[2024-01-24 12:36:54,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:54,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:54,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference
[2024-01-24 12:36:57,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:57,083] [INFO] Task started: Prodigal
[2024-01-24 12:36:57,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf3d9519-01dc-474d-98f9-5844ca1b206d/GCF_014699035.1_ASM1469903v1_genomic.fna.gz | prodigal -d GCF_014699035.1_ASM1469903v1_genomic.fna/cds.fna -a GCF_014699035.1_ASM1469903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:32,197] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:32,197] [INFO] Task started: HMMsearch
[2024-01-24 12:37:32,198] [INFO] Running command: hmmsearch --tblout GCF_014699035.1_ASM1469903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/reference_markers.hmm GCF_014699035.1_ASM1469903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:32,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:32,644] [INFO] Found 6/6 markers.
[2024-01-24 12:37:32,706] [INFO] Query marker FASTA was written to GCF_014699035.1_ASM1469903v1_genomic.fna/markers.fasta
[2024-01-24 12:37:32,706] [INFO] Task started: Blastn
[2024-01-24 12:37:32,706] [INFO] Running command: blastn -query GCF_014699035.1_ASM1469903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/reference_markers.fasta -out GCF_014699035.1_ASM1469903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:33,290] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:33,294] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:33,294] [INFO] Target genome list was writen to GCF_014699035.1_ASM1469903v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:33,303] [INFO] Task started: fastANI
[2024-01-24 12:37:33,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf3d9519-01dc-474d-98f9-5844ca1b206d/GCF_014699035.1_ASM1469903v1_genomic.fna.gz --refList GCF_014699035.1_ASM1469903v1_genomic.fna/target_genomes.txt --output GCF_014699035.1_ASM1469903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:56,950] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:56,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:56,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:56,976] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:56,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:56,977] [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 validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	100.0	2716	2720	95	conclusive
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	78.6306	905	2720	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.9636	716	2720	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.7795	576	2720	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.6976	676	2720	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.6412	547	2720	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.6182	521	2720	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.5485	595	2720	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.4821	548	2720	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.4095	561	2720	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	77.2453	475	2720	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.0495	422	2720	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	76.9963	363	2720	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.8064	320	2720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:56,979] [INFO] DFAST Taxonomy check result was written to GCF_014699035.1_ASM1469903v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:56,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:56,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:56,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/checkm_data
[2024-01-24 12:37:56,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:57,064] [INFO] Task started: CheckM
[2024-01-24 12:37:57,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014699035.1_ASM1469903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014699035.1_ASM1469903v1_genomic.fna/checkm_input GCF_014699035.1_ASM1469903v1_genomic.fna/checkm_result
[2024-01-24 12:39:33,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:33,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:33,092] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:33,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:33,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014699035.1_ASM1469903v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:33,094] [INFO] Task started: Blastn
[2024-01-24 12:39:33,094] [INFO] Running command: blastn -query GCF_014699035.1_ASM1469903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35c6dfcf-f8df-4a41-9919-5de1d36640ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014699035.1_ASM1469903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:33,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:33,869] [INFO] Selected 19 target genomes.
[2024-01-24 12:39:33,869] [INFO] Target genome list was writen to GCF_014699035.1_ASM1469903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:33,889] [INFO] Task started: fastANI
[2024-01-24 12:39:33,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf3d9519-01dc-474d-98f9-5844ca1b206d/GCF_014699035.1_ASM1469903v1_genomic.fna.gz --refList GCF_014699035.1_ASM1469903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014699035.1_ASM1469903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:07,278] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:07,294] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:07,295] [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_014699035.1	s__Spirosoma validum	100.0	2716	2720	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_900112365.1	s__Spirosoma endophyticum	78.6397	903	2720	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	78.2412	494	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965485.1	s__Spirosoma sp006965485	78.0388	697	2720	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	77.9638	716	2720	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	77.7787	576	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754945.1	s__Spirosoma sp009754945	77.6976	676	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117325.1	s__Spirosoma sp014117325	77.688	667	2720	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	77.6582	562	2720	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	77.6399	548	2720	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	77.5588	593	2720	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	77.4753	550	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898575.1	s__Spirosoma sp001898575	77.4627	572	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000374085.1	s__Spirosoma spitsbergense	77.2515	473	2720	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	77.0491	423	2720	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	77.0174	360	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849055.1	s__Spirosoma sp012849055	76.9826	315	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296815.2	s__Fibrisoma limi	76.8064	320	2720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377625.1	s__Spirosoma sp014377625	76.5835	237	2720	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 12:40:07,297] [INFO] GTDB search result was written to GCF_014699035.1_ASM1469903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:07,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:07,304] [INFO] DFAST_QC result json was written to GCF_014699035.1_ASM1469903v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:07,305] [INFO] DFAST_QC completed!
[2024-01-24 12:40:07,305] [INFO] Total running time: 0h3m13s