[2023-06-29 23:45:44,980] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:45:44,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:45:44,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference
[2023-06-29 23:45:46,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:45:46,175] [INFO] Task started: Prodigal
[2023-06-29 23:45:46,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d23628d-8a49-4cbf-87e0-09e4eb2ef8ce/GCA_900769345.1_SRS476193_84_genomic.fna.gz | prodigal -d GCA_900769345.1_SRS476193_84_genomic.fna/cds.fna -a GCA_900769345.1_SRS476193_84_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:46:03,599] [INFO] Task succeeded: Prodigal
[2023-06-29 23:46:03,600] [INFO] Task started: HMMsearch
[2023-06-29 23:46:03,600] [INFO] Running command: hmmsearch --tblout GCA_900769345.1_SRS476193_84_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/reference_markers.hmm GCA_900769345.1_SRS476193_84_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:46:03,843] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:46:03,845] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d23628d-8a49-4cbf-87e0-09e4eb2ef8ce/GCA_900769345.1_SRS476193_84_genomic.fna.gz]
[2023-06-29 23:46:03,891] [INFO] Query marker FASTA was written to GCA_900769345.1_SRS476193_84_genomic.fna/markers.fasta
[2023-06-29 23:46:03,892] [INFO] Task started: Blastn
[2023-06-29 23:46:03,892] [INFO] Running command: blastn -query GCA_900769345.1_SRS476193_84_genomic.fna/markers.fasta -db /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/reference_markers.fasta -out GCA_900769345.1_SRS476193_84_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:46:04,494] [INFO] Task succeeded: Blastn
[2023-06-29 23:46:04,499] [INFO] Selected 25 target genomes.
[2023-06-29 23:46:04,500] [INFO] Target genome list was writen to GCA_900769345.1_SRS476193_84_genomic.fna/target_genomes.txt
[2023-06-29 23:46:04,503] [INFO] Task started: fastANI
[2023-06-29 23:46:04,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d23628d-8a49-4cbf-87e0-09e4eb2ef8ce/GCA_900769345.1_SRS476193_84_genomic.fna.gz --refList GCA_900769345.1_SRS476193_84_genomic.fna/target_genomes.txt --output GCA_900769345.1_SRS476193_84_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:46:16,782] [INFO] Task succeeded: fastANI
[2023-06-29 23:46:16,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:46:16,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:46:16,788] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:46:16,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:46:16,789] [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	76.0219	56	874	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	75.9214	55	874	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:46:16,791] [INFO] DFAST Taxonomy check result was written to GCA_900769345.1_SRS476193_84_genomic.fna/tc_result.tsv
[2023-06-29 23:46:16,792] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:46:16,792] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:46:16,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/checkm_data
[2023-06-29 23:46:16,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:46:16,829] [INFO] Task started: CheckM
[2023-06-29 23:46:16,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900769345.1_SRS476193_84_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900769345.1_SRS476193_84_genomic.fna/checkm_input GCA_900769345.1_SRS476193_84_genomic.fna/checkm_result
[2023-06-29 23:47:06,623] [INFO] Task succeeded: CheckM
[2023-06-29 23:47:06,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:47:06,658] [INFO] ===== Completeness check finished =====
[2023-06-29 23:47:06,659] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:47:06,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900769345.1_SRS476193_84_genomic.fna/markers.fasta)
[2023-06-29 23:47:06,660] [INFO] Task started: Blastn
[2023-06-29 23:47:06,660] [INFO] Running command: blastn -query GCA_900769345.1_SRS476193_84_genomic.fna/markers.fasta -db /var/lib/cwl/stg73263b15-0bae-41e6-9135-045b63d3220d/dqc_reference/reference_markers_gtdb.fasta -out GCA_900769345.1_SRS476193_84_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:47:07,502] [INFO] Task succeeded: Blastn
[2023-06-29 23:47:07,506] [INFO] Selected 13 target genomes.
[2023-06-29 23:47:07,507] [INFO] Target genome list was writen to GCA_900769345.1_SRS476193_84_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:47:07,509] [INFO] Task started: fastANI
[2023-06-29 23:47:07,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d23628d-8a49-4cbf-87e0-09e4eb2ef8ce/GCA_900769345.1_SRS476193_84_genomic.fna.gz --refList GCA_900769345.1_SRS476193_84_genomic.fna/target_genomes_gtdb.txt --output GCA_900769345.1_SRS476193_84_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:47:13,812] [INFO] Task succeeded: fastANI
[2023-06-29 23:47:13,825] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:47:13,825] [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
GCA_900769345.1	s__SFTJ01 sp900769345	100.0	866	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004563195.1	s__SFTJ01 sp004563195	88.1183	644	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557385.1	s__SFTJ01 sp004557385	80.509	261	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	97.97	96.18	0.87	0.82	3	-
GCA_905210415.1	s__SFTJ01 sp905210415	78.5589	180	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501735.1	s__RGIG4576 sp904501735	76.5894	56	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__RGIG4576	95.0	99.07	98.15	0.95	0.90	3	-
GCA_004557565.1	s__Sodaliphilus sp004557565	76.5866	84	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.84	96.54	0.87	0.65	13	-
GCA_900770215.1	s__Sodaliphilus sp900770215	76.0954	50	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768435.1	s__Sodaliphilus sp902768435	75.6284	51	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:47:13,828] [INFO] GTDB search result was written to GCA_900769345.1_SRS476193_84_genomic.fna/result_gtdb.tsv
[2023-06-29 23:47:13,828] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:47:13,832] [INFO] DFAST_QC result json was written to GCA_900769345.1_SRS476193_84_genomic.fna/dqc_result.json
[2023-06-29 23:47:13,832] [INFO] DFAST_QC completed!
[2023-06-29 23:47:13,832] [INFO] Total running time: 0h1m29s