[2024-01-24 11:34:52,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:52,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:52,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference
[2024-01-24 11:34:55,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,643] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg444f0e81-775b-429e-be9a-171e7a62b1ff/GCF_009909205.1_ASM990920v1_genomic.fna.gz | prodigal -d GCF_009909205.1_ASM990920v1_genomic.fna/cds.fna -a GCF_009909205.1_ASM990920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,997] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,997] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,997] [INFO] Running command: hmmsearch --tblout GCF_009909205.1_ASM990920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/reference_markers.hmm GCF_009909205.1_ASM990920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:09,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:09,310] [INFO] Found 6/6 markers.
[2024-01-24 11:35:09,343] [INFO] Query marker FASTA was written to GCF_009909205.1_ASM990920v1_genomic.fna/markers.fasta
[2024-01-24 11:35:09,343] [INFO] Task started: Blastn
[2024-01-24 11:35:09,343] [INFO] Running command: blastn -query GCF_009909205.1_ASM990920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/reference_markers.fasta -out GCF_009909205.1_ASM990920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,435] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,438] [INFO] Selected 12 target genomes.
[2024-01-24 11:35:10,438] [INFO] Target genome list was writen to GCF_009909205.1_ASM990920v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,443] [INFO] Task started: fastANI
[2024-01-24 11:35:10,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg444f0e81-775b-429e-be9a-171e7a62b1ff/GCF_009909205.1_ASM990920v1_genomic.fna.gz --refList GCF_009909205.1_ASM990920v1_genomic.fna/target_genomes.txt --output GCF_009909205.1_ASM990920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:20,937] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:20,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:20,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:20,953] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:20,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:20,953] [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
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	100.0	1200	1201	95	conclusive
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	82.5308	701	1201	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	82.2741	674	1201	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	82.2388	672	1201	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	81.8195	607	1201	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	81.6274	657	1201	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.7326	482	1201	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.6719	477	1201	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.5486	483	1201	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.2944	465	1201	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.2914	456	1201	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.0799	436	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:20,955] [INFO] DFAST Taxonomy check result was written to GCF_009909205.1_ASM990920v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:20,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:20,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:20,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/checkm_data
[2024-01-24 11:35:20,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:21,000] [INFO] Task started: CheckM
[2024-01-24 11:35:21,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009909205.1_ASM990920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009909205.1_ASM990920v1_genomic.fna/checkm_input GCF_009909205.1_ASM990920v1_genomic.fna/checkm_result
[2024-01-24 11:36:33,190] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:33,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:33,213] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:33,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:33,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009909205.1_ASM990920v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:33,214] [INFO] Task started: Blastn
[2024-01-24 11:36:33,214] [INFO] Running command: blastn -query GCF_009909205.1_ASM990920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg619bba99-d6f1-46a3-bde9-dba85c91a251/dqc_reference/reference_markers_gtdb.fasta -out GCF_009909205.1_ASM990920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:35,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:35,443] [INFO] Selected 18 target genomes.
[2024-01-24 11:36:35,443] [INFO] Target genome list was writen to GCF_009909205.1_ASM990920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:35,460] [INFO] Task started: fastANI
[2024-01-24 11:36:35,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg444f0e81-775b-429e-be9a-171e7a62b1ff/GCF_009909205.1_ASM990920v1_genomic.fna.gz --refList GCF_009909205.1_ASM990920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009909205.1_ASM990920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:51,258] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:51,277] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:51,277] [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_009909205.1	s__Aquabacterium fontiphilum	100.0	1200	1201	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_001770725.1	s__Aquabacterium sp001770725	82.9069	715	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502875.1	s__Aquabacterium sp005502875	82.7421	691	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447195.1	s__Aquabacterium parvum	82.5315	701	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCA_016000265.1	s__Aquabacterium sp016000265	82.3353	662	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.96	99.96	0.95	0.95	2	-
GCF_003100395.1	s__Aquabacterium olei	82.2795	673	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362855.1	s__Aquabacterium commune	82.2101	675	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	95.44	95.44	0.90	0.90	2	-
GCF_000768065.1	s__Aquabacterium sp000768065	81.8033	693	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894125.1	s__Aquabacterium sp903894125	81.8023	484	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.35	99.35	0.82	0.82	2	-
GCF_004310865.1	s__Aquabacterium lacunae	81.7858	611	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933735.1	s__Aquabacterium sp003933735	81.6409	656	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989885.1	s__Aquabacterium sp017989885	81.5715	344	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	98.47	98.47	0.69	0.69	2	-
GCA_019112875.1	s__Aquabacterium excrementipullorum	81.5452	633	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195855.1	s__Aquabacterium sp016195855	81.544	669	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963115.1	s__Aquabacterium sp003963115	81.2411	684	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017994835.1	s__Aquabacterium sp017994835	80.9253	419	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.70	99.70	0.89	0.89	2	-
GCF_018069755.1	s__Ideonella sp018069755	79.2613	496	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	79.002	436	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:51,279] [INFO] GTDB search result was written to GCF_009909205.1_ASM990920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:51,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:51,283] [INFO] DFAST_QC result json was written to GCF_009909205.1_ASM990920v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:51,283] [INFO] DFAST_QC completed!
[2024-01-24 11:36:51,283] [INFO] Total running time: 0h1m59s