[2023-06-30 18:53:30,129] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:53:30,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:53:30,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference
[2023-06-30 18:53:32,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:53:32,566] [INFO] Task started: Prodigal
[2023-06-30 18:53:32,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc8275a3-f673-4e02-8c3e-4fa04c3eb625/GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna.gz | prodigal -d GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/cds.fna -a GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:53:50,824] [INFO] Task succeeded: Prodigal
[2023-06-30 18:53:50,824] [INFO] Task started: HMMsearch
[2023-06-30 18:53:50,824] [INFO] Running command: hmmsearch --tblout GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/reference_markers.hmm GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:53:51,049] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:53:51,051] [INFO] Found 6/6 markers.
[2023-06-30 18:53:51,085] [INFO] Query marker FASTA was written to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/markers.fasta
[2023-06-30 18:53:51,085] [INFO] Task started: Blastn
[2023-06-30 18:53:51,085] [INFO] Running command: blastn -query GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/reference_markers.fasta -out GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:53:51,660] [INFO] Task succeeded: Blastn
[2023-06-30 18:53:51,663] [INFO] Selected 28 target genomes.
[2023-06-30 18:53:51,664] [INFO] Target genome list was writen to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/target_genomes.txt
[2023-06-30 18:53:51,665] [INFO] Task started: fastANI
[2023-06-30 18:53:51,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8275a3-f673-4e02-8c3e-4fa04c3eb625/GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna.gz --refList GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/target_genomes.txt --output GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:54:17,883] [INFO] Task succeeded: fastANI
[2023-06-30 18:54:17,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:54:17,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:54:17,888] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:54:17,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:54:17,889] [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
Flavipsychrobacter stenotrophus	strain=RB1R16	GCA_002954265.1	2077091	2077091	type	True	76.4988	118	1093	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:54:17,891] [INFO] DFAST Taxonomy check result was written to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/tc_result.tsv
[2023-06-30 18:54:17,891] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:54:17,891] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:54:17,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/checkm_data
[2023-06-30 18:54:17,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:54:17,934] [INFO] Task started: CheckM
[2023-06-30 18:54:17,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/checkm_input GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/checkm_result
[2023-06-30 18:55:10,321] [INFO] Task succeeded: CheckM
[2023-06-30 18:55:10,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 4.17%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-30 18:55:10,342] [INFO] ===== Completeness check finished =====
[2023-06-30 18:55:10,342] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:55:10,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/markers.fasta)
[2023-06-30 18:55:10,343] [INFO] Task started: Blastn
[2023-06-30 18:55:10,343] [INFO] Running command: blastn -query GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ffe09f7-60ef-4d1b-8242-c913574cb19e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:55:11,092] [INFO] Task succeeded: Blastn
[2023-06-30 18:55:11,096] [INFO] Selected 26 target genomes.
[2023-06-30 18:55:11,096] [INFO] Target genome list was writen to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:55:11,102] [INFO] Task started: fastANI
[2023-06-30 18:55:11,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8275a3-f673-4e02-8c3e-4fa04c3eb625/GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna.gz --refList GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/target_genomes_gtdb.txt --output GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:55:27,066] [INFO] Task succeeded: fastANI
[2023-06-30 18:55:27,077] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:55:27,077] [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_903835145.1	s__Flavipsychrobacter sp903835145	98.9842	700	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.38	99.38	0.87	0.87	2	conclusive
GCA_903877645.1	s__Flavipsychrobacter sp903877645	76.6105	79	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.60	99.21	0.95	0.89	10	-
GCA_903903635.1	s__Flavipsychrobacter sp903903635	76.5791	77	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882805.1	s__Flavipsychrobacter sp903882805	76.5292	77	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786565.1	s__Flavipsychrobacter sp016786565	76.5264	58	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954265.1	s__Flavipsychrobacter stenotrophus	76.5162	117	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882965.1	s__Flavipsychrobacter sp903882965	76.3338	69	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377675.1	s__Flavipsychrobacter sp014377675	76.2792	78	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303395.1	s__Flavipsychrobacter sp017303395	76.229	65	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483105.1	s__Flavipsychrobacter sp002483105	76.1268	51	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824665.1	s__Flavipsychrobacter sp903824665	76.0903	71	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.94	99.86	0.99	0.98	5	-
GCA_903906615.1	s__Flavipsychrobacter sp903906615	75.747	50	1093	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:55:27,079] [INFO] GTDB search result was written to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/result_gtdb.tsv
[2023-06-30 18:55:27,080] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:55:27,083] [INFO] DFAST_QC result json was written to GCA_903900985.1_freshwater_MAG_---_Umea_bin-01022_genomic.fna/dqc_result.json
[2023-06-30 18:55:27,083] [INFO] DFAST_QC completed!
[2023-06-30 18:55:27,083] [INFO] Total running time: 0h1m57s