[2024-01-24 10:48:09,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg523d6da6-62cc-428a-80fa-a8b47043f4f5/GCF_017353255.1_ASM1735325v1_genomic.fna.gz | prodigal -d GCF_017353255.1_ASM1735325v1_genomic.fna/cds.fna -a GCF_017353255.1_ASM1735325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:02,352] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:02,353] [INFO] Task started: HMMsearch
[2024-01-24 10:49:02,353] [INFO] Running command: hmmsearch --tblout GCF_017353255.1_ASM1735325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/reference_markers.hmm GCF_017353255.1_ASM1735325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:02,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:02,919] [INFO] Found 6/6 markers.
[2024-01-24 10:49:03,051] [INFO] Query marker FASTA was written to GCF_017353255.1_ASM1735325v1_genomic.fna/markers.fasta
[2024-01-24 10:49:03,051] [INFO] Task started: Blastn
[2024-01-24 10:49:03,051] [INFO] Running command: blastn -query GCF_017353255.1_ASM1735325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/reference_markers.fasta -out GCF_017353255.1_ASM1735325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:03,969] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:03,973] [INFO] Selected 21 target genomes.
[2024-01-24 10:49:03,973] [INFO] Target genome list was writen to GCF_017353255.1_ASM1735325v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:03,981] [INFO] Task started: fastANI
[2024-01-24 10:49:03,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg523d6da6-62cc-428a-80fa-a8b47043f4f5/GCF_017353255.1_ASM1735325v1_genomic.fna.gz --refList GCF_017353255.1_ASM1735325v1_genomic.fna/target_genomes.txt --output GCF_017353255.1_ASM1735325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:32,699] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:32,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:32,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:32,729] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:32,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:32,730] [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 aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	100.0	2228	2232	95	conclusive
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	83.2493	1453	2232	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	78.1883	728	2232	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.8764	360	2232	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	76.4304	329	2232	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.4062	296	2232	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	76.2958	257	2232	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	76.2483	239	2232	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.1698	237	2232	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	76.1697	285	2232	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	76.1487	239	2232	95	below_threshold
Larkinella soli	strain=MIMbqt9	GCA_003703975.1	1770527	1770527	type	True	75.9926	201	2232	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	75.9508	175	2232	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	75.903	150	2232	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	75.765	188	2232	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.4277	107	2232	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	75.4096	90	2232	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	75.0722	50	2232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:32,732] [INFO] DFAST Taxonomy check result was written to GCF_017353255.1_ASM1735325v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:32,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:32,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:32,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/checkm_data
[2024-01-24 10:49:32,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:32,810] [INFO] Task started: CheckM
[2024-01-24 10:49:32,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017353255.1_ASM1735325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017353255.1_ASM1735325v1_genomic.fna/checkm_input GCF_017353255.1_ASM1735325v1_genomic.fna/checkm_result
[2024-01-24 10:51:10,155] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:10,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:10,182] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:10,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:10,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017353255.1_ASM1735325v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:10,183] [INFO] Task started: Blastn
[2024-01-24 10:51:10,183] [INFO] Running command: blastn -query GCF_017353255.1_ASM1735325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bed7bd7-6e7a-4a63-aec4-db6f1a0920af/dqc_reference/reference_markers_gtdb.fasta -out GCF_017353255.1_ASM1735325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:11,020] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:11,024] [INFO] Selected 15 target genomes.
[2024-01-24 10:51:11,024] [INFO] Target genome list was writen to GCF_017353255.1_ASM1735325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:11,035] [INFO] Task started: fastANI
[2024-01-24 10:51:11,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg523d6da6-62cc-428a-80fa-a8b47043f4f5/GCF_017353255.1_ASM1735325v1_genomic.fna.gz --refList GCF_017353255.1_ASM1735325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017353255.1_ASM1735325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:28,708] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:28,720] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:28,721] [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_017353255.1	s__Fibrella sp017353255	100.0	2228	2232	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_017353185.1	s__Fibrella sp017353185	83.2404	1454	2232	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	78.198	725	2232	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	77.4816	580	2232	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	77.4321	525	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001988955.1	s__Spirosoma montaniterrae	76.8776	360	2232	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	76.8142	338	2232	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	76.5869	288	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383955.1	s__Rudanella lutea	76.5615	327	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374065.1	s__Spirosoma luteum	76.2416	240	2232	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	76.1632	238	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	76.1588	287	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	76.1422	240	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271695.1	s__Rufibacter sp008271695	75.0722	50	2232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:28,722] [INFO] GTDB search result was written to GCF_017353255.1_ASM1735325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:28,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:28,727] [INFO] DFAST_QC result json was written to GCF_017353255.1_ASM1735325v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:28,727] [INFO] DFAST_QC completed!
[2024-01-24 10:51:28,727] [INFO] Total running time: 0h3m19s