[2023-06-30 15:35:42,672] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:35:42,675] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:35:42,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference
[2023-06-30 15:35:43,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:35:44,000] [INFO] Task started: Prodigal
[2023-06-30 15:35:44,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg34d206c6-1074-4068-9363-532341a31b20/GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna.gz | prodigal -d GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/cds.fna -a GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:36:10,888] [INFO] Task succeeded: Prodigal
[2023-06-30 15:36:10,889] [INFO] Task started: HMMsearch
[2023-06-30 15:36:10,889] [INFO] Running command: hmmsearch --tblout GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/reference_markers.hmm GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:36:11,278] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:36:11,279] [INFO] Found 6/6 markers.
[2023-06-30 15:36:11,344] [INFO] Query marker FASTA was written to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/markers.fasta
[2023-06-30 15:36:11,345] [INFO] Task started: Blastn
[2023-06-30 15:36:11,345] [INFO] Running command: blastn -query GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/reference_markers.fasta -out GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:36:12,415] [INFO] Task succeeded: Blastn
[2023-06-30 15:36:12,420] [INFO] Selected 11 target genomes.
[2023-06-30 15:36:12,421] [INFO] Target genome list was writen to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/target_genomes.txt
[2023-06-30 15:36:12,423] [INFO] Task started: fastANI
[2023-06-30 15:36:12,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d206c6-1074-4068-9363-532341a31b20/GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna.gz --refList GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/target_genomes.txt --output GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:36:34,450] [INFO] Task succeeded: fastANI
[2023-06-30 15:36:34,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:36:34,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:36:34,465] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:36:34,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:36:34,465] [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
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	91.4407	2205	2830	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	90.8904	1964	2830	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	90.8711	1959	2830	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	89.433	1906	2830	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	89.2118	1954	2830	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.47	1545	2830	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.6254	1813	2830	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.523	1629	2830	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.3081	1761	2830	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.6732	1323	2830	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.2249	1476	2830	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:36:34,467] [INFO] DFAST Taxonomy check result was written to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/tc_result.tsv
[2023-06-30 15:36:34,468] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:36:34,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:36:34,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/checkm_data
[2023-06-30 15:36:34,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:36:34,552] [INFO] Task started: CheckM
[2023-06-30 15:36:34,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/checkm_input GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/checkm_result
[2023-06-30 15:37:47,703] [INFO] Task succeeded: CheckM
[2023-06-30 15:37:47,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:37:47,729] [INFO] ===== Completeness check finished =====
[2023-06-30 15:37:47,729] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:37:47,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/markers.fasta)
[2023-06-30 15:37:47,730] [INFO] Task started: Blastn
[2023-06-30 15:37:47,730] [INFO] Running command: blastn -query GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f056f83-9ad5-4165-a6c0-942a6be42fcf/dqc_reference/reference_markers_gtdb.fasta -out GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:37:49,700] [INFO] Task succeeded: Blastn
[2023-06-30 15:37:49,706] [INFO] Selected 9 target genomes.
[2023-06-30 15:37:49,706] [INFO] Target genome list was writen to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:37:49,712] [INFO] Task started: fastANI
[2023-06-30 15:37:49,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d206c6-1074-4068-9363-532341a31b20/GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna.gz --refList GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/target_genomes_gtdb.txt --output GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:38:08,392] [INFO] Task succeeded: fastANI
[2023-06-30 15:38:08,405] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:38:08,405] [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_900104795.1	s__Paraburkholderia sp900104795	98.4659	2433	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.49	98.44	0.88	0.86	5	conclusive
GCF_002278075.1	s__Paraburkholderia aromaticivorans	91.4329	2206	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459535.1	s__Paraburkholderia sp000178415	90.9225	2009	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_000013645.1	s__Paraburkholderia xenovorans	90.8616	1960	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_004339745.1	s__Paraburkholderia sp004339745	89.9575	1988	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	89.6935	1990	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	89.4279	1907	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_003002025.1	s__Paraburkholderia sp003002025	89.1085	1915	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_902859915.1	s__Paraburkholderia ultramafica	87.4588	1547	2830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:38:08,407] [INFO] GTDB search result was written to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/result_gtdb.tsv
[2023-06-30 15:38:08,408] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:38:08,412] [INFO] DFAST_QC result json was written to GCA_903869145.1_freshwater_MAG_---_MJ130617B_bin-119_genomic.fna/dqc_result.json
[2023-06-30 15:38:08,412] [INFO] DFAST_QC completed!
[2023-06-30 15:38:08,412] [INFO] Total running time: 0h2m26s