[2023-06-30 14:31:37,218] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:31:37,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:31:37,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference
[2023-06-30 14:31:38,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:31:38,441] [INFO] Task started: Prodigal
[2023-06-30 14:31:38,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e25b89b-1306-49ae-a173-2bfabcd8966b/GCA_024275895.1_ASM2427589v1_genomic.fna.gz | prodigal -d GCA_024275895.1_ASM2427589v1_genomic.fna/cds.fna -a GCA_024275895.1_ASM2427589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:31:45,420] [INFO] Task succeeded: Prodigal
[2023-06-30 14:31:45,421] [INFO] Task started: HMMsearch
[2023-06-30 14:31:45,421] [INFO] Running command: hmmsearch --tblout GCA_024275895.1_ASM2427589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/reference_markers.hmm GCA_024275895.1_ASM2427589v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:31:45,680] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:31:45,682] [INFO] Found 6/6 markers.
[2023-06-30 14:31:45,717] [INFO] Query marker FASTA was written to GCA_024275895.1_ASM2427589v1_genomic.fna/markers.fasta
[2023-06-30 14:31:45,718] [INFO] Task started: Blastn
[2023-06-30 14:31:45,718] [INFO] Running command: blastn -query GCA_024275895.1_ASM2427589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/reference_markers.fasta -out GCA_024275895.1_ASM2427589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:31:46,456] [INFO] Task succeeded: Blastn
[2023-06-30 14:31:46,461] [INFO] Selected 30 target genomes.
[2023-06-30 14:31:46,461] [INFO] Target genome list was writen to GCA_024275895.1_ASM2427589v1_genomic.fna/target_genomes.txt
[2023-06-30 14:31:46,468] [INFO] Task started: fastANI
[2023-06-30 14:31:46,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e25b89b-1306-49ae-a173-2bfabcd8966b/GCA_024275895.1_ASM2427589v1_genomic.fna.gz --refList GCA_024275895.1_ASM2427589v1_genomic.fna/target_genomes.txt --output GCA_024275895.1_ASM2427589v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:32:06,867] [INFO] Task succeeded: fastANI
[2023-06-30 14:32:06,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:32:06,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:32:06,883] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:32:06,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:32:06,883] [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
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.3774	54	748	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.3447	77	748	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.3199	78	748	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.3094	77	748	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.3071	57	748	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.2739	58	748	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	76.2459	59	748	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1121	54	748	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.1103	53	748	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.0518	70	748	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	75.8233	66	748	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:32:06,886] [INFO] DFAST Taxonomy check result was written to GCA_024275895.1_ASM2427589v1_genomic.fna/tc_result.tsv
[2023-06-30 14:32:06,886] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:32:06,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:32:06,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/checkm_data
[2023-06-30 14:32:06,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:32:06,921] [INFO] Task started: CheckM
[2023-06-30 14:32:06,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024275895.1_ASM2427589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024275895.1_ASM2427589v1_genomic.fna/checkm_input GCA_024275895.1_ASM2427589v1_genomic.fna/checkm_result
[2023-06-30 14:32:33,617] [INFO] Task succeeded: CheckM
[2023-06-30 14:32:33,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:32:33,639] [INFO] ===== Completeness check finished =====
[2023-06-30 14:32:33,640] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:32:33,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024275895.1_ASM2427589v1_genomic.fna/markers.fasta)
[2023-06-30 14:32:33,640] [INFO] Task started: Blastn
[2023-06-30 14:32:33,640] [INFO] Running command: blastn -query GCA_024275895.1_ASM2427589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91eb990-3430-4e7a-ad93-141a7b4c5520/dqc_reference/reference_markers_gtdb.fasta -out GCA_024275895.1_ASM2427589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:32:34,906] [INFO] Task succeeded: Blastn
[2023-06-30 14:32:34,911] [INFO] Selected 25 target genomes.
[2023-06-30 14:32:34,911] [INFO] Target genome list was writen to GCA_024275895.1_ASM2427589v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:32:34,969] [INFO] Task started: fastANI
[2023-06-30 14:32:34,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e25b89b-1306-49ae-a173-2bfabcd8966b/GCA_024275895.1_ASM2427589v1_genomic.fna.gz --refList GCA_024275895.1_ASM2427589v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024275895.1_ASM2427589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:32:50,286] [INFO] Task succeeded: fastANI
[2023-06-30 14:32:50,306] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:32:50,307] [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_002869085.1	s__BM303 sp002869085	78.1521	269	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__BM303;g__BM303	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015482775.1	s__Kaustia mangrovi	76.5266	69	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	76.2901	72	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	76.2881	78	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_012848855.1	s__Pyruvatibacter mobilis	76.2459	59	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002389665.1	s__Tepidicaulis sp002389665	76.134	53	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281615.1	s__Rhodoligotrophos sp005281615	76.1121	54	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228955.1	s__UBA2767 sp003228955	76.0454	61	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__UBA2767	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574785.1	s__Nordella sp003574785	75.9645	71	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873435.1	s__Nordella sp014873435	75.7149	57	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046175.1	s__Bosea sp003046175	75.5285	53	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:32:50,309] [INFO] GTDB search result was written to GCA_024275895.1_ASM2427589v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:32:50,310] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:32:50,314] [INFO] DFAST_QC result json was written to GCA_024275895.1_ASM2427589v1_genomic.fna/dqc_result.json
[2023-06-30 14:32:50,314] [INFO] DFAST_QC completed!
[2023-06-30 14:32:50,314] [INFO] Total running time: 0h1m13s