[2024-01-25 20:23:50,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:50,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:50,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference
[2024-01-25 20:23:51,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:51,731] [INFO] Task started: Prodigal
[2024-01-25 20:23:51,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg37c752cd-663f-43eb-bf87-7ca7f0c1a037/GCF_017353175.1_ASM1735317v1_genomic.fna.gz | prodigal -d GCF_017353175.1_ASM1735317v1_genomic.fna/cds.fna -a GCF_017353175.1_ASM1735317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:22,942] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:22,942] [INFO] Task started: HMMsearch
[2024-01-25 20:24:22,942] [INFO] Running command: hmmsearch --tblout GCF_017353175.1_ASM1735317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/reference_markers.hmm GCF_017353175.1_ASM1735317v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:23,253] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:23,255] [INFO] Found 6/6 markers.
[2024-01-25 20:24:23,327] [INFO] Query marker FASTA was written to GCF_017353175.1_ASM1735317v1_genomic.fna/markers.fasta
[2024-01-25 20:24:23,327] [INFO] Task started: Blastn
[2024-01-25 20:24:23,327] [INFO] Running command: blastn -query GCF_017353175.1_ASM1735317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/reference_markers.fasta -out GCF_017353175.1_ASM1735317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:23,949] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:23,952] [INFO] Selected 20 target genomes.
[2024-01-25 20:24:23,952] [INFO] Target genome list was writen to GCF_017353175.1_ASM1735317v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:23,977] [INFO] Task started: fastANI
[2024-01-25 20:24:23,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c752cd-663f-43eb-bf87-7ca7f0c1a037/GCF_017353175.1_ASM1735317v1_genomic.fna.gz --refList GCF_017353175.1_ASM1735317v1_genomic.fna/target_genomes.txt --output GCF_017353175.1_ASM1735317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:47,771] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:47,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:47,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:47,782] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:24:47,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:24:47,782] [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 aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	77.8987	671	2556	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	77.622	567	2556	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	77.5312	567	2556	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.8855	281	2556	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	76.7405	265	2556	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	76.7157	301	2556	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	76.6574	255	2556	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	76.6199	251	2556	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	76.5767	258	2556	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	76.3873	253	2556	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	76.3584	201	2556	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.2689	227	2556	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	76.111	212	2556	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.0988	217	2556	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	76.0522	222	2556	95	below_threshold
Siphonobacter aquaeclarae	strain=DSM 21668	GCA_900103285.1	563176	563176	type	True	75.6731	58	2556	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.462	78	2556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:47,783] [INFO] DFAST Taxonomy check result was written to GCF_017353175.1_ASM1735317v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:47,784] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:47,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:47,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/checkm_data
[2024-01-25 20:24:47,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:47,856] [INFO] Task started: CheckM
[2024-01-25 20:24:47,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017353175.1_ASM1735317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017353175.1_ASM1735317v1_genomic.fna/checkm_input GCF_017353175.1_ASM1735317v1_genomic.fna/checkm_result
[2024-01-25 20:26:12,618] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:12,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:12,639] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:12,640] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:12,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017353175.1_ASM1735317v1_genomic.fna/markers.fasta)
[2024-01-25 20:26:12,641] [INFO] Task started: Blastn
[2024-01-25 20:26:12,641] [INFO] Running command: blastn -query GCF_017353175.1_ASM1735317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg215e46c4-7c0d-4e1c-bc00-f2c2af42248e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017353175.1_ASM1735317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:13,458] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:13,461] [INFO] Selected 15 target genomes.
[2024-01-25 20:26:13,461] [INFO] Target genome list was writen to GCF_017353175.1_ASM1735317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:13,475] [INFO] Task started: fastANI
[2024-01-25 20:26:13,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c752cd-663f-43eb-bf87-7ca7f0c1a037/GCF_017353175.1_ASM1735317v1_genomic.fna.gz --refList GCF_017353175.1_ASM1735317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017353175.1_ASM1735317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:26:31,065] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:31,074] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:26:31,074] [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_017353175.1	s__Fibrella sp017353175	100.0	2554	2556	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_002108455.1	s__Fibrella sp002108455	80.7148	1233	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	98.52	98.52	0.95	0.95	2	-
GCF_000331105.1	s__Fibrella aestuarina	77.8967	672	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353185.1	s__Fibrella sp017353185	77.6064	570	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353255.1	s__Fibrella sp017353255	77.5318	567	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	76.7436	209	2556	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	76.6493	257	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184635.1	s__Rudanella paleaurantiibacter	76.6275	252	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	76.5775	259	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377625.1	s__Spirosoma sp014377625	76.4117	177	2556	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	76.2636	229	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	76.116	214	2556	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	76.0944	209	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	75.4514	69	2556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:26:31,075] [INFO] GTDB search result was written to GCF_017353175.1_ASM1735317v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:26:31,076] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:26:31,078] [INFO] DFAST_QC result json was written to GCF_017353175.1_ASM1735317v1_genomic.fna/dqc_result.json
[2024-01-25 20:26:31,079] [INFO] DFAST_QC completed!
[2024-01-25 20:26:31,079] [INFO] Total running time: 0h2m40s