[2024-01-24 13:25:30,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference
[2024-01-24 13:25:31,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,842] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb1acfcb-9afa-4dd1-83e2-410b9f205a37/GCF_004340905.1_ASM434090v1_genomic.fna.gz | prodigal -d GCF_004340905.1_ASM434090v1_genomic.fna/cds.fna -a GCF_004340905.1_ASM434090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:45,645] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:45,645] [INFO] Task started: HMMsearch
[2024-01-24 13:25:45,645] [INFO] Running command: hmmsearch --tblout GCF_004340905.1_ASM434090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/reference_markers.hmm GCF_004340905.1_ASM434090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:45,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:45,960] [INFO] Found 6/6 markers.
[2024-01-24 13:25:46,007] [INFO] Query marker FASTA was written to GCF_004340905.1_ASM434090v1_genomic.fna/markers.fasta
[2024-01-24 13:25:46,008] [INFO] Task started: Blastn
[2024-01-24 13:25:46,008] [INFO] Running command: blastn -query GCF_004340905.1_ASM434090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/reference_markers.fasta -out GCF_004340905.1_ASM434090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,101] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:47,101] [INFO] Target genome list was writen to GCF_004340905.1_ASM434090v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:47,113] [INFO] Task started: fastANI
[2024-01-24 13:25:47,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1acfcb-9afa-4dd1-83e2-410b9f205a37/GCF_004340905.1_ASM434090v1_genomic.fna.gz --refList GCF_004340905.1_ASM434090v1_genomic.fna/target_genomes.txt --output GCF_004340905.1_ASM434090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:04,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:04,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:04,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:04,556] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:04,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:04,556] [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
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	100.0	1673	1674	95	conclusive
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	99.9708	1620	1674	95	conclusive
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	93.0853	1224	1674	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	93.0711	1152	1674	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.066	725	1674	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.7528	753	1674	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.4962	898	1674	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.2555	693	1674	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.2018	887	1674	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.1987	730	1674	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.2764	674	1674	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.1046	643	1674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:04,559] [INFO] DFAST Taxonomy check result was written to GCF_004340905.1_ASM434090v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:04,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:04,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:04,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/checkm_data
[2024-01-24 13:26:04,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:04,620] [INFO] Task started: CheckM
[2024-01-24 13:26:04,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340905.1_ASM434090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340905.1_ASM434090v1_genomic.fna/checkm_input GCF_004340905.1_ASM434090v1_genomic.fna/checkm_result
[2024-01-24 13:27:17,652] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:17,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:17,675] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:17,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:17,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340905.1_ASM434090v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:17,676] [INFO] Task started: Blastn
[2024-01-24 13:27:17,676] [INFO] Running command: blastn -query GCF_004340905.1_ASM434090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bae94ae-517d-439c-ada9-92a15b2d2d7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340905.1_ASM434090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:19,938] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:19,942] [INFO] Selected 9 target genomes.
[2024-01-24 13:27:19,943] [INFO] Target genome list was writen to GCF_004340905.1_ASM434090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:19,977] [INFO] Task started: fastANI
[2024-01-24 13:27:19,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1acfcb-9afa-4dd1-83e2-410b9f205a37/GCF_004340905.1_ASM434090v1_genomic.fna.gz --refList GCF_004340905.1_ASM434090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340905.1_ASM434090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:34,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:34,259] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:34,259] [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_004340905.1	s__Rubrivivax gelatinosus	100.0	1673	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000284255.1	s__Rubrivivax gelatinosus_A	93.1677	1413	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	93.0139	1155	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	90.0576	1336	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
GCA_001725505.1	s__Rubrivivax sp001725505	82.8025	701	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	81.5913	848	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_018971105.1	s__Rubrivivax sp018971105	81.4501	729	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.9556	661	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223165.1	s__Rubrivivax sp016223165	80.3202	935	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:34,260] [INFO] GTDB search result was written to GCF_004340905.1_ASM434090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:34,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:34,264] [INFO] DFAST_QC result json was written to GCF_004340905.1_ASM434090v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:34,264] [INFO] DFAST_QC completed!
[2024-01-24 13:27:34,264] [INFO] Total running time: 0h2m4s