[2024-01-24 13:58:55,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,839] [INFO] DQC Reference Directory: /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference
[2024-01-24 13:58:57,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,125] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,125] [INFO] Running command: gunzip -c /var/lib/cwl/stgde932367-cdb9-4318-94ce-ccccee802daa/GCF_000429665.1_ASM42966v1_genomic.fna.gz | prodigal -d GCF_000429665.1_ASM42966v1_genomic.fna/cds.fna -a GCF_000429665.1_ASM42966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:09,438] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:09,438] [INFO] Task started: HMMsearch
[2024-01-24 13:59:09,438] [INFO] Running command: hmmsearch --tblout GCF_000429665.1_ASM42966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/reference_markers.hmm GCF_000429665.1_ASM42966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:09,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:09,790] [INFO] Found 6/6 markers.
[2024-01-24 13:59:09,833] [INFO] Query marker FASTA was written to GCF_000429665.1_ASM42966v1_genomic.fna/markers.fasta
[2024-01-24 13:59:09,833] [INFO] Task started: Blastn
[2024-01-24 13:59:09,834] [INFO] Running command: blastn -query GCF_000429665.1_ASM42966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/reference_markers.fasta -out GCF_000429665.1_ASM42966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:10,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:10,800] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:10,801] [INFO] Target genome list was writen to GCF_000429665.1_ASM42966v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:10,816] [INFO] Task started: fastANI
[2024-01-24 13:59:10,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgde932367-cdb9-4318-94ce-ccccee802daa/GCF_000429665.1_ASM42966v1_genomic.fna.gz --refList GCF_000429665.1_ASM42966v1_genomic.fna/target_genomes.txt --output GCF_000429665.1_ASM42966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:23,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:23,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:23,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:23,979] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:23,979] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:23,979] [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
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	81.3399	616	1314	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	79.4442	458	1314	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	79.0837	430	1314	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	78.7709	380	1314	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	78.7397	390	1314	95	below_threshold
Azospira inquinata	strain=Azo-3	GCA_018905915.1	2785627	2785627	type	True	78.6802	413	1314	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	78.3236	345	1314	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.0837	270	1314	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.0569	275	1314	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.932	222	1314	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.8782	228	1314	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.5794	259	1314	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	77.2744	274	1314	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.2658	193	1314	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.9149	247	1314	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.7839	252	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:23,981] [INFO] DFAST Taxonomy check result was written to GCF_000429665.1_ASM42966v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:23,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:23,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:23,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/checkm_data
[2024-01-24 13:59:23,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:24,027] [INFO] Task started: CheckM
[2024-01-24 13:59:24,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429665.1_ASM42966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429665.1_ASM42966v1_genomic.fna/checkm_input GCF_000429665.1_ASM42966v1_genomic.fna/checkm_result
[2024-01-24 14:00:02,573] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:02,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:02,600] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:02,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:02,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429665.1_ASM42966v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:02,601] [INFO] Task started: Blastn
[2024-01-24 14:00:02,601] [INFO] Running command: blastn -query GCF_000429665.1_ASM42966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91f686b-e498-4fd7-b717-51a130965806/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429665.1_ASM42966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:04,575] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:04,578] [INFO] Selected 14 target genomes.
[2024-01-24 14:00:04,579] [INFO] Target genome list was writen to GCF_000429665.1_ASM42966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:04,625] [INFO] Task started: fastANI
[2024-01-24 14:00:04,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgde932367-cdb9-4318-94ce-ccccee802daa/GCF_000429665.1_ASM42966v1_genomic.fna.gz --refList GCF_000429665.1_ASM42966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429665.1_ASM42966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:16,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:16,700] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:16,700] [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_000429665.1	s__Azovibrio restrictus	100.0	1311	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002340095.1	s__Azovibrio sp002340095	85.4188	662	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252145.1	s__Azovibrio restrictus_A	82.5384	324	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217225.1	s__Azospira oryzae	81.3477	616	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira	95.0	98.24	98.03	0.94	0.90	6	-
GCF_008274805.1	s__Oryzomicrobium terrae	80.0002	483	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Oryzomicrobium	95.0	98.48	98.48	0.93	0.93	2	-
GCA_018261935.1	s__JAGTRP01 sp018261935	79.9172	495	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAGTRP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720065.1	s__SSSZ01 sp016720065	79.7928	448	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__SSSZ01	95.0	99.85	99.82	0.99	0.97	4	-
GCF_003634965.1	s__Azonexus fungiphilus	79.4654	456	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_009469585.1	s__Azonexus sp009469585	79.2451	434	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	79.2407	396	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470165.1	s__Azonexus sp002470165	79.1041	302	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897745.1	s__66-26 sp001897745	78.5792	369	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
GCA_907163075.1	s__Propionivibrio sp907163075	77.2747	217	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886975.1	s__Propionivibrio sp903886975	77.0232	170	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:16,702] [INFO] GTDB search result was written to GCF_000429665.1_ASM42966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:16,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:16,707] [INFO] DFAST_QC result json was written to GCF_000429665.1_ASM42966v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:16,707] [INFO] DFAST_QC completed!
[2024-01-24 14:00:16,707] [INFO] Total running time: 0h1m21s