[2023-06-16 20:50:18,564] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:50:18,569] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:50:18,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference
[2023-06-16 20:50:19,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:50:19,769] [INFO] Task started: Prodigal
[2023-06-16 20:50:19,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg76a6bf3f-3ffc-4b33-812b-8d5388be1374/GCA_009928075.1_ASM992807v1_genomic.fna.gz | prodigal -d GCA_009928075.1_ASM992807v1_genomic.fna/cds.fna -a GCA_009928075.1_ASM992807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:50:24,772] [INFO] Task succeeded: Prodigal
[2023-06-16 20:50:24,772] [INFO] Task started: HMMsearch
[2023-06-16 20:50:24,772] [INFO] Running command: hmmsearch --tblout GCA_009928075.1_ASM992807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/reference_markers.hmm GCA_009928075.1_ASM992807v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:50:24,941] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:50:24,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg76a6bf3f-3ffc-4b33-812b-8d5388be1374/GCA_009928075.1_ASM992807v1_genomic.fna.gz]
[2023-06-16 20:50:24,964] [INFO] Query marker FASTA was written to GCA_009928075.1_ASM992807v1_genomic.fna/markers.fasta
[2023-06-16 20:50:24,964] [INFO] Task started: Blastn
[2023-06-16 20:50:24,964] [INFO] Running command: blastn -query GCA_009928075.1_ASM992807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/reference_markers.fasta -out GCA_009928075.1_ASM992807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:50:25,766] [INFO] Task succeeded: Blastn
[2023-06-16 20:50:25,770] [INFO] Selected 23 target genomes.
[2023-06-16 20:50:25,770] [INFO] Target genome list was writen to GCA_009928075.1_ASM992807v1_genomic.fna/target_genomes.txt
[2023-06-16 20:50:25,791] [INFO] Task started: fastANI
[2023-06-16 20:50:25,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a6bf3f-3ffc-4b33-812b-8d5388be1374/GCA_009928075.1_ASM992807v1_genomic.fna.gz --refList GCA_009928075.1_ASM992807v1_genomic.fna/target_genomes.txt --output GCA_009928075.1_ASM992807v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:50:39,885] [INFO] Task succeeded: fastANI
[2023-06-16 20:50:39,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:50:39,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:50:39,901] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:50:39,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:50:39,901] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.785	88	393	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.6395	75	393	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.6189	74	393	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.371	81	393	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.3212	85	393	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.2403	63	393	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.1315	80	393	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.0653	78	393	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.0259	80	393	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	76.9939	81	393	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.9533	79	393	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.8174	62	393	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	76.7612	62	393	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.7594	59	393	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.7483	80	393	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	76.668	81	393	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	76.6427	69	393	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.5814	80	393	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	76.4886	67	393	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2677	57	393	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:50:39,903] [INFO] DFAST Taxonomy check result was written to GCA_009928075.1_ASM992807v1_genomic.fna/tc_result.tsv
[2023-06-16 20:50:39,904] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:50:39,904] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:50:39,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/checkm_data
[2023-06-16 20:50:39,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:50:39,934] [INFO] Task started: CheckM
[2023-06-16 20:50:39,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009928075.1_ASM992807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009928075.1_ASM992807v1_genomic.fna/checkm_input GCA_009928075.1_ASM992807v1_genomic.fna/checkm_result
[2023-06-16 20:51:00,516] [INFO] Task succeeded: CheckM
[2023-06-16 20:51:00,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.74%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:51:00,535] [INFO] ===== Completeness check finished =====
[2023-06-16 20:51:00,536] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:51:00,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009928075.1_ASM992807v1_genomic.fna/markers.fasta)
[2023-06-16 20:51:00,536] [INFO] Task started: Blastn
[2023-06-16 20:51:00,536] [INFO] Running command: blastn -query GCA_009928075.1_ASM992807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e83da46-30bd-4407-9deb-fd92194f35e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_009928075.1_ASM992807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:01,925] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:01,929] [INFO] Selected 20 target genomes.
[2023-06-16 20:51:01,929] [INFO] Target genome list was writen to GCA_009928075.1_ASM992807v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:51:01,951] [INFO] Task started: fastANI
[2023-06-16 20:51:01,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a6bf3f-3ffc-4b33-812b-8d5388be1374/GCA_009928075.1_ASM992807v1_genomic.fna.gz --refList GCA_009928075.1_ASM992807v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009928075.1_ASM992807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:51:11,192] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:11,205] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:51:11,206] [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_009927815.1	s__UBA3065 sp002367415	99.0598	298	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	99.03	98.97	0.84	0.74	6	conclusive
GCA_018882975.1	s__UBA3065 sp018882975	81.3426	220	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923755.1	s__UBA3065 sp009923755	81.0553	203	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858125.1	s__Azospira_A restricta	77.9357	91	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012745.1	s__Thiobacillus denitrificans_B	77.6293	70	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	77.5185	54	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCA_016183655.1	s__Azospira_A sp016183655	77.3714	87	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653115.1	s__Rhodocyclus purpureus	77.3212	85	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	77.1771	80	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCF_004337445.1	s__Parasulfuritortus cantonensis	76.9456	65	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	76.8151	81	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628555.1	s__Aromatoleum sp003628555	76.6282	79	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	76.5518	79	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	76.5228	79	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:51:11,208] [INFO] GTDB search result was written to GCA_009928075.1_ASM992807v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:51:11,208] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:51:11,212] [INFO] DFAST_QC result json was written to GCA_009928075.1_ASM992807v1_genomic.fna/dqc_result.json
[2023-06-16 20:51:11,213] [INFO] DFAST_QC completed!
[2023-06-16 20:51:11,213] [INFO] Total running time: 0h0m53s