[2024-01-24 12:44:06,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:06,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:06,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference
[2024-01-24 12:44:07,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:07,218] [INFO] Task started: Prodigal
[2024-01-24 12:44:07,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg647afa1f-a925-4ff0-ba02-667851af2997/GCF_017353185.1_ASM1735318v1_genomic.fna.gz | prodigal -d GCF_017353185.1_ASM1735318v1_genomic.fna/cds.fna -a GCF_017353185.1_ASM1735318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:41,551] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:41,552] [INFO] Task started: HMMsearch
[2024-01-24 12:44:41,552] [INFO] Running command: hmmsearch --tblout GCF_017353185.1_ASM1735318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/reference_markers.hmm GCF_017353185.1_ASM1735318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:41,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:41,959] [INFO] Found 6/6 markers.
[2024-01-24 12:44:42,019] [INFO] Query marker FASTA was written to GCF_017353185.1_ASM1735318v1_genomic.fna/markers.fasta
[2024-01-24 12:44:42,020] [INFO] Task started: Blastn
[2024-01-24 12:44:42,020] [INFO] Running command: blastn -query GCF_017353185.1_ASM1735318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/reference_markers.fasta -out GCF_017353185.1_ASM1735318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:42,681] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:42,687] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:42,687] [INFO] Target genome list was writen to GCF_017353185.1_ASM1735318v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:42,706] [INFO] Task started: fastANI
[2024-01-24 12:44:42,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg647afa1f-a925-4ff0-ba02-667851af2997/GCF_017353185.1_ASM1735318v1_genomic.fna.gz --refList GCF_017353185.1_ASM1735318v1_genomic.fna/target_genomes.txt --output GCF_017353185.1_ASM1735318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:02,660] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:02,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:02,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:02,672] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:02,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:02,672] [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
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	100.0	2096	2098	95	conclusive
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	83.2594	1441	2098	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	78.9441	343	2098	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	77.8807	720	2098	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	76.6696	324	2098	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.6073	330	2098	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.5527	292	2098	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	76.3525	247	2098	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	76.1727	266	2098	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	76.1104	176	2098	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	76.0818	254	2098	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	76.0601	174	2098	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.0556	228	2098	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.5126	70	2098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:02,674] [INFO] DFAST Taxonomy check result was written to GCF_017353185.1_ASM1735318v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:02,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:02,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:02,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/checkm_data
[2024-01-24 12:45:02,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:02,737] [INFO] Task started: CheckM
[2024-01-24 12:45:02,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017353185.1_ASM1735318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017353185.1_ASM1735318v1_genomic.fna/checkm_input GCF_017353185.1_ASM1735318v1_genomic.fna/checkm_result
[2024-01-24 12:46:34,461] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:34,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:34,485] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:34,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:34,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017353185.1_ASM1735318v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:34,486] [INFO] Task started: Blastn
[2024-01-24 12:46:34,487] [INFO] Running command: blastn -query GCF_017353185.1_ASM1735318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b360e31-0577-478f-8871-f0ed85c66d6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017353185.1_ASM1735318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:35,275] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:35,281] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:35,281] [INFO] Target genome list was writen to GCF_017353185.1_ASM1735318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:35,312] [INFO] Task started: fastANI
[2024-01-24 12:46:35,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg647afa1f-a925-4ff0-ba02-667851af2997/GCF_017353185.1_ASM1735318v1_genomic.fna.gz --refList GCF_017353185.1_ASM1735318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017353185.1_ASM1735318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:50,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:50,334] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:50,335] [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_017353185.1	s__Fibrella sp017353185	100.0	2096	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017353255.1	s__Fibrella sp017353255	83.2693	1439	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	77.8854	719	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353175.1	s__Fibrella sp017353175	77.6728	557	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002108455.1	s__Fibrella sp002108455	77.399	525	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	98.52	98.52	0.95	0.95	2	-
GCF_009184635.1	s__Rudanella paleaurantiibacter	76.6762	323	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292855.1	s__Rudanella sp004292855	76.3196	335	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
GCF_003583365.1	s__Fibrisoma montanum	76.1737	266	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296815.2	s__Fibrisoma limi	76.0622	227	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	75.9782	206	2098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:50,337] [INFO] GTDB search result was written to GCF_017353185.1_ASM1735318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:50,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:50,344] [INFO] DFAST_QC result json was written to GCF_017353185.1_ASM1735318v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:50,345] [INFO] DFAST_QC completed!
[2024-01-24 12:46:50,345] [INFO] Total running time: 0h2m44s