[2023-06-30 09:06:41,967] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:41,969] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:41,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference
[2023-06-30 09:06:45,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:45,209] [INFO] Task started: Prodigal
[2023-06-30 09:06:45,211] [INFO] Running command: gunzip -c /var/lib/cwl/stga878c9d9-bcba-4f2d-9575-822c26eb2120/GCA_024653675.1_ASM2465367v1_genomic.fna.gz | prodigal -d GCA_024653675.1_ASM2465367v1_genomic.fna/cds.fna -a GCA_024653675.1_ASM2465367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:06:53,277] [INFO] Task succeeded: Prodigal
[2023-06-30 09:06:53,278] [INFO] Task started: HMMsearch
[2023-06-30 09:06:53,278] [INFO] Running command: hmmsearch --tblout GCA_024653675.1_ASM2465367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/reference_markers.hmm GCA_024653675.1_ASM2465367v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:06:53,529] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:06:53,531] [INFO] Found 6/6 markers.
[2023-06-30 09:06:53,579] [INFO] Query marker FASTA was written to GCA_024653675.1_ASM2465367v1_genomic.fna/markers.fasta
[2023-06-30 09:06:53,580] [INFO] Task started: Blastn
[2023-06-30 09:06:53,580] [INFO] Running command: blastn -query GCA_024653675.1_ASM2465367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/reference_markers.fasta -out GCA_024653675.1_ASM2465367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:06:54,405] [INFO] Task succeeded: Blastn
[2023-06-30 09:06:54,409] [INFO] Selected 25 target genomes.
[2023-06-30 09:06:54,409] [INFO] Target genome list was writen to GCA_024653675.1_ASM2465367v1_genomic.fna/target_genomes.txt
[2023-06-30 09:06:54,418] [INFO] Task started: fastANI
[2023-06-30 09:06:54,418] [INFO] Running command: fastANI --query /var/lib/cwl/stga878c9d9-bcba-4f2d-9575-822c26eb2120/GCA_024653675.1_ASM2465367v1_genomic.fna.gz --refList GCA_024653675.1_ASM2465367v1_genomic.fna/target_genomes.txt --output GCA_024653675.1_ASM2465367v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:07:14,202] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:14,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:07:14,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:07:14,220] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:07:14,220] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:07:14,220] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	79.9288	330	821	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.2642	127	821	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.2256	155	821	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	77.218	132	821	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	77.1612	110	821	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.0307	118	821	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	76.9938	161	821	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	76.9015	85	821	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	76.8955	160	821	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	76.629	101	821	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	76.4745	108	821	95	below_threshold
Novimethylophilus kurashikiensis	strain=La2-4	GCA_003112435.1	1825523	1825523	type	True	76.4726	77	821	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.4065	85	821	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	76.323	131	821	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.275	116	821	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.2704	111	821	95	below_threshold
Cupriavidus basilensis	strain=DSM 11853	GCA_008801925.2	68895	68895	suspected-type	True	76.2203	105	821	95	below_threshold
Caballeronia choica		GCA_001544535.2	326476	326476	type	True	76.1563	78	821	95	below_threshold
Caballeronia glathei	strain=DSM 50014	GCA_000698595.1	60547	60547	type	True	76.0527	78	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:07:14,222] [INFO] DFAST Taxonomy check result was written to GCA_024653675.1_ASM2465367v1_genomic.fna/tc_result.tsv
[2023-06-30 09:07:14,223] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:07:14,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:07:14,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/checkm_data
[2023-06-30 09:07:14,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:07:14,258] [INFO] Task started: CheckM
[2023-06-30 09:07:14,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024653675.1_ASM2465367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024653675.1_ASM2465367v1_genomic.fna/checkm_input GCA_024653675.1_ASM2465367v1_genomic.fna/checkm_result
[2023-06-30 09:07:42,962] [INFO] Task succeeded: CheckM
[2023-06-30 09:07:42,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:07:42,988] [INFO] ===== Completeness check finished =====
[2023-06-30 09:07:42,988] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:07:42,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024653675.1_ASM2465367v1_genomic.fna/markers.fasta)
[2023-06-30 09:07:42,989] [INFO] Task started: Blastn
[2023-06-30 09:07:42,989] [INFO] Running command: blastn -query GCA_024653675.1_ASM2465367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e72cbcc-9f5f-4d6d-a46c-593c205e52d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_024653675.1_ASM2465367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:44,377] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:44,383] [INFO] Selected 23 target genomes.
[2023-06-30 09:07:44,383] [INFO] Target genome list was writen to GCA_024653675.1_ASM2465367v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:07:44,422] [INFO] Task started: fastANI
[2023-06-30 09:07:44,423] [INFO] Running command: fastANI --query /var/lib/cwl/stga878c9d9-bcba-4f2d-9575-822c26eb2120/GCA_024653675.1_ASM2465367v1_genomic.fna.gz --refList GCA_024653675.1_ASM2465367v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024653675.1_ASM2465367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:07:55,763] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:55,778] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:07:55,778] [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_003134595.1	s__Gallionella sp003134595	81.6401	383	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403995.1	s__Gallionella sp002403995	81.5098	377	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153155.1	s__Gallionella sp003153155	81.4723	439	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801175.1	s__Gallionella sp001801175	81.4716	427	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880945.1	s__Gallionella sp017880945	81.1653	291	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177795.1	s__Gallionella sp016177795	81.1425	284	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183575.1	s__Gallionella sp016183575	81.0206	272	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880865.1	s__Gallionella sp017880865	80.6654	372	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298605.1	s__Gallionella sp004298605	80.6258	281	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218415.1	s__Gallionella sp016218415	80.5039	366	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218475.1	s__Gallionella sp016218475	80.4932	319	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577345.1	s__Gallionella acididurans	80.468	341	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218445.1	s__CAITJF01 sp016218445	80.3881	286	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__CAITJF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858965.1	s__Gallionella sp903858965	79.9755	307	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.89	99.89	0.95	0.95	2	-
GCF_018324385.1	s__Gallionella kumadai	79.9197	331	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934275.1	s__Gallionella sp903934275	79.646	271	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885195.1	s__Nitrotoga sp009885195	78.6521	178	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Nitrotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847155.1	s__Sideroxydans sp903847155	78.3269	237	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:07:55,780] [INFO] GTDB search result was written to GCA_024653675.1_ASM2465367v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:07:55,781] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:07:55,785] [INFO] DFAST_QC result json was written to GCA_024653675.1_ASM2465367v1_genomic.fna/dqc_result.json
[2023-06-30 09:07:55,786] [INFO] DFAST_QC completed!
[2023-06-30 09:07:55,786] [INFO] Total running time: 0h1m14s