[2024-01-24 13:01:11,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:11,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:11,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference
[2024-01-24 13:01:13,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,363] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d620f87-0193-48c4-b035-54b8cdf73938/GCF_006337085.1_ASM633708v1_genomic.fna.gz | prodigal -d GCF_006337085.1_ASM633708v1_genomic.fna/cds.fna -a GCF_006337085.1_ASM633708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:21,831] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:21,832] [INFO] Task started: HMMsearch
[2024-01-24 13:01:21,832] [INFO] Running command: hmmsearch --tblout GCF_006337085.1_ASM633708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/reference_markers.hmm GCF_006337085.1_ASM633708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:22,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:22,142] [INFO] Found 6/6 markers.
[2024-01-24 13:01:22,170] [INFO] Query marker FASTA was written to GCF_006337085.1_ASM633708v1_genomic.fna/markers.fasta
[2024-01-24 13:01:22,170] [INFO] Task started: Blastn
[2024-01-24 13:01:22,171] [INFO] Running command: blastn -query GCF_006337085.1_ASM633708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/reference_markers.fasta -out GCF_006337085.1_ASM633708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:22,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:22,974] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:22,974] [INFO] Target genome list was writen to GCF_006337085.1_ASM633708v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:22,985] [INFO] Task started: fastANI
[2024-01-24 13:01:22,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d620f87-0193-48c4-b035-54b8cdf73938/GCF_006337085.1_ASM633708v1_genomic.fna.gz --refList GCF_006337085.1_ASM633708v1_genomic.fna/target_genomes.txt --output GCF_006337085.1_ASM633708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:40,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:40,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:40,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:40,113] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:40,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:40,114] [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 faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	100.0	994	995	95	conclusive
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	79.5605	315	995	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	79.3837	293	995	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	79.1483	290	995	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	79.0705	280	995	95	below_threshold
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	78.019	125	995	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.6694	51	995	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	76.5481	75	995	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	75.9662	64	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:40,119] [INFO] DFAST Taxonomy check result was written to GCF_006337085.1_ASM633708v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:40,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:40,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:40,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/checkm_data
[2024-01-24 13:01:40,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:40,164] [INFO] Task started: CheckM
[2024-01-24 13:01:40,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006337085.1_ASM633708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006337085.1_ASM633708v1_genomic.fna/checkm_input GCF_006337085.1_ASM633708v1_genomic.fna/checkm_result
[2024-01-24 13:02:08,795] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:08,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:08,818] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:08,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:08,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006337085.1_ASM633708v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:08,819] [INFO] Task started: Blastn
[2024-01-24 13:02:08,819] [INFO] Running command: blastn -query GCF_006337085.1_ASM633708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfba7c45a-b030-470b-92b4-280f9010d72f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006337085.1_ASM633708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:09,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:09,916] [INFO] Selected 10 target genomes.
[2024-01-24 13:02:09,916] [INFO] Target genome list was writen to GCF_006337085.1_ASM633708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:09,925] [INFO] Task started: fastANI
[2024-01-24 13:02:09,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d620f87-0193-48c4-b035-54b8cdf73938/GCF_006337085.1_ASM633708v1_genomic.fna.gz --refList GCF_006337085.1_ASM633708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006337085.1_ASM633708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:17,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:17,140] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:17,140] [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_006337085.1	s__Sutterella faecalis	100.0	994	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.36	97.93	0.96	0.93	5	conclusive
GCF_009183815.1	s__Sutterella seckii_A	90.9948	698	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.09	95.34	0.87	0.81	4	-
GCA_905198475.1	s__Sutterella sp905198475	81.4695	437	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770335.1	s__Sutterella sp900770335	80.6363	359	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609995.1	s__Sutterella megalosphaeroides	79.5525	314	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905213905.1	s__Sutterella sp905213905	79.3001	299	995	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	79.2261	274	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.47	98.47	0.94	0.94	2	-
GCF_003315195.1	s__Sutterella wadsworthensis	79.0705	280	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.28	97.53	0.92	0.89	35	-
GCF_000430725.1	s__Azohydromonas australica	76.0142	62	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:17,142] [INFO] GTDB search result was written to GCF_006337085.1_ASM633708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:17,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:17,147] [INFO] DFAST_QC result json was written to GCF_006337085.1_ASM633708v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:17,147] [INFO] DFAST_QC completed!
[2024-01-24 13:02:17,147] [INFO] Total running time: 0h1m5s