[2023-06-12 23:51:14,243] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:51:14,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:51:14,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference
[2023-06-12 23:51:15,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:51:15,472] [INFO] Task started: Prodigal
[2023-06-12 23:51:15,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgb377bee1-f97f-47b8-9a71-7f77e13ebf27/GCA_022448405.1_ASM2244840v1_genomic.fna.gz | prodigal -d GCA_022448405.1_ASM2244840v1_genomic.fna/cds.fna -a GCA_022448405.1_ASM2244840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:51:22,673] [INFO] Task succeeded: Prodigal
[2023-06-12 23:51:22,674] [INFO] Task started: HMMsearch
[2023-06-12 23:51:22,674] [INFO] Running command: hmmsearch --tblout GCA_022448405.1_ASM2244840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/reference_markers.hmm GCA_022448405.1_ASM2244840v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:51:22,925] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:51:22,927] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb377bee1-f97f-47b8-9a71-7f77e13ebf27/GCA_022448405.1_ASM2244840v1_genomic.fna.gz]
[2023-06-12 23:51:22,992] [INFO] Query marker FASTA was written to GCA_022448405.1_ASM2244840v1_genomic.fna/markers.fasta
[2023-06-12 23:51:22,993] [INFO] Task started: Blastn
[2023-06-12 23:51:22,993] [INFO] Running command: blastn -query GCA_022448405.1_ASM2244840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/reference_markers.fasta -out GCA_022448405.1_ASM2244840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:51:23,928] [INFO] Task succeeded: Blastn
[2023-06-12 23:51:23,933] [INFO] Selected 17 target genomes.
[2023-06-12 23:51:23,934] [INFO] Target genome list was writen to GCA_022448405.1_ASM2244840v1_genomic.fna/target_genomes.txt
[2023-06-12 23:51:23,939] [INFO] Task started: fastANI
[2023-06-12 23:51:23,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgb377bee1-f97f-47b8-9a71-7f77e13ebf27/GCA_022448405.1_ASM2244840v1_genomic.fna.gz --refList GCA_022448405.1_ASM2244840v1_genomic.fna/target_genomes.txt --output GCA_022448405.1_ASM2244840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:51:40,132] [INFO] Task succeeded: fastANI
[2023-06-12 23:51:40,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:51:40,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:51:40,155] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:51:40,155] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:51:40,155] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	82.5753	377	609	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	82.4981	385	609	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	82.4496	382	609	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	81.8217	386	609	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	81.6705	378	609	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	81.6381	374	609	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	81.6187	401	609	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	81.6171	396	609	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	81.5293	402	609	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	81.4588	379	609	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	81.4497	384	609	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	81.3863	374	609	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	81.1776	370	609	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	81.0695	351	609	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	80.91	363	609	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	80.8242	375	609	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.4636	342	609	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:51:40,158] [INFO] DFAST Taxonomy check result was written to GCA_022448405.1_ASM2244840v1_genomic.fna/tc_result.tsv
[2023-06-12 23:51:40,158] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:51:40,158] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:51:40,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/checkm_data
[2023-06-12 23:51:40,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:51:40,218] [INFO] Task started: CheckM
[2023-06-12 23:51:40,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448405.1_ASM2244840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448405.1_ASM2244840v1_genomic.fna/checkm_input GCA_022448405.1_ASM2244840v1_genomic.fna/checkm_result
[2023-06-12 23:52:08,172] [INFO] Task succeeded: CheckM
[2023-06-12 23:52:08,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:52:08,196] [INFO] ===== Completeness check finished =====
[2023-06-12 23:52:08,196] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:52:08,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448405.1_ASM2244840v1_genomic.fna/markers.fasta)
[2023-06-12 23:52:08,197] [INFO] Task started: Blastn
[2023-06-12 23:52:08,197] [INFO] Running command: blastn -query GCA_022448405.1_ASM2244840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b0323b5-611f-4118-b6df-9f0a2a814d1e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448405.1_ASM2244840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:52:10,079] [INFO] Task succeeded: Blastn
[2023-06-12 23:52:10,084] [INFO] Selected 18 target genomes.
[2023-06-12 23:52:10,085] [INFO] Target genome list was writen to GCA_022448405.1_ASM2244840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:52:10,102] [INFO] Task started: fastANI
[2023-06-12 23:52:10,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgb377bee1-f97f-47b8-9a71-7f77e13ebf27/GCA_022448405.1_ASM2244840v1_genomic.fna.gz --refList GCA_022448405.1_ASM2244840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448405.1_ASM2244840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:52:26,243] [INFO] Task succeeded: fastANI
[2023-06-12 23:52:26,265] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:52:26,265] [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_016219375.1	s__Aquabacterium sp016219375	97.5226	543	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004322345.1	s__Aquabacterium sp004322345	83.3304	395	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.53	97.53	0.87	0.87	2	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	82.4787	385	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_018069875.1	s__Ideonella sp018069875	82.0693	384	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_001770725.1	s__Aquabacterium sp001770725	81.9424	405	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	81.9294	385	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	81.8621	385	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	81.845	389	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	81.6486	387	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	81.631	416	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201595.1	s__Sphaerotilus hippei	81.537	379	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	81.2366	346	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	81.1265	348	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339015.1	s__Aquabacterium sp002339015	81.0769	380	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.88	99.88	0.91	0.91	2	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.9558	384	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894125.1	s__Aquabacterium sp903894125	80.9422	287	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.35	99.35	0.82	0.82	2	-
GCF_900142965.1	s__Rhizobacter sp900142965	80.9208	387	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	80.8399	385	609	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-12 23:52:26,267] [INFO] GTDB search result was written to GCA_022448405.1_ASM2244840v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:52:26,268] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:52:26,274] [INFO] DFAST_QC result json was written to GCA_022448405.1_ASM2244840v1_genomic.fna/dqc_result.json
[2023-06-12 23:52:26,274] [INFO] DFAST_QC completed!
[2023-06-12 23:52:26,274] [INFO] Total running time: 0h1m12s