[2024-01-24 11:44:05,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference
[2024-01-24 11:44:08,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,837] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,837] [INFO] Running command: gunzip -c /var/lib/cwl/stga5a1c863-75c4-415e-aadf-a6ce36e2c1ca/GCF_003259745.1_ASM325974v1_genomic.fna.gz | prodigal -d GCF_003259745.1_ASM325974v1_genomic.fna/cds.fna -a GCF_003259745.1_ASM325974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:43,104] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:43,104] [INFO] Task started: HMMsearch
[2024-01-24 11:44:43,105] [INFO] Running command: hmmsearch --tblout GCF_003259745.1_ASM325974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/reference_markers.hmm GCF_003259745.1_ASM325974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:43,423] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:43,424] [INFO] Found 6/6 markers.
[2024-01-24 11:44:43,479] [INFO] Query marker FASTA was written to GCF_003259745.1_ASM325974v1_genomic.fna/markers.fasta
[2024-01-24 11:44:43,479] [INFO] Task started: Blastn
[2024-01-24 11:44:43,479] [INFO] Running command: blastn -query GCF_003259745.1_ASM325974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/reference_markers.fasta -out GCF_003259745.1_ASM325974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:44,056] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:44,060] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:44,061] [INFO] Target genome list was writen to GCF_003259745.1_ASM325974v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:44,066] [INFO] Task started: fastANI
[2024-01-24 11:44:44,066] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a1c863-75c4-415e-aadf-a6ce36e2c1ca/GCF_003259745.1_ASM325974v1_genomic.fna.gz --refList GCF_003259745.1_ASM325974v1_genomic.fna/target_genomes.txt --output GCF_003259745.1_ASM325974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:58,686] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:58,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:58,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:58,699] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:58,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:58,700] [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
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	100.0	2319	2319	95	conclusive
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	80.1253	1278	2319	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	80.0444	1281	2319	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	80.0121	1274	2319	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	79.8587	1234	2319	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	79.7278	1236	2319	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	76.381	275	2319	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	76.1108	208	2319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:58,701] [INFO] DFAST Taxonomy check result was written to GCF_003259745.1_ASM325974v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:58,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:58,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:58,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/checkm_data
[2024-01-24 11:44:58,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:58,766] [INFO] Task started: CheckM
[2024-01-24 11:44:58,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259745.1_ASM325974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259745.1_ASM325974v1_genomic.fna/checkm_input GCF_003259745.1_ASM325974v1_genomic.fna/checkm_result
[2024-01-24 11:46:30,433] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:30,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:30,454] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:30,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:30,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259745.1_ASM325974v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:30,455] [INFO] Task started: Blastn
[2024-01-24 11:46:30,456] [INFO] Running command: blastn -query GCF_003259745.1_ASM325974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb11be73b-a8fe-459f-b11a-b239b0baf7f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259745.1_ASM325974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:31,258] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:31,262] [INFO] Selected 11 target genomes.
[2024-01-24 11:46:31,263] [INFO] Target genome list was writen to GCF_003259745.1_ASM325974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:31,272] [INFO] Task started: fastANI
[2024-01-24 11:46:31,272] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a1c863-75c4-415e-aadf-a6ce36e2c1ca/GCF_003259745.1_ASM325974v1_genomic.fna.gz --refList GCF_003259745.1_ASM325974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259745.1_ASM325974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:46,978] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:46,994] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:46,995] [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_003259745.1	s__Larkinella arboricola	100.0	2319	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004366505.1	s__Larkinella sp004366505	84.2043	1674	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003334855.1	s__Larkinella punicea	80.1195	1280	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	80.0812	1293	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	80.0412	1281	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	80.0155	1274	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009668025.1	s__Larkinella terrae	79.877	1230	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858635.1	s__Larkinella rosea	79.7127	1240	2319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	76.3743	276	2319	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	76.1108	208	2319	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 11:46:47,000] [INFO] GTDB search result was written to GCF_003259745.1_ASM325974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:47,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:47,006] [INFO] DFAST_QC result json was written to GCF_003259745.1_ASM325974v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:47,006] [INFO] DFAST_QC completed!
[2024-01-24 11:46:47,006] [INFO] Total running time: 0h2m42s