[2023-06-29 23:16:23,945] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:16:23,948] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:16:23,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference
[2023-06-29 23:16:25,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:16:25,211] [INFO] Task started: Prodigal
[2023-06-29 23:16:25,211] [INFO] Running command: gunzip -c /var/lib/cwl/stgc52e0f09-6729-4828-9a9f-a15d69e9cf7d/GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna.gz | prodigal -d GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/cds.fna -a GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:34,535] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:34,535] [INFO] Task started: HMMsearch
[2023-06-29 23:16:34,535] [INFO] Running command: hmmsearch --tblout GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/reference_markers.hmm GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:34,800] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:34,802] [INFO] Found 6/6 markers.
[2023-06-29 23:16:34,839] [INFO] Query marker FASTA was written to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/markers.fasta
[2023-06-29 23:16:34,839] [INFO] Task started: Blastn
[2023-06-29 23:16:34,840] [INFO] Running command: blastn -query GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/reference_markers.fasta -out GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:35,525] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:35,529] [INFO] Selected 32 target genomes.
[2023-06-29 23:16:35,529] [INFO] Target genome list was writen to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/target_genomes.txt
[2023-06-29 23:16:35,531] [INFO] Task started: fastANI
[2023-06-29 23:16:35,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52e0f09-6729-4828-9a9f-a15d69e9cf7d/GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna.gz --refList GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/target_genomes.txt --output GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:16:57,526] [INFO] Task succeeded: fastANI
[2023-06-29 23:16:57,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:16:57,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:16:57,533] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:16:57,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:16:57,534] [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
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	75.6921	51	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:16:57,536] [INFO] DFAST Taxonomy check result was written to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/tc_result.tsv
[2023-06-29 23:16:57,537] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:16:57,537] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:16:57,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/checkm_data
[2023-06-29 23:16:57,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:16:57,581] [INFO] Task started: CheckM
[2023-06-29 23:16:57,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/checkm_input GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/checkm_result
[2023-06-29 23:17:28,753] [INFO] Task succeeded: CheckM
[2023-06-29 23:17:28,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:17:28,780] [INFO] ===== Completeness check finished =====
[2023-06-29 23:17:28,780] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:17:28,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/markers.fasta)
[2023-06-29 23:17:28,781] [INFO] Task started: Blastn
[2023-06-29 23:17:28,781] [INFO] Running command: blastn -query GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ab7f58a-2423-4ffb-93ce-f6b381ca39a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:29,773] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:29,778] [INFO] Selected 27 target genomes.
[2023-06-29 23:17:29,779] [INFO] Target genome list was writen to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:17:29,795] [INFO] Task started: fastANI
[2023-06-29 23:17:29,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52e0f09-6729-4828-9a9f-a15d69e9cf7d/GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna.gz --refList GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/target_genomes_gtdb.txt --output GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:17:45,948] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:45,960] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:17:45,960] [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_903908265.1	s__CAIYLH01 sp903908265	99.8018	840	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.59	99.26	0.90	0.86	35	conclusive
GCA_903879335.1	s__CAIYLH01 sp903879335	78.3606	200	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.91	99.87	0.98	0.96	13	-
GCA_903927005.1	s__CAIYLH01 sp903927005	77.6689	138	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.60	99.60	0.92	0.92	2	-
GCA_903884235.1	s__CAIYLH01 sp903884235	76.7646	126	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	-
GCA_018241525.1	s__SZAS-83 sp018241525	76.5329	117	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241545.1	s__SZAS-83 sp018241545	75.8637	73	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138485.1	s__Steroidobacter_A soli	75.6921	51	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:17:45,962] [INFO] GTDB search result was written to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/result_gtdb.tsv
[2023-06-29 23:17:45,963] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:17:45,965] [INFO] DFAST_QC result json was written to GCA_903883215.1_freshwater_MAG_---_Ki2-D4_bin-0800_genomic.fna/dqc_result.json
[2023-06-29 23:17:45,965] [INFO] DFAST_QC completed!
[2023-06-29 23:17:45,965] [INFO] Total running time: 0h1m22s