[2024-01-24 13:18:26,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,095] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference
[2024-01-24 13:18:27,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,494] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,494] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc1c4d64-ebbf-4a33-abcb-7d511a9b16a7/GCF_009696565.1_ASM969656v1_genomic.fna.gz | prodigal -d GCF_009696565.1_ASM969656v1_genomic.fna/cds.fna -a GCF_009696565.1_ASM969656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:50,616] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:50,616] [INFO] Task started: HMMsearch
[2024-01-24 13:18:50,616] [INFO] Running command: hmmsearch --tblout GCF_009696565.1_ASM969656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/reference_markers.hmm GCF_009696565.1_ASM969656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:50,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:50,887] [INFO] Found 6/6 markers.
[2024-01-24 13:18:50,916] [INFO] Query marker FASTA was written to GCF_009696565.1_ASM969656v1_genomic.fna/markers.fasta
[2024-01-24 13:18:50,917] [INFO] Task started: Blastn
[2024-01-24 13:18:50,917] [INFO] Running command: blastn -query GCF_009696565.1_ASM969656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/reference_markers.fasta -out GCF_009696565.1_ASM969656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:51,542] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:51,545] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:51,546] [INFO] Target genome list was writen to GCF_009696565.1_ASM969656v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:51,560] [INFO] Task started: fastANI
[2024-01-24 13:18:51,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1c4d64-ebbf-4a33-abcb-7d511a9b16a7/GCF_009696565.1_ASM969656v1_genomic.fna.gz --refList GCF_009696565.1_ASM969656v1_genomic.fna/target_genomes.txt --output GCF_009696565.1_ASM969656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:03,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:03,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:03,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:03,687] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:03,687] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:03,687] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	100.0	1067	1069	95	conclusive
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	99.9808	1068	1069	95	conclusive
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	78.7457	89	1069	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.1225	56	1069	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.9848	53	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,689] [INFO] DFAST Taxonomy check result was written to GCF_009696565.1_ASM969656v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:03,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:03,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:03,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/checkm_data
[2024-01-24 13:19:03,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:03,730] [INFO] Task started: CheckM
[2024-01-24 13:19:03,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696565.1_ASM969656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696565.1_ASM969656v1_genomic.fna/checkm_input GCF_009696565.1_ASM969656v1_genomic.fna/checkm_result
[2024-01-24 13:20:07,501] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:07,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:07,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:07,523] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:07,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696565.1_ASM969656v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:07,524] [INFO] Task started: Blastn
[2024-01-24 13:20:07,524] [INFO] Running command: blastn -query GCF_009696565.1_ASM969656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe5c7f75-8ca0-41cf-8f99-30d34ae38be2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696565.1_ASM969656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:08,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:08,642] [INFO] Selected 14 target genomes.
[2024-01-24 13:20:08,642] [INFO] Target genome list was writen to GCF_009696565.1_ASM969656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:08,690] [INFO] Task started: fastANI
[2024-01-24 13:20:08,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1c4d64-ebbf-4a33-abcb-7d511a9b16a7/GCF_009696565.1_ASM969656v1_genomic.fna.gz --refList GCF_009696565.1_ASM969656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696565.1_ASM969656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:16,833] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:16,845] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:16,846] [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_009676955.1	s__Sodaliphilus pleomorphus	99.9983	1067	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.46	98.06	0.93	0.87	18	conclusive
GCA_900770215.1	s__Sodaliphilus sp900770215	90.6135	780	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314215.1	s__Sodaliphilus sp900314215	84.7185	609	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902768435.1	s__Sodaliphilus sp902768435	77.8053	261	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619355.1	s__Sodaliphilus sp017619355	77.7428	229	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318255.1	s__Sodaliphilus sp900318255	77.6946	217	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_016287065.1	s__Sodaliphilus sp016287065	77.6781	175	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318865.1	s__Sodaliphilus sp900318865	77.6166	228	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.72	97.82	0.92	0.87	5	-
GCA_902776835.1	s__Sodaliphilus sp902776835	77.565	237	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_902760865.1	s__Sodaliphilus sp902760865	77.5173	201	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318065.1	s__Sodaliphilus sp900318065	77.4317	201	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_902776955.1	s__Sodaliphilus sp902776955	77.2898	162	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557665.1	s__Sodaliphilus sp017557665	77.0441	161	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002476625.1	s__Sodaliphilus sp002476625	77.0178	141	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,848] [INFO] GTDB search result was written to GCF_009696565.1_ASM969656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:16,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:16,852] [INFO] DFAST_QC result json was written to GCF_009696565.1_ASM969656v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:16,852] [INFO] DFAST_QC completed!
[2024-01-24 13:20:16,852] [INFO] Total running time: 0h1m51s