[2023-06-27 23:24:49,310] [INFO] DFAST_QC pipeline started.
[2023-06-27 23:24:49,312] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 23:24:49,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference
[2023-06-27 23:24:51,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 23:24:51,683] [INFO] Task started: Prodigal
[2023-06-27 23:24:51,683] [INFO] Running command: gunzip -c /var/lib/cwl/stge419f2aa-15f2-42c0-9165-40009d1a1b16/GCA_002367415.1_ASM236741v1_genomic.fna.gz | prodigal -d GCA_002367415.1_ASM236741v1_genomic.fna/cds.fna -a GCA_002367415.1_ASM236741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 23:24:56,135] [INFO] Task succeeded: Prodigal
[2023-06-27 23:24:56,136] [INFO] Task started: HMMsearch
[2023-06-27 23:24:56,136] [INFO] Running command: hmmsearch --tblout GCA_002367415.1_ASM236741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/reference_markers.hmm GCA_002367415.1_ASM236741v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 23:24:56,319] [INFO] Task succeeded: HMMsearch
[2023-06-27 23:24:56,323] [INFO] Found 6/6 markers.
[2023-06-27 23:24:56,347] [INFO] Query marker FASTA was written to GCA_002367415.1_ASM236741v1_genomic.fna/markers.fasta
[2023-06-27 23:24:56,348] [INFO] Task started: Blastn
[2023-06-27 23:24:56,348] [INFO] Running command: blastn -query GCA_002367415.1_ASM236741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/reference_markers.fasta -out GCA_002367415.1_ASM236741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:24:57,145] [INFO] Task succeeded: Blastn
[2023-06-27 23:24:57,150] [INFO] Selected 24 target genomes.
[2023-06-27 23:24:57,150] [INFO] Target genome list was writen to GCA_002367415.1_ASM236741v1_genomic.fna/target_genomes.txt
[2023-06-27 23:24:57,151] [INFO] Task started: fastANI
[2023-06-27 23:24:57,151] [INFO] Running command: fastANI --query /var/lib/cwl/stge419f2aa-15f2-42c0-9165-40009d1a1b16/GCA_002367415.1_ASM236741v1_genomic.fna.gz --refList GCA_002367415.1_ASM236741v1_genomic.fna/target_genomes.txt --output GCA_002367415.1_ASM236741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 23:25:10,724] [INFO] Task succeeded: fastANI
[2023-06-27 23:25:10,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 23:25:10,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 23:25:10,744] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 23:25:10,744] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 23:25:10,744] [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	77.9497	105	449	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.4013	99	449	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.3409	82	449	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.3239	106	449	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.3201	93	449	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.3112	92	449	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.2209	104	449	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.1683	99	449	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	77.1496	83	449	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.1413	100	449	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	77.1083	100	449	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.0705	82	449	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.0204	82	449	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.9666	94	449	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	76.9629	94	449	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.9096	92	449	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	76.8815	98	449	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.8207	89	449	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	76.768	98	449	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.7545	71	449	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.7418	98	449	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.7413	97	449	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	76.5876	78	449	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	76.5473	84	449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 23:25:10,747] [INFO] DFAST Taxonomy check result was written to GCA_002367415.1_ASM236741v1_genomic.fna/tc_result.tsv
[2023-06-27 23:25:10,747] [INFO] ===== Taxonomy check completed =====
[2023-06-27 23:25:10,748] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 23:25:10,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/checkm_data
[2023-06-27 23:25:10,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 23:25:10,769] [INFO] Task started: CheckM
[2023-06-27 23:25:10,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002367415.1_ASM236741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002367415.1_ASM236741v1_genomic.fna/checkm_input GCA_002367415.1_ASM236741v1_genomic.fna/checkm_result
[2023-06-27 23:25:28,800] [INFO] Task succeeded: CheckM
[2023-06-27 23:25:28,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 23:25:28,822] [INFO] ===== Completeness check finished =====
[2023-06-27 23:25:28,822] [INFO] ===== Start GTDB Search =====
[2023-06-27 23:25:28,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002367415.1_ASM236741v1_genomic.fna/markers.fasta)
[2023-06-27 23:25:28,823] [INFO] Task started: Blastn
[2023-06-27 23:25:28,823] [INFO] Running command: blastn -query GCA_002367415.1_ASM236741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77bd6f92-cf56-414d-b8ac-86ea86f43dc2/dqc_reference/reference_markers_gtdb.fasta -out GCA_002367415.1_ASM236741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:25:30,304] [INFO] Task succeeded: Blastn
[2023-06-27 23:25:30,308] [INFO] Selected 17 target genomes.
[2023-06-27 23:25:30,308] [INFO] Target genome list was writen to GCA_002367415.1_ASM236741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 23:25:30,314] [INFO] Task started: fastANI
[2023-06-27 23:25:30,314] [INFO] Running command: fastANI --query /var/lib/cwl/stge419f2aa-15f2-42c0-9165-40009d1a1b16/GCA_002367415.1_ASM236741v1_genomic.fna.gz --refList GCA_002367415.1_ASM236741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002367415.1_ASM236741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 23:25:38,984] [INFO] Task succeeded: fastANI
[2023-06-27 23:25:38,998] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 23:25:38,999] [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	98.9671	386	449	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	81.4932	279	449	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	81.4314	246	449	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	77.8243	117	449	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	77.5401	75	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	77.3095	117	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429605.1	s__Azonexus hydrophilus	77.3078	83	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCA_018240785.1	s__Thauera sp018240785	77.2262	88	449	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	77.2247	97	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	77.149	81	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	77.1083	100	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335435.1	s__Parasulfuritortus sp013335435	76.9974	88	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	76.8653	98	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337445.1	s__Parasulfuritortus cantonensis	76.7825	88	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967275.1	s__Sulfuritortus calidifontis	76.7413	97	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001808185.1	s__Jeongeupia sp001808185	76.3363	84	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791205.1	s__Desulfobacillus sp016791205	76.3255	83	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 23:25:39,000] [INFO] GTDB search result was written to GCA_002367415.1_ASM236741v1_genomic.fna/result_gtdb.tsv
[2023-06-27 23:25:39,001] [INFO] ===== GTDB Search completed =====
[2023-06-27 23:25:39,008] [INFO] DFAST_QC result json was written to GCA_002367415.1_ASM236741v1_genomic.fna/dqc_result.json
[2023-06-27 23:25:39,009] [INFO] DFAST_QC completed!
[2023-06-27 23:25:39,009] [INFO] Total running time: 0h0m50s