[2023-06-05 19:00:42,752] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:00:42,754] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:00:42,754] [INFO] DQC Reference Directory: /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference
[2023-06-05 19:00:43,867] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:00:43,867] [INFO] Task started: Prodigal
[2023-06-05 19:00:43,868] [INFO] Running command: gunzip -c /var/lib/cwl/stgcacdea11-8d3c-49e3-af6c-62a24cd0ec19/GCA_004211355.1_ASM421135v1_genomic.fna.gz | prodigal -d GCA_004211355.1_ASM421135v1_genomic.fna/cds.fna -a GCA_004211355.1_ASM421135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:00:59,827] [INFO] Task succeeded: Prodigal
[2023-06-05 19:00:59,828] [INFO] Task started: HMMsearch
[2023-06-05 19:00:59,828] [INFO] Running command: hmmsearch --tblout GCA_004211355.1_ASM421135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/reference_markers.hmm GCA_004211355.1_ASM421135v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:00,071] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:00,072] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcacdea11-8d3c-49e3-af6c-62a24cd0ec19/GCA_004211355.1_ASM421135v1_genomic.fna.gz]
[2023-06-05 19:01:00,108] [INFO] Query marker FASTA was written to GCA_004211355.1_ASM421135v1_genomic.fna/markers.fasta
[2023-06-05 19:01:00,108] [INFO] Task started: Blastn
[2023-06-05 19:01:00,108] [INFO] Running command: blastn -query GCA_004211355.1_ASM421135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/reference_markers.fasta -out GCA_004211355.1_ASM421135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:00,758] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:00,761] [INFO] Selected 11 target genomes.
[2023-06-05 19:01:00,761] [INFO] Target genome list was writen to GCA_004211355.1_ASM421135v1_genomic.fna/target_genomes.txt
[2023-06-05 19:01:00,762] [INFO] Task started: fastANI
[2023-06-05 19:01:00,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacdea11-8d3c-49e3-af6c-62a24cd0ec19/GCA_004211355.1_ASM421135v1_genomic.fna.gz --refList GCA_004211355.1_ASM421135v1_genomic.fna/target_genomes.txt --output GCA_004211355.1_ASM421135v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:01:11,488] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:11,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:01:11,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:01:11,496] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:01:11,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:01:11,497] [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 soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	81.8929	702	1414	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	81.4848	609	1414	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	81.1274	601	1414	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	80.8934	581	1414	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	80.6394	599	1414	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	80.381	516	1414	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.0513	465	1414	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.7761	419	1414	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.6428	394	1414	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.6311	443	1414	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.2091	430	1414	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:01:11,498] [INFO] DFAST Taxonomy check result was written to GCA_004211355.1_ASM421135v1_genomic.fna/tc_result.tsv
[2023-06-05 19:01:11,499] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:01:11,499] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:01:11,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/checkm_data
[2023-06-05 19:01:11,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:01:11,544] [INFO] Task started: CheckM
[2023-06-05 19:01:11,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004211355.1_ASM421135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004211355.1_ASM421135v1_genomic.fna/checkm_input GCA_004211355.1_ASM421135v1_genomic.fna/checkm_result
[2023-06-05 19:02:54,961] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:54,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.86%
Contamintation: 16.67%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:54,981] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:54,981] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:54,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004211355.1_ASM421135v1_genomic.fna/markers.fasta)
[2023-06-05 19:02:54,983] [INFO] Task started: Blastn
[2023-06-05 19:02:54,983] [INFO] Running command: blastn -query GCA_004211355.1_ASM421135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8baf8f2-1dbe-4ef9-86a3-2caab3d776d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_004211355.1_ASM421135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:56,117] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:56,120] [INFO] Selected 14 target genomes.
[2023-06-05 19:02:56,120] [INFO] Target genome list was writen to GCA_004211355.1_ASM421135v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:56,154] [INFO] Task started: fastANI
[2023-06-05 19:02:56,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacdea11-8d3c-49e3-af6c-62a24cd0ec19/GCA_004211355.1_ASM421135v1_genomic.fna.gz --refList GCA_004211355.1_ASM421135v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004211355.1_ASM421135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:03:08,199] [INFO] Task succeeded: fastANI
[2023-06-05 19:03:08,208] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 19:03:08,208] [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_013822685.1	s__Aquabacterium sp013822685	86.0065	974	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378415.1	s__Aquabacterium sp014378415	85.4355	832	1414	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	81.9105	700	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112875.1	s__Aquabacterium excrementipullorum	81.7689	717	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770725.1	s__Aquabacterium sp001770725	81.6171	619	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768065.1	s__Aquabacterium sp000768065	81.3484	674	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000265.1	s__Aquabacterium sp016000265	81.2515	581	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903894125.1	s__Aquabacterium sp903894125	81.1785	454	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.35	99.35	0.82	0.82	2	-
GCF_001447195.1	s__Aquabacterium parvum	81.1388	600	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCA_002339015.1	s__Aquabacterium sp002339015	81.1219	653	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.88	99.88	0.91	0.91	2	-
GCA_003963115.1	s__Aquabacterium sp003963115	81.0008	648	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871865.1	s__Aquabacterium sp903871865	80.5557	392	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	80.387	515	1414	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	80.0349	390	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.70	99.70	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-05 19:03:08,210] [INFO] GTDB search result was written to GCA_004211355.1_ASM421135v1_genomic.fna/result_gtdb.tsv
[2023-06-05 19:03:08,211] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:03:08,214] [INFO] DFAST_QC result json was written to GCA_004211355.1_ASM421135v1_genomic.fna/dqc_result.json
[2023-06-05 19:03:08,214] [INFO] DFAST_QC completed!
[2023-06-05 19:03:08,214] [INFO] Total running time: 0h2m25s