[2024-01-24 12:47:25,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:25,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:25,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference
[2024-01-24 12:47:27,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:27,172] [INFO] Task started: Prodigal
[2024-01-24 12:47:27,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a0bfe37-5348-44d1-8f3e-b5bea50d6a4e/GCF_010747415.1_ASM1074741v1_genomic.fna.gz | prodigal -d GCF_010747415.1_ASM1074741v1_genomic.fna/cds.fna -a GCF_010747415.1_ASM1074741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:02,046] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:02,047] [INFO] Task started: HMMsearch
[2024-01-24 12:48:02,047] [INFO] Running command: hmmsearch --tblout GCF_010747415.1_ASM1074741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/reference_markers.hmm GCF_010747415.1_ASM1074741v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:02,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:02,426] [INFO] Found 6/6 markers.
[2024-01-24 12:48:02,487] [INFO] Query marker FASTA was written to GCF_010747415.1_ASM1074741v1_genomic.fna/markers.fasta
[2024-01-24 12:48:02,487] [INFO] Task started: Blastn
[2024-01-24 12:48:02,487] [INFO] Running command: blastn -query GCF_010747415.1_ASM1074741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/reference_markers.fasta -out GCF_010747415.1_ASM1074741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:03,133] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:03,136] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:03,137] [INFO] Target genome list was writen to GCF_010747415.1_ASM1074741v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:03,159] [INFO] Task started: fastANI
[2024-01-24 12:48:03,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a0bfe37-5348-44d1-8f3e-b5bea50d6a4e/GCF_010747415.1_ASM1074741v1_genomic.fna.gz --refList GCF_010747415.1_ASM1074741v1_genomic.fna/target_genomes.txt --output GCF_010747415.1_ASM1074741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:25,933] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:25,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:25,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:25,955] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:25,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:25,955] [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
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	100.0	2378	2378	95	conclusive
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	79.062	1036	2378	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	78.9649	986	2378	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	77.4721	408	2378	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.4483	524	2378	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.3999	474	2378	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.3888	396	2378	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.2845	501	2378	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.2749	417	2378	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	77.1381	410	2378	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.0459	432	2378	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.016	424	2378	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.7868	368	2378	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.2325	262	2378	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	76.1969	224	2378	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	76.0996	158	2378	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	76.0602	213	2378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:25,957] [INFO] DFAST Taxonomy check result was written to GCF_010747415.1_ASM1074741v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:25,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:25,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:25,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/checkm_data
[2024-01-24 12:48:25,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:26,025] [INFO] Task started: CheckM
[2024-01-24 12:48:26,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010747415.1_ASM1074741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010747415.1_ASM1074741v1_genomic.fna/checkm_input GCF_010747415.1_ASM1074741v1_genomic.fna/checkm_result
[2024-01-24 12:49:57,276] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:57,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:57,301] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:57,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:57,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010747415.1_ASM1074741v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:57,302] [INFO] Task started: Blastn
[2024-01-24 12:49:57,302] [INFO] Running command: blastn -query GCF_010747415.1_ASM1074741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafdac55e-8508-4fe6-a9b7-8b711ccd23e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_010747415.1_ASM1074741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:58,116] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:58,120] [INFO] Selected 15 target genomes.
[2024-01-24 12:49:58,120] [INFO] Target genome list was writen to GCF_010747415.1_ASM1074741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:58,157] [INFO] Task started: fastANI
[2024-01-24 12:49:58,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a0bfe37-5348-44d1-8f3e-b5bea50d6a4e/GCF_010747415.1_ASM1074741v1_genomic.fna.gz --refList GCF_010747415.1_ASM1074741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010747415.1_ASM1074741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:17,647] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:17,668] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:17,668] [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_010747415.1	s__Spirosoma agri	100.0	2378	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010233585.1	s__Spirosoma endbachense	79.056	1037	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	78.9688	985	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000024525.1	s__Spirosoma linguale	77.6584	563	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003259005.1	s__Spirosoma sp003259005	77.5428	533	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006965485.1	s__Spirosoma sp006965485	77.4684	546	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002825.1	s__Spirosoma oryzae	77.4647	409	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.4107	474	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.4035	393	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	77.2883	415	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	77.034	434	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374065.1	s__Spirosoma luteum	77.01	425	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001988955.1	s__Spirosoma montaniterrae	76.7868	368	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	76.1831	226	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292855.1	s__Rudanella sp004292855	75.9648	182	2378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:17,670] [INFO] GTDB search result was written to GCF_010747415.1_ASM1074741v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:17,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:17,675] [INFO] DFAST_QC result json was written to GCF_010747415.1_ASM1074741v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:17,676] [INFO] DFAST_QC completed!
[2024-01-24 12:50:17,676] [INFO] Total running time: 0h2m52s