[2024-01-25 18:52:35,603] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:35,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:35,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference
[2024-01-25 18:52:36,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:36,696] [INFO] Task started: Prodigal
[2024-01-25 18:52:36,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d87a173-b157-49cc-9935-1d18d04b49a7/GCF_009676955.1_ASM967695v1_genomic.fna.gz | prodigal -d GCF_009676955.1_ASM967695v1_genomic.fna/cds.fna -a GCF_009676955.1_ASM967695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:55,995] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:55,995] [INFO] Task started: HMMsearch
[2024-01-25 18:52:55,995] [INFO] Running command: hmmsearch --tblout GCF_009676955.1_ASM967695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/reference_markers.hmm GCF_009676955.1_ASM967695v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:56,208] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:56,209] [INFO] Found 6/6 markers.
[2024-01-25 18:52:56,236] [INFO] Query marker FASTA was written to GCF_009676955.1_ASM967695v1_genomic.fna/markers.fasta
[2024-01-25 18:52:56,236] [INFO] Task started: Blastn
[2024-01-25 18:52:56,236] [INFO] Running command: blastn -query GCF_009676955.1_ASM967695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/reference_markers.fasta -out GCF_009676955.1_ASM967695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:56,810] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:56,813] [INFO] Selected 17 target genomes.
[2024-01-25 18:52:56,813] [INFO] Target genome list was writen to GCF_009676955.1_ASM967695v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:56,830] [INFO] Task started: fastANI
[2024-01-25 18:52:56,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d87a173-b157-49cc-9935-1d18d04b49a7/GCF_009676955.1_ASM967695v1_genomic.fna.gz --refList GCF_009676955.1_ASM967695v1_genomic.fna/target_genomes.txt --output GCF_009676955.1_ASM967695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:08,104] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:08,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:08,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:08,110] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:08,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:08,110] [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_009676955.1	2606626	2606626	type	True	100.0	1113	1113	95	conclusive
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	99.9555	1067	1113	95	conclusive
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	79.0871	95	1113	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	78.1836	62	1113	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8709	55	1113	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.69	53	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:08,112] [INFO] DFAST Taxonomy check result was written to GCF_009676955.1_ASM967695v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:08,112] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:08,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:08,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/checkm_data
[2024-01-25 18:53:08,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:08,149] [INFO] Task started: CheckM
[2024-01-25 18:53:08,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009676955.1_ASM967695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009676955.1_ASM967695v1_genomic.fna/checkm_input GCF_009676955.1_ASM967695v1_genomic.fna/checkm_result
[2024-01-25 18:54:01,510] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:01,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:01,532] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:01,532] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:01,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009676955.1_ASM967695v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:01,533] [INFO] Task started: Blastn
[2024-01-25 18:54:01,534] [INFO] Running command: blastn -query GCF_009676955.1_ASM967695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4553c3f7-e5b8-4ce6-bd58-3488f3094acd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009676955.1_ASM967695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:02,496] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:02,499] [INFO] Selected 14 target genomes.
[2024-01-25 18:54:02,499] [INFO] Target genome list was writen to GCF_009676955.1_ASM967695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:02,517] [INFO] Task started: fastANI
[2024-01-25 18:54:02,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d87a173-b157-49cc-9935-1d18d04b49a7/GCF_009676955.1_ASM967695v1_genomic.fna.gz --refList GCF_009676955.1_ASM967695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009676955.1_ASM967695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:11,119] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:11,129] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:11,129] [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	100.0	1113	1113	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	90.5135	805	1113	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	84.6317	618	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900318255.1	s__Sodaliphilus sp900318255	77.8321	226	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_902768435.1	s__Sodaliphilus sp902768435	77.8203	273	1113	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	77.7703	233	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.72	97.82	0.92	0.87	5	-
GCA_900318065.1	s__Sodaliphilus sp900318065	77.5967	206	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_017619355.1	s__Sodaliphilus sp017619355	77.5881	247	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776835.1	s__Sodaliphilus sp902776835	77.4973	245	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_016287065.1	s__Sodaliphilus sp016287065	77.406	190	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760865.1	s__Sodaliphilus sp902760865	77.3799	207	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776955.1	s__Sodaliphilus sp902776955	77.1908	175	1113	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	77.0586	160	1113	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	76.9815	142	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:11,130] [INFO] GTDB search result was written to GCF_009676955.1_ASM967695v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:11,131] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:11,133] [INFO] DFAST_QC result json was written to GCF_009676955.1_ASM967695v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:11,133] [INFO] DFAST_QC completed!
[2024-01-25 18:54:11,134] [INFO] Total running time: 0h1m36s