[2023-06-29 04:57:20,264] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:57:20,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:57:20,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference
[2023-06-29 04:57:21,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:57:21,564] [INFO] Task started: Prodigal
[2023-06-29 04:57:21,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg779b8563-1106-4279-a4ae-e6c8b4a51ea0/GCA_020025965.1_ASM2002596v1_genomic.fna.gz | prodigal -d GCA_020025965.1_ASM2002596v1_genomic.fna/cds.fna -a GCA_020025965.1_ASM2002596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:57:26,983] [INFO] Task succeeded: Prodigal
[2023-06-29 04:57:26,984] [INFO] Task started: HMMsearch
[2023-06-29 04:57:26,984] [INFO] Running command: hmmsearch --tblout GCA_020025965.1_ASM2002596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/reference_markers.hmm GCA_020025965.1_ASM2002596v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:57:27,268] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:57:27,270] [INFO] Found 6/6 markers.
[2023-06-29 04:57:27,300] [INFO] Query marker FASTA was written to GCA_020025965.1_ASM2002596v1_genomic.fna/markers.fasta
[2023-06-29 04:57:27,301] [INFO] Task started: Blastn
[2023-06-29 04:57:27,301] [INFO] Running command: blastn -query GCA_020025965.1_ASM2002596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/reference_markers.fasta -out GCA_020025965.1_ASM2002596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:57:27,977] [INFO] Task succeeded: Blastn
[2023-06-29 04:57:27,984] [INFO] Selected 26 target genomes.
[2023-06-29 04:57:27,984] [INFO] Target genome list was writen to GCA_020025965.1_ASM2002596v1_genomic.fna/target_genomes.txt
[2023-06-29 04:57:27,989] [INFO] Task started: fastANI
[2023-06-29 04:57:27,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg779b8563-1106-4279-a4ae-e6c8b4a51ea0/GCA_020025965.1_ASM2002596v1_genomic.fna.gz --refList GCA_020025965.1_ASM2002596v1_genomic.fna/target_genomes.txt --output GCA_020025965.1_ASM2002596v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:57:47,992] [INFO] Task succeeded: fastANI
[2023-06-29 04:57:47,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:57:47,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:57:48,001] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:57:48,001] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:57:48,002] [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 megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	78.5135	125	630	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	77.6504	102	630	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	77.3511	87	630	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.2073	85	630	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	77.1823	85	630	95	below_threshold
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	76.5791	52	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:57:48,004] [INFO] DFAST Taxonomy check result was written to GCA_020025965.1_ASM2002596v1_genomic.fna/tc_result.tsv
[2023-06-29 04:57:48,005] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:57:48,005] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:57:48,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/checkm_data
[2023-06-29 04:57:48,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:57:48,033] [INFO] Task started: CheckM
[2023-06-29 04:57:48,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025965.1_ASM2002596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025965.1_ASM2002596v1_genomic.fna/checkm_input GCA_020025965.1_ASM2002596v1_genomic.fna/checkm_result
[2023-06-29 04:58:11,465] [INFO] Task succeeded: CheckM
[2023-06-29 04:58:11,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:58:11,487] [INFO] ===== Completeness check finished =====
[2023-06-29 04:58:11,487] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:58:11,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025965.1_ASM2002596v1_genomic.fna/markers.fasta)
[2023-06-29 04:58:11,488] [INFO] Task started: Blastn
[2023-06-29 04:58:11,488] [INFO] Running command: blastn -query GCA_020025965.1_ASM2002596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1665cbb-9ffa-4e24-993c-5b05ff40f4d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025965.1_ASM2002596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:58:12,372] [INFO] Task succeeded: Blastn
[2023-06-29 04:58:12,376] [INFO] Selected 20 target genomes.
[2023-06-29 04:58:12,376] [INFO] Target genome list was writen to GCA_020025965.1_ASM2002596v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:58:12,397] [INFO] Task started: fastANI
[2023-06-29 04:58:12,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg779b8563-1106-4279-a4ae-e6c8b4a51ea0/GCA_020025965.1_ASM2002596v1_genomic.fna.gz --refList GCA_020025965.1_ASM2002596v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025965.1_ASM2002596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:58:23,021] [INFO] Task succeeded: fastANI
[2023-06-29 04:58:23,044] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:58:23,044] [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_017936545.1	s__Sutterella sp017936545	78.6711	141	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905186105.1	s__Sutterella sp905186105	78.6149	135	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	97.95	97.93	0.89	0.89	3	-
GCF_000297775.1	s__Sutterella wadsworthensis_A	78.5912	158	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.94	98.60	0.92	0.86	8	-
GCA_900764215.1	s__Sutterella sp900764215	78.5404	135	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.09	99.09	0.76	0.76	2	-
GCF_003609995.1	s__Sutterella megalosphaeroides	78.5135	125	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754475.1	s__Sutterella sp900754475	78.5083	108	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.47	98.47	0.94	0.94	2	-
GCA_900543805.1	s__Sutterella merdavium	78.1022	111	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.29	97.30	0.92	0.87	4	-
GCA_900762445.1	s__Sutterella sp900762445	77.9455	81	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.95	99.93	0.98	0.98	3	-
GCA_900545275.1	s__Sutterella sp900545275	77.8275	113	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.03	98.03	0.94	0.94	2	-
GCA_905194315.1	s__Sutterella sp905194315	77.8129	87	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250875.1	s__Sutterella parvirubra	77.6967	100	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.34	98.52	0.95	0.91	4	-
GCA_905198475.1	s__Sutterella sp905198475	77.3952	70	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905202595.1	s__Sutterella sp905202595	76.3189	78	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:58:23,047] [INFO] GTDB search result was written to GCA_020025965.1_ASM2002596v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:58:23,047] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:58:23,050] [INFO] DFAST_QC result json was written to GCA_020025965.1_ASM2002596v1_genomic.fna/dqc_result.json
[2023-06-29 04:58:23,051] [INFO] DFAST_QC completed!
[2023-06-29 04:58:23,051] [INFO] Total running time: 0h1m3s