76.2425	70	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	97.14	97.14	0.85	0.85	2	-
GCA_004193595.1	s__S5133MH16 sp004193595	76.0253	69	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792055.1	s__B13-G4 sp013792055	75.7713	61	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	99.03	97.50	0.88	0.84	10	-
GCA_013791935.1	s__VMSV01 sp013791935	75.763	51	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5616;g__VMSV01	95.0	97.02	95.73	0.86	0.82	4	-
GCA_016743945.1	s__NBML01 sp016743945	74.906	61	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744295.1	s__NBML01 sp016744295	74.7214	57	2302	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:54,191] [INFO] GTDB search result was written to GCF_017377355.1_ASM1737735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:54,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:54,196] [INFO] DFAST_QC result json was written to GCF_017377355.1_ASM1737735v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:54,196] [INFO] DFAST_QC completed!
[2024-01-24 14:07:54,196] [INFO] Total running time: 0h1m48s