[2023-06-30 11:15:53,755] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:15:53,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:15:53,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference
[2023-06-30 11:15:56,833] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:15:56,834] [INFO] Task started: Prodigal
[2023-06-30 11:15:56,834] [INFO] Running command: gunzip -c /var/lib/cwl/stge4be0b69-050d-4141-9ae9-88f2d3095a3c/GCA_016708385.1_ASM1670838v1_genomic.fna.gz | prodigal -d GCA_016708385.1_ASM1670838v1_genomic.fna/cds.fna -a GCA_016708385.1_ASM1670838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:16:09,442] [INFO] Task succeeded: Prodigal
[2023-06-30 11:16:09,443] [INFO] Task started: HMMsearch
[2023-06-30 11:16:09,443] [INFO] Running command: hmmsearch --tblout GCA_016708385.1_ASM1670838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/reference_markers.hmm GCA_016708385.1_ASM1670838v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:16:09,734] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:16:09,736] [INFO] Found 6/6 markers.
[2023-06-30 11:16:09,775] [INFO] Query marker FASTA was written to GCA_016708385.1_ASM1670838v1_genomic.fna/markers.fasta
[2023-06-30 11:16:09,776] [INFO] Task started: Blastn
[2023-06-30 11:16:09,776] [INFO] Running command: blastn -query GCA_016708385.1_ASM1670838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/reference_markers.fasta -out GCA_016708385.1_ASM1670838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:16:10,842] [INFO] Task succeeded: Blastn
[2023-06-30 11:16:10,847] [INFO] Selected 29 target genomes.
[2023-06-30 11:16:10,848] [INFO] Target genome list was writen to GCA_016708385.1_ASM1670838v1_genomic.fna/target_genomes.txt
[2023-06-30 11:16:10,852] [INFO] Task started: fastANI
[2023-06-30 11:16:10,852] [INFO] Running command: fastANI --query /var/lib/cwl/stge4be0b69-050d-4141-9ae9-88f2d3095a3c/GCA_016708385.1_ASM1670838v1_genomic.fna.gz --refList GCA_016708385.1_ASM1670838v1_genomic.fna/target_genomes.txt --output GCA_016708385.1_ASM1670838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:16:33,254] [INFO] Task succeeded: fastANI
[2023-06-30 11:16:33,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:16:33,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:16:33,281] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:16:33,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 11:16:33,281] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.0821	335	1505	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.8197	346	1505	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.8003	362	1505	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.6057	331	1505	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.5999	372	1505	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.5565	335	1505	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.4858	324	1505	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.4584	322	1505	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	77.4549	294	1505	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.364	321	1505	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.3313	331	1505	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.29	361	1505	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	77.2142	305	1505	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.1807	446	1505	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.1699	349	1505	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.1233	305	1505	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.0662	314	1505	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.789	408	1505	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	76.7673	236	1505	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	76.6777	249	1505	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.6614	462	1505	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	76.5548	435	1505	95	below_threshold
Pelomicrobium methylotrophicum	strain=SM250	GCA_008014345.1	2602750	2602750	type	True	76.5548	139	1505	95	below_threshold
Burkholderia catarinensis	strain=89	GCA_001883705.2	1108140	1108140	type	True	76.5171	378	1505	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.508	429	1505	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	76.4705	254	1505	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	76.1924	123	1505	95	below_threshold
Novimethylophilus kurashikiensis	strain=La2-4	GCA_003112435.1	1825523	1825523	type	True	76.1637	75	1505	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.0188	135	1505	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:16:33,283] [INFO] DFAST Taxonomy check result was written to GCA_016708385.1_ASM1670838v1_genomic.fna/tc_result.tsv
[2023-06-30 11:16:33,284] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:16:33,284] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:16:33,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/checkm_data
[2023-06-30 11:16:33,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:16:33,333] [INFO] Task started: CheckM
[2023-06-30 11:16:33,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708385.1_ASM1670838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708385.1_ASM1670838v1_genomic.fna/checkm_input GCA_016708385.1_ASM1670838v1_genomic.fna/checkm_result
[2023-06-30 11:17:33,192] [INFO] Task succeeded: CheckM
[2023-06-30 11:17:33,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:17:33,217] [INFO] ===== Completeness check finished =====
[2023-06-30 11:17:33,217] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:17:33,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708385.1_ASM1670838v1_genomic.fna/markers.fasta)
[2023-06-30 11:17:33,218] [INFO] Task started: Blastn
[2023-06-30 11:17:33,218] [INFO] Running command: blastn -query GCA_016708385.1_ASM1670838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg095b5819-5e56-49d5-be02-5100f341723e/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708385.1_ASM1670838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:17:35,336] [INFO] Task succeeded: Blastn
[2023-06-30 11:17:35,341] [INFO] Selected 13 target genomes.
[2023-06-30 11:17:35,341] [INFO] Target genome list was writen to GCA_016708385.1_ASM1670838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:17:35,350] [INFO] Task started: fastANI
[2023-06-30 11:17:35,350] [INFO] Running command: fastANI --query /var/lib/cwl/stge4be0b69-050d-4141-9ae9-88f2d3095a3c/GCA_016708385.1_ASM1670838v1_genomic.fna.gz --refList GCA_016708385.1_ASM1670838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708385.1_ASM1670838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:17:46,352] [INFO] Task succeeded: fastANI
[2023-06-30 11:17:46,370] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:17:46,371] [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_016720425.1	s__CAIWHR01 sp016720425	98.9599	1313	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	conclusive
GCA_903912485.1	s__CAIWHR01 sp903912485	81.4071	614	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	99.88	99.81	0.92	0.91	3	-
GCA_016716425.1	s__VBCG01 sp016716425	80.8267	733	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704895.1	s__VBCG01 sp016704895	80.6916	638	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	96.62	96.45	0.90	0.90	3	-
GCA_010365205.1	s__CAIWHR01 sp010365205	80.1531	378	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	80.0213	645	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339295.1	s__VBCG01 sp905339295	80.0034	633	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971195.1	s__VBCG01 sp018971195	79.7598	423	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241745.1	s__VBCG01 sp018241745	79.5373	466	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868295.1	s__Desulfobacillus sp016868295	78.2632	323	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235765.1	s__Fen-999 sp016235765	77.4498	296	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	77.3661	298	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_008801915.1	s__Cupriavidus gilardii	77.3373	377	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
--------------------------------------------------------------------------------
[2023-06-30 11:17:46,373] [INFO] GTDB search result was written to GCA_016708385.1_ASM1670838v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:17:46,374] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:17:46,379] [INFO] DFAST_QC result json was written to GCA_016708385.1_ASM1670838v1_genomic.fna/dqc_result.json
[2023-06-30 11:17:46,379] [INFO] DFAST_QC completed!
[2023-06-30 11:17:46,379] [INFO] Total running time: 0h1m53s