[2023-06-28 20:27:13,433] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:27:13,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:27:13,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference
[2023-06-28 20:27:14,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:27:14,926] [INFO] Task started: Prodigal
[2023-06-28 20:27:14,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f4394f6-60ae-49f3-9bba-f5adf6abad7f/GCA_012799495.1_ASM1279949v1_genomic.fna.gz | prodigal -d GCA_012799495.1_ASM1279949v1_genomic.fna/cds.fna -a GCA_012799495.1_ASM1279949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:27:18,977] [INFO] Task succeeded: Prodigal
[2023-06-28 20:27:18,977] [INFO] Task started: HMMsearch
[2023-06-28 20:27:18,977] [INFO] Running command: hmmsearch --tblout GCA_012799495.1_ASM1279949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/reference_markers.hmm GCA_012799495.1_ASM1279949v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:27:19,249] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:27:19,251] [INFO] Found 6/6 markers.
[2023-06-28 20:27:19,282] [INFO] Query marker FASTA was written to GCA_012799495.1_ASM1279949v1_genomic.fna/markers.fasta
[2023-06-28 20:27:19,283] [INFO] Task started: Blastn
[2023-06-28 20:27:19,283] [INFO] Running command: blastn -query GCA_012799495.1_ASM1279949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/reference_markers.fasta -out GCA_012799495.1_ASM1279949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:19,883] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:19,887] [INFO] Selected 22 target genomes.
[2023-06-28 20:27:19,887] [INFO] Target genome list was writen to GCA_012799495.1_ASM1279949v1_genomic.fna/target_genomes.txt
[2023-06-28 20:27:19,896] [INFO] Task started: fastANI
[2023-06-28 20:27:19,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4394f6-60ae-49f3-9bba-f5adf6abad7f/GCA_012799495.1_ASM1279949v1_genomic.fna.gz --refList GCA_012799495.1_ASM1279949v1_genomic.fna/target_genomes.txt --output GCA_012799495.1_ASM1279949v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:27:35,214] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:35,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:27:35,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:27:35,220] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:27:35,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:27:35,221] [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
Desulfitobacterium chlororespirans	strain=DSM 11544	GCA_900143285.1	51616	51616	type	True	76.6792	63	538	95	below_threshold
Desulfitobacterium dehalogenans	strain=ATCC 51507	GCA_000243155.3	36854	36854	type	True	76.6548	89	538	95	below_threshold
Desulfitobacterium hafniense	strain=DCB-2	GCA_000021925.1	49338	49338	type	True	76.4981	68	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:27:35,223] [INFO] DFAST Taxonomy check result was written to GCA_012799495.1_ASM1279949v1_genomic.fna/tc_result.tsv
[2023-06-28 20:27:35,223] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:27:35,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:27:35,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/checkm_data
[2023-06-28 20:27:35,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:27:35,259] [INFO] Task started: CheckM
[2023-06-28 20:27:35,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012799495.1_ASM1279949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012799495.1_ASM1279949v1_genomic.fna/checkm_input GCA_012799495.1_ASM1279949v1_genomic.fna/checkm_result
[2023-06-28 20:27:55,219] [INFO] Task succeeded: CheckM
[2023-06-28 20:27:55,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:27:55,249] [INFO] ===== Completeness check finished =====
[2023-06-28 20:27:55,250] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:27:55,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012799495.1_ASM1279949v1_genomic.fna/markers.fasta)
[2023-06-28 20:27:55,251] [INFO] Task started: Blastn
[2023-06-28 20:27:55,251] [INFO] Running command: blastn -query GCA_012799495.1_ASM1279949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73ef9a9-fd6e-4b1e-9085-45dab3908ffe/dqc_reference/reference_markers_gtdb.fasta -out GCA_012799495.1_ASM1279949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:56,030] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:56,036] [INFO] Selected 20 target genomes.
[2023-06-28 20:27:56,037] [INFO] Target genome list was writen to GCA_012799495.1_ASM1279949v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:27:56,049] [INFO] Task started: fastANI
[2023-06-28 20:27:56,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4394f6-60ae-49f3-9bba-f5adf6abad7f/GCA_012799495.1_ASM1279949v1_genomic.fna.gz --refList GCA_012799495.1_ASM1279949v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012799495.1_ASM1279949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:28:06,911] [INFO] Task succeeded: fastANI
[2023-06-28 20:28:06,920] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:28:06,921] [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_012799495.1	s__Desulfitobacterium sp012799495	100.0	524	538	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900143285.1	s__Desulfitobacterium chlororespirans	76.6753	62	538	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243155.2	s__Desulfitobacterium dehalogenans	76.6548	89	538	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.36	95.71	0.90	0.87	3	-
GCF_000021925.1	s__Desulfitobacterium hafniense	76.4981	68	538	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.85	96.87	0.87	0.83	9	-
GCF_000243135.2	s__Desulfitobacterium dichloroeliminans	76.4071	64	538	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:28:06,924] [INFO] GTDB search result was written to GCA_012799495.1_ASM1279949v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:28:06,925] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:28:06,928] [INFO] DFAST_QC result json was written to GCA_012799495.1_ASM1279949v1_genomic.fna/dqc_result.json
[2023-06-28 20:28:06,928] [INFO] DFAST_QC completed!
[2023-06-28 20:28:06,928] [INFO] Total running time: 0h0m53s