[2024-01-24 11:27:04,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference
[2024-01-24 11:27:05,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,724] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c50f273-54e8-4b05-a966-6cf846353671/GCF_001633165.1_ASM163316v1_genomic.fna.gz | prodigal -d GCF_001633165.1_ASM163316v1_genomic.fna/cds.fna -a GCF_001633165.1_ASM163316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:18,115] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:18,116] [INFO] Task started: HMMsearch
[2024-01-24 11:27:18,116] [INFO] Running command: hmmsearch --tblout GCF_001633165.1_ASM163316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/reference_markers.hmm GCF_001633165.1_ASM163316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:18,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:18,386] [INFO] Found 6/6 markers.
[2024-01-24 11:27:18,422] [INFO] Query marker FASTA was written to GCF_001633165.1_ASM163316v1_genomic.fna/markers.fasta
[2024-01-24 11:27:18,422] [INFO] Task started: Blastn
[2024-01-24 11:27:18,422] [INFO] Running command: blastn -query GCF_001633165.1_ASM163316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/reference_markers.fasta -out GCF_001633165.1_ASM163316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:19,465] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:19,469] [INFO] Selected 14 target genomes.
[2024-01-24 11:27:19,470] [INFO] Target genome list was writen to GCF_001633165.1_ASM163316v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:19,479] [INFO] Task started: fastANI
[2024-01-24 11:27:19,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c50f273-54e8-4b05-a966-6cf846353671/GCF_001633165.1_ASM163316v1_genomic.fna.gz --refList GCF_001633165.1_ASM163316v1_genomic.fna/target_genomes.txt --output GCF_001633165.1_ASM163316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:31,966] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:31,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:31,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:31,990] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:31,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:31,990] [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
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	100.0	1446	1448	95	conclusive
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	99.9863	1433	1448	95	conclusive
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	88.7736	1017	1448	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	82.1153	687	1448	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	81.9848	714	1448	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	81.9488	691	1448	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	81.4721	734	1448	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.6039	595	1448	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	79.1222	576	1448	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	79.0888	563	1448	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6118	580	1448	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.5226	449	1448	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.4859	440	1448	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8108	383	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,992] [INFO] DFAST Taxonomy check result was written to GCF_001633165.1_ASM163316v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:31,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:31,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:31,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/checkm_data
[2024-01-24 11:27:31,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:32,034] [INFO] Task started: CheckM
[2024-01-24 11:27:32,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001633165.1_ASM163316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001633165.1_ASM163316v1_genomic.fna/checkm_input GCF_001633165.1_ASM163316v1_genomic.fna/checkm_result
[2024-01-24 11:28:15,993] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:15,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:16,012] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:16,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:16,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001633165.1_ASM163316v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:16,014] [INFO] Task started: Blastn
[2024-01-24 11:28:16,014] [INFO] Running command: blastn -query GCF_001633165.1_ASM163316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe79b09c-e16e-4295-adc2-3927a5c7b068/dqc_reference/reference_markers_gtdb.fasta -out GCF_001633165.1_ASM163316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:17,921] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:17,925] [INFO] Selected 8 target genomes.
[2024-01-24 11:28:17,925] [INFO] Target genome list was writen to GCF_001633165.1_ASM163316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:17,935] [INFO] Task started: fastANI
[2024-01-24 11:28:17,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c50f273-54e8-4b05-a966-6cf846353671/GCF_001633165.1_ASM163316v1_genomic.fna.gz --refList GCF_001633165.1_ASM163316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001633165.1_ASM163316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:26,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:26,245] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:26,245] [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_001633165.1	s__Rhodovulum sulfidophilum	100.0	1446	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	conclusive
GCF_002073975.1	s__Rhodovulum sp002073975	92.1701	1203	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	88.7211	1021	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003053725.1	s__Rhodovulum kholense	88.6643	1061	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_004339675.1	s__Rhodovulum steppense	81.9805	717	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	81.9537	690	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	81.4475	741	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	79.1012	576	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:26,247] [INFO] GTDB search result was written to GCF_001633165.1_ASM163316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:26,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:26,251] [INFO] DFAST_QC result json was written to GCF_001633165.1_ASM163316v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:26,251] [INFO] DFAST_QC completed!
[2024-01-24 11:28:26,251] [INFO] Total running time: 0h1m22s