[2024-01-24 13:55:44,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:44,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:44,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference
[2024-01-24 13:55:45,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:45,242] [INFO] Task started: Prodigal
[2024-01-24 13:55:45,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg28ccf531-38a5-4626-9301-4c5a5b5d77db/GCF_014282275.1_ASM1428227v1_genomic.fna.gz | prodigal -d GCF_014282275.1_ASM1428227v1_genomic.fna/cds.fna -a GCF_014282275.1_ASM1428227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:17,223] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:17,224] [INFO] Task started: HMMsearch
[2024-01-24 13:56:17,225] [INFO] Running command: hmmsearch --tblout GCF_014282275.1_ASM1428227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/reference_markers.hmm GCF_014282275.1_ASM1428227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:17,573] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:17,574] [INFO] Found 6/6 markers.
[2024-01-24 13:56:17,631] [INFO] Query marker FASTA was written to GCF_014282275.1_ASM1428227v1_genomic.fna/markers.fasta
[2024-01-24 13:56:17,631] [INFO] Task started: Blastn
[2024-01-24 13:56:17,632] [INFO] Running command: blastn -query GCF_014282275.1_ASM1428227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/reference_markers.fasta -out GCF_014282275.1_ASM1428227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:18,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:18,238] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:18,239] [INFO] Target genome list was writen to GCF_014282275.1_ASM1428227v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:18,245] [INFO] Task started: fastANI
[2024-01-24 13:56:18,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ccf531-38a5-4626-9301-4c5a5b5d77db/GCF_014282275.1_ASM1428227v1_genomic.fna.gz --refList GCF_014282275.1_ASM1428227v1_genomic.fna/target_genomes.txt --output GCF_014282275.1_ASM1428227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:42,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:42,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:42,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:42,251] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:42,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:42,251] [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 utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	100.0	2194	2201	95	conclusive
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	80.3251	1086	2201	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.9877	583	2201	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.66	573	2201	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.5382	524	2201	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.4691	454	2201	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.4401	373	2201	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.3784	410	2201	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	77.2374	429	2201	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.2235	431	2201	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.0366	436	2201	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.0185	342	2201	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	76.9975	400	2201	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	76.9352	363	2201	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	76.9263	337	2201	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	76.8805	300	2201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:42,253] [INFO] DFAST Taxonomy check result was written to GCF_014282275.1_ASM1428227v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:42,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:42,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:42,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/checkm_data
[2024-01-24 13:56:42,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:42,318] [INFO] Task started: CheckM
[2024-01-24 13:56:42,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014282275.1_ASM1428227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014282275.1_ASM1428227v1_genomic.fna/checkm_input GCF_014282275.1_ASM1428227v1_genomic.fna/checkm_result
[2024-01-24 13:58:09,032] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:09,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,053] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:09,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:09,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014282275.1_ASM1428227v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:09,055] [INFO] Task started: Blastn
[2024-01-24 13:58:09,055] [INFO] Running command: blastn -query GCF_014282275.1_ASM1428227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5381d798-c490-45b4-a942-2535a4803701/dqc_reference/reference_markers_gtdb.fasta -out GCF_014282275.1_ASM1428227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:09,896] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:09,899] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:09,900] [INFO] Target genome list was writen to GCF_014282275.1_ASM1428227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:09,922] [INFO] Task started: fastANI
[2024-01-24 13:58:09,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ccf531-38a5-4626-9301-4c5a5b5d77db/GCF_014282275.1_ASM1428227v1_genomic.fna.gz --refList GCF_014282275.1_ASM1428227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014282275.1_ASM1428227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:32,882] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:32,897] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:32,897] [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_014282275.1	s__Spirosoma utsteinense	100.0	2194	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	conclusive
GCF_002067135.1	s__Spirosoma rigui	80.3279	1085	2201	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	78.0191	561	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	77.9939	582	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.6654	572	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_013127955.1	s__Spirosoma taeanense	77.5381	524	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974425.1	s__Spirosoma radiotolerans	77.4751	453	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	77.3855	409	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	77.3463	373	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374085.1	s__Spirosoma spitsbergense	77.243	426	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	77.224	431	2201	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	77.0576	434	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002056795.1	s__Spirosoma aerolatum	77.0169	341	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	76.9858	402	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	76.9276	336	2201	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	76.9218	365	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435915.1	s__Spirosoma terrae	76.8969	298	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,899] [INFO] GTDB search result was written to GCF_014282275.1_ASM1428227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:32,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:32,903] [INFO] DFAST_QC result json was written to GCF_014282275.1_ASM1428227v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:32,903] [INFO] DFAST_QC completed!
[2024-01-24 13:58:32,903] [INFO] Total running time: 0h2m49s