[2023-06-29 21:20:39,864] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:20:39,867] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:20:39,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference
[2023-06-29 21:20:41,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:20:41,112] [INFO] Task started: Prodigal
[2023-06-29 21:20:41,112] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f4db2d6-aa01-45aa-96cd-14f2642f4bd4/GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna.gz | prodigal -d GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/cds.fna -a GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:20:47,294] [INFO] Task succeeded: Prodigal
[2023-06-29 21:20:47,294] [INFO] Task started: HMMsearch
[2023-06-29 21:20:47,295] [INFO] Running command: hmmsearch --tblout GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/reference_markers.hmm GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:20:47,556] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:20:47,558] [INFO] Found 6/6 markers.
[2023-06-29 21:20:47,588] [INFO] Query marker FASTA was written to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/markers.fasta
[2023-06-29 21:20:47,588] [INFO] Task started: Blastn
[2023-06-29 21:20:47,588] [INFO] Running command: blastn -query GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/reference_markers.fasta -out GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:20:48,201] [INFO] Task succeeded: Blastn
[2023-06-29 21:20:48,205] [INFO] Selected 26 target genomes.
[2023-06-29 21:20:48,205] [INFO] Target genome list was writen to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/target_genomes.txt
[2023-06-29 21:20:48,212] [INFO] Task started: fastANI
[2023-06-29 21:20:48,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f4db2d6-aa01-45aa-96cd-14f2642f4bd4/GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna.gz --refList GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/target_genomes.txt --output GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:20:59,075] [INFO] Task succeeded: fastANI
[2023-06-29 21:20:59,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:20:59,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:20:59,079] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:20:59,079] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:20:59,079] [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
Sulfuricurvum kujiense	strain=DSM 16994	GCA_000183725.1	148813	148813	type	True	77.5992	181	846	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:20:59,081] [INFO] DFAST Taxonomy check result was written to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/tc_result.tsv
[2023-06-29 21:20:59,082] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:20:59,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:20:59,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/checkm_data
[2023-06-29 21:20:59,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:20:59,118] [INFO] Task started: CheckM
[2023-06-29 21:20:59,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/checkm_input GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/checkm_result
[2023-06-29 21:21:24,428] [INFO] Task succeeded: CheckM
[2023-06-29 21:21:24,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:21:24,452] [INFO] ===== Completeness check finished =====
[2023-06-29 21:21:24,452] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:21:24,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/markers.fasta)
[2023-06-29 21:21:24,453] [INFO] Task started: Blastn
[2023-06-29 21:21:24,453] [INFO] Running command: blastn -query GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd8a5e0-0845-4ddb-9c91-542f3ed6153c/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:21:25,288] [INFO] Task succeeded: Blastn
[2023-06-29 21:21:25,294] [INFO] Selected 12 target genomes.
[2023-06-29 21:21:25,295] [INFO] Target genome list was writen to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:21:25,299] [INFO] Task started: fastANI
[2023-06-29 21:21:25,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f4db2d6-aa01-45aa-96cd-14f2642f4bd4/GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna.gz --refList GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/target_genomes_gtdb.txt --output GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:21:30,033] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:30,048] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:21:30,048] [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_903844635.1	s__Sulfuricurvum sp903844635	100.0	841	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011391735.1	s__Sulfuricurvum sp011391735	79.1703	208	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000310245.1	s__Sulfuricurvum sp000310245	78.1076	232	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.06	98.44	0.95	0.92	4	-
GCA_019163035.1	s__Sulfuricurvum sp019163035	78.0927	196	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282015.1	s__Sulfuricurvum sp002282015	78.0639	230	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002742695.1	s__Sulfuricurvum kujiense_A	77.8267	183	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.70	99.66	0.87	0.87	4	-
GCF_000183725.1	s__Sulfuricurvum kujiense	77.6153	180	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002633015.1	s__Sulfuricurvum sp002633015	77.2229	194	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014764105.1	s__Sulfuricurvum sp014764105	77.0959	104	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.42	99.42	0.84	0.84	2	-
GCF_004347735.1	s__Sulfuricurvum sp002327465	76.9468	71	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	98.67	98.67	0.93	0.93	2	-
GCA_903892995.1	s__CAITKP01 sp903892995	76.7792	53	846	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.47	98.97	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:21:30,050] [INFO] GTDB search result was written to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/result_gtdb.tsv
[2023-06-29 21:21:30,051] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:21:30,055] [INFO] DFAST_QC result json was written to GCA_903844635.1_freshwater_MAG_---_MJ-time_bin-9098_genomic.fna/dqc_result.json
[2023-06-29 21:21:30,055] [INFO] DFAST_QC completed!
[2023-06-29 21:21:30,055] [INFO] Total running time: 0h0m50s