[2023-06-05 18:04:04,273] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:04:04,282] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:04:04,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference
[2023-06-05 18:04:05,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:04:05,735] [INFO] Task started: Prodigal
[2023-06-05 18:04:05,735] [INFO] Running command: gunzip -c /var/lib/cwl/stga40432d8-733a-4a61-a2a6-fef40f21d064/GCA_934277635.1_ERR7738583_bin.31_genomic.fna.gz | prodigal -d GCA_934277635.1_ERR7738583_bin.31_genomic.fna/cds.fna -a GCA_934277635.1_ERR7738583_bin.31_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:04:17,534] [INFO] Task succeeded: Prodigal
[2023-06-05 18:04:17,534] [INFO] Task started: HMMsearch
[2023-06-05 18:04:17,535] [INFO] Running command: hmmsearch --tblout GCA_934277635.1_ERR7738583_bin.31_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/reference_markers.hmm GCA_934277635.1_ERR7738583_bin.31_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:04:17,871] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:04:17,873] [INFO] Found 6/6 markers.
[2023-06-05 18:04:17,910] [INFO] Query marker FASTA was written to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/markers.fasta
[2023-06-05 18:04:17,910] [INFO] Task started: Blastn
[2023-06-05 18:04:17,911] [INFO] Running command: blastn -query GCA_934277635.1_ERR7738583_bin.31_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/reference_markers.fasta -out GCA_934277635.1_ERR7738583_bin.31_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:04:19,087] [INFO] Task succeeded: Blastn
[2023-06-05 18:04:19,091] [INFO] Selected 14 target genomes.
[2023-06-05 18:04:19,091] [INFO] Target genome list was writen to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/target_genomes.txt
[2023-06-05 18:04:19,092] [INFO] Task started: fastANI
[2023-06-05 18:04:19,092] [INFO] Running command: fastANI --query /var/lib/cwl/stga40432d8-733a-4a61-a2a6-fef40f21d064/GCA_934277635.1_ERR7738583_bin.31_genomic.fna.gz --refList GCA_934277635.1_ERR7738583_bin.31_genomic.fna/target_genomes.txt --output GCA_934277635.1_ERR7738583_bin.31_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:04:30,828] [INFO] Task succeeded: fastANI
[2023-06-05 18:04:30,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:04:30,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:04:30,844] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-05 18:04:30,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:04:30,844] [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
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	98.816	875	921	95	conclusive
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	98.8049	860	921	95	conclusive
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.9511	279	921	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	78.4017	141	921	95	below_threshold
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	78.3557	145	921	95	below_threshold
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	77.1556	92	921	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:04:30,847] [INFO] DFAST Taxonomy check result was written to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/tc_result.tsv
[2023-06-05 18:04:30,848] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:04:30,848] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:04:30,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/checkm_data
[2023-06-05 18:04:30,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:04:30,889] [INFO] Task started: CheckM
[2023-06-05 18:04:30,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934277635.1_ERR7738583_bin.31_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934277635.1_ERR7738583_bin.31_genomic.fna/checkm_input GCA_934277635.1_ERR7738583_bin.31_genomic.fna/checkm_result
[2023-06-05 18:05:07,334] [INFO] Task succeeded: CheckM
[2023-06-05 18:05:07,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:05:07,367] [INFO] ===== Completeness check finished =====
[2023-06-05 18:05:07,367] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:05:07,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934277635.1_ERR7738583_bin.31_genomic.fna/markers.fasta)
[2023-06-05 18:05:07,367] [INFO] Task started: Blastn
[2023-06-05 18:05:07,368] [INFO] Running command: blastn -query GCA_934277635.1_ERR7738583_bin.31_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6f9426-d922-4076-a487-8875744f9aa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934277635.1_ERR7738583_bin.31_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:08,380] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:08,384] [INFO] Selected 17 target genomes.
[2023-06-05 18:05:08,384] [INFO] Target genome list was writen to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:05:08,388] [INFO] Task started: fastANI
[2023-06-05 18:05:08,388] [INFO] Running command: fastANI --query /var/lib/cwl/stga40432d8-733a-4a61-a2a6-fef40f21d064/GCA_934277635.1_ERR7738583_bin.31_genomic.fna.gz --refList GCA_934277635.1_ERR7738583_bin.31_genomic.fna/target_genomes_gtdb.txt --output GCA_934277635.1_ERR7738583_bin.31_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:05:20,696] [INFO] Task succeeded: fastANI
[2023-06-05 18:05:20,705] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:05:20,705] [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_003315195.1	s__Sutterella wadsworthensis	98.8049	860	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.28	97.53	0.92	0.89	35	conclusive
GCF_009183815.1	s__Sutterella seckii_A	79.6059	274	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.09	95.34	0.87	0.81	4	-
GCA_905213905.1	s__Sutterella sp905213905	79.5632	177	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899755.1	s__Sutterella massiliensis	79.5233	194	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.18	98.18	0.90	0.90	2	-
GCA_905198475.1	s__Sutterella sp905198475	79.011	248	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337085.1	s__Sutterella faecalis	78.9994	276	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.36	97.93	0.96	0.93	5	-
GCA_900770335.1	s__Sutterella sp900770335	78.6147	185	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764215.1	s__Sutterella sp900764215	78.1725	115	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.09	99.09	0.76	0.76	2	-
GCA_905202595.1	s__Sutterella sp905202595	78.0895	166	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:05:20,714] [INFO] GTDB search result was written to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/result_gtdb.tsv
[2023-06-05 18:05:20,715] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:05:20,728] [INFO] DFAST_QC result json was written to GCA_934277635.1_ERR7738583_bin.31_genomic.fna/dqc_result.json
[2023-06-05 18:05:20,728] [INFO] DFAST_QC completed!
[2023-06-05 18:05:20,728] [INFO] Total running time: 0h1m16s