[2024-01-24 12:37:09,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference
[2024-01-24 12:37:10,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,872] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg085cd38e-d98b-482a-991f-007588230040/GCF_010233585.1_ASM1023358v1_genomic.fna.gz | prodigal -d GCF_010233585.1_ASM1023358v1_genomic.fna/cds.fna -a GCF_010233585.1_ASM1023358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:56,135] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:56,136] [INFO] Task started: HMMsearch
[2024-01-24 12:37:56,136] [INFO] Running command: hmmsearch --tblout GCF_010233585.1_ASM1023358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/reference_markers.hmm GCF_010233585.1_ASM1023358v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:56,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:56,526] [INFO] Found 6/6 markers.
[2024-01-24 12:37:56,602] [INFO] Query marker FASTA was written to GCF_010233585.1_ASM1023358v1_genomic.fna/markers.fasta
[2024-01-24 12:37:56,603] [INFO] Task started: Blastn
[2024-01-24 12:37:56,603] [INFO] Running command: blastn -query GCF_010233585.1_ASM1023358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/reference_markers.fasta -out GCF_010233585.1_ASM1023358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:57,194] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:57,199] [INFO] Selected 16 target genomes.
[2024-01-24 12:37:57,200] [INFO] Target genome list was writen to GCF_010233585.1_ASM1023358v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:57,217] [INFO] Task started: fastANI
[2024-01-24 12:37:57,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg085cd38e-d98b-482a-991f-007588230040/GCF_010233585.1_ASM1023358v1_genomic.fna.gz --refList GCF_010233585.1_ASM1023358v1_genomic.fna/target_genomes.txt --output GCF_010233585.1_ASM1023358v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:19,783] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:19,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:19,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:19,803] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:19,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:19,803] [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 endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	100.0	3442	3442	95	conclusive
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	92.7971	2680	3442	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	79.0794	1039	3442	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	77.8726	702	3442	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.5363	537	3442	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.4067	592	3442	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.3684	555	3442	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.3248	567	3442	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	77.2254	428	3442	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.1813	368	3442	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.131	415	3442	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.1264	537	3442	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.0603	381	3442	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.1767	275	3442	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	75.8018	163	3442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:19,805] [INFO] DFAST Taxonomy check result was written to GCF_010233585.1_ASM1023358v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:19,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:19,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:19,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/checkm_data
[2024-01-24 12:38:19,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:19,896] [INFO] Task started: CheckM
[2024-01-24 12:38:19,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010233585.1_ASM1023358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010233585.1_ASM1023358v1_genomic.fna/checkm_input GCF_010233585.1_ASM1023358v1_genomic.fna/checkm_result
[2024-01-24 12:40:23,375] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:23,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:23,399] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:23,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:23,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010233585.1_ASM1023358v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:23,401] [INFO] Task started: Blastn
[2024-01-24 12:40:23,401] [INFO] Running command: blastn -query GCF_010233585.1_ASM1023358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb3f693-ebbe-4269-8580-2b39d51f5524/dqc_reference/reference_markers_gtdb.fasta -out GCF_010233585.1_ASM1023358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:24,230] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:24,233] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:24,233] [INFO] Target genome list was writen to GCF_010233585.1_ASM1023358v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:24,242] [INFO] Task started: fastANI
[2024-01-24 12:40:24,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg085cd38e-d98b-482a-991f-007588230040/GCF_010233585.1_ASM1023358v1_genomic.fna.gz --refList GCF_010233585.1_ASM1023358v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010233585.1_ASM1023358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:45,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:45,997] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:45,998] [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_010233585.1	s__Spirosoma endbachense	100.0	3442	3442	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_011604685.1	s__Spirosoma aureum	92.7969	2681	3442	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	79.0794	1039	3442	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	77.8634	704	3442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699005.1	s__Spirosoma profusum	77.5494	537	3442	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	77.5239	500	3442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	77.4063	592	3442	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	77.3755	556	3442	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	77.3301	564	3442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282275.1	s__Spirosoma utsteinense	77.2254	428	3442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.1943	367	3442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000374065.1	s__Spirosoma luteum	77.1314	416	3442	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	77.1262	537	3442	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	77.0534	382	3442	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 12:40:45,999] [INFO] GTDB search result was written to GCF_010233585.1_ASM1023358v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:46,001] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:46,005] [INFO] DFAST_QC result json was written to GCF_010233585.1_ASM1023358v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:46,005] [INFO] DFAST_QC completed!
[2024-01-24 12:40:46,005] [INFO] Total running time: 0h3m36s