[2024-01-24 13:43:26,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference
[2024-01-24 13:43:27,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:27,687] [INFO] Task started: Prodigal
[2024-01-24 13:43:27,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f348790-f6ad-4d71-a90b-4b0ae36b2c4f/GCF_000974685.2_FaOYT1_2.0_genomic.fna.gz | prodigal -d GCF_000974685.2_FaOYT1_2.0_genomic.fna/cds.fna -a GCF_000974685.2_FaOYT1_2.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:36,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:36,191] [INFO] Task started: HMMsearch
[2024-01-24 13:43:36,191] [INFO] Running command: hmmsearch --tblout GCF_000974685.2_FaOYT1_2.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/reference_markers.hmm GCF_000974685.2_FaOYT1_2.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:36,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:36,404] [INFO] Found 6/6 markers.
[2024-01-24 13:43:36,429] [INFO] Query marker FASTA was written to GCF_000974685.2_FaOYT1_2.0_genomic.fna/markers.fasta
[2024-01-24 13:43:36,429] [INFO] Task started: Blastn
[2024-01-24 13:43:36,429] [INFO] Running command: blastn -query GCF_000974685.2_FaOYT1_2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/reference_markers.fasta -out GCF_000974685.2_FaOYT1_2.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:37,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:37,202] [INFO] Selected 25 target genomes.
[2024-01-24 13:43:37,202] [INFO] Target genome list was writen to GCF_000974685.2_FaOYT1_2.0_genomic.fna/target_genomes.txt
[2024-01-24 13:43:37,236] [INFO] Task started: fastANI
[2024-01-24 13:43:37,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f348790-f6ad-4d71-a90b-4b0ae36b2c4f/GCF_000974685.2_FaOYT1_2.0_genomic.fna.gz --refList GCF_000974685.2_FaOYT1_2.0_genomic.fna/target_genomes.txt --output GCF_000974685.2_FaOYT1_2.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:53,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:53,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:53,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:53,269] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:53,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:53,269] [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
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	100.0	905	905	95	conclusive
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	78.9853	261	905	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	77.4006	118	905	95	below_threshold
Paraburkholderia phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	77.3201	65	905	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.2831	92	905	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.2198	133	905	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.1996	94	905	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	77.1761	69	905	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.0383	103	905	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	76.918	120	905	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.875	89	905	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	76.8439	98	905	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	76.8188	99	905	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.7727	82	905	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.7456	109	905	95	below_threshold
Thauera terpenica	strain=58Eu	GCA_000443165.1	76113	76113	type	True	76.6067	78	905	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.6037	84	905	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	76.5691	79	905	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	76.5155	94	905	95	below_threshold
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	76.3873	61	905	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.2435	80	905	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.1981	106	905	95	below_threshold
Cupriavidus plantarum	strain=LMG 26296	GCA_905397285.1	942865	942865	type	True	76.1625	74	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:53,272] [INFO] DFAST Taxonomy check result was written to GCF_000974685.2_FaOYT1_2.0_genomic.fna/tc_result.tsv
[2024-01-24 13:43:53,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:53,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:53,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/checkm_data
[2024-01-24 13:43:53,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:53,299] [INFO] Task started: CheckM
[2024-01-24 13:43:53,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000974685.2_FaOYT1_2.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000974685.2_FaOYT1_2.0_genomic.fna/checkm_input GCF_000974685.2_FaOYT1_2.0_genomic.fna/checkm_result
[2024-01-24 13:44:22,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:22,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:22,211] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:22,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:22,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000974685.2_FaOYT1_2.0_genomic.fna/markers.fasta)
[2024-01-24 13:44:22,211] [INFO] Task started: Blastn
[2024-01-24 13:44:22,212] [INFO] Running command: blastn -query GCF_000974685.2_FaOYT1_2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg019e2673-2c6b-44c7-ac52-b525b412dde5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000974685.2_FaOYT1_2.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:23,541] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:23,545] [INFO] Selected 12 target genomes.
[2024-01-24 13:44:23,545] [INFO] Target genome list was writen to GCF_000974685.2_FaOYT1_2.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:23,560] [INFO] Task started: fastANI
[2024-01-24 13:44:23,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f348790-f6ad-4d71-a90b-4b0ae36b2c4f/GCF_000974685.2_FaOYT1_2.0_genomic.fna.gz --refList GCF_000974685.2_FaOYT1_2.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000974685.2_FaOYT1_2.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:29,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:29,240] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:29,240] [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_000974685.2	s__Ferriphaselus amnicola	100.0	905	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Ferriphaselus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000746095.1	s__Ferriphaselus sp000746095	83.7538	544	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Ferriphaselus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234685.1	s__Ferriphaselus sp016234685	80.9325	376	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Ferriphaselus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324385.1	s__Gallionella kumadai	78.9677	262	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620315.1	s__Sideroxydans sp011620315	78.5416	247	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	78.396	253	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297065.1	s__PALSA-1006 sp004297065	78.2675	244	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__PALSA-1006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018814405.1	s__Sideroxydans sp018814405	78.225	229	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	100.00	100.00	0.99	0.99	3	-
GCA_001801105.1	s__Gallionella sp001801105	78.2027	202	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218055.1	s__Sideroxydans sp006218055	77.9757	118	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414205.1	s__Gallionella sp002414205	77.189	123	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.54	99.54	0.86	0.86	2	-
GCA_002787455.1	s__Sideroxydans sp002787455	77.1461	114	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.23	98.87	0.83	0.78	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:29,242] [INFO] GTDB search result was written to GCF_000974685.2_FaOYT1_2.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:29,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:29,246] [INFO] DFAST_QC result json was written to GCF_000974685.2_FaOYT1_2.0_genomic.fna/dqc_result.json
[2024-01-24 13:44:29,247] [INFO] DFAST_QC completed!
[2024-01-24 13:44:29,247] [INFO] Total running time: 0h1m3s