[2023-06-13 17:12:08,442] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:12:08,444] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:12:08,444] [INFO] DQC Reference Directory: /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference
[2023-06-13 17:12:09,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:12:09,598] [INFO] Task started: Prodigal
[2023-06-13 17:12:09,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg74af364c-9265-48c5-8f19-230e6f93a2f0/GCA_022778865.1_ASM2277886v1_genomic.fna.gz | prodigal -d GCA_022778865.1_ASM2277886v1_genomic.fna/cds.fna -a GCA_022778865.1_ASM2277886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:25,578] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:25,579] [INFO] Task started: HMMsearch
[2023-06-13 17:12:25,579] [INFO] Running command: hmmsearch --tblout GCA_022778865.1_ASM2277886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/reference_markers.hmm GCA_022778865.1_ASM2277886v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:25,804] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:25,805] [INFO] Found 6/6 markers.
[2023-06-13 17:12:25,829] [INFO] Query marker FASTA was written to GCA_022778865.1_ASM2277886v1_genomic.fna/markers.fasta
[2023-06-13 17:12:25,829] [INFO] Task started: Blastn
[2023-06-13 17:12:25,829] [INFO] Running command: blastn -query GCA_022778865.1_ASM2277886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/reference_markers.fasta -out GCA_022778865.1_ASM2277886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:26,405] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:26,408] [INFO] Selected 26 target genomes.
[2023-06-13 17:12:26,409] [INFO] Target genome list was writen to GCA_022778865.1_ASM2277886v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:26,410] [INFO] Task started: fastANI
[2023-06-13 17:12:26,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg74af364c-9265-48c5-8f19-230e6f93a2f0/GCA_022778865.1_ASM2277886v1_genomic.fna.gz --refList GCA_022778865.1_ASM2277886v1_genomic.fna/target_genomes.txt --output GCA_022778865.1_ASM2277886v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:39,388] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:39,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:39,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:39,393] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:39,393] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:39,393] [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	77.227	129	718	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	77.1701	128	718	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:39,395] [INFO] DFAST Taxonomy check result was written to GCA_022778865.1_ASM2277886v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:39,396] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:39,396] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:39,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/checkm_data
[2023-06-13 17:12:39,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:39,424] [INFO] Task started: CheckM
[2023-06-13 17:12:39,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022778865.1_ASM2277886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022778865.1_ASM2277886v1_genomic.fna/checkm_input GCA_022778865.1_ASM2277886v1_genomic.fna/checkm_result
[2023-06-13 17:13:26,503] [INFO] Task succeeded: CheckM
[2023-06-13 17:13:26,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:13:26,522] [INFO] ===== Completeness check finished =====
[2023-06-13 17:13:26,522] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:13:26,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022778865.1_ASM2277886v1_genomic.fna/markers.fasta)
[2023-06-13 17:13:26,523] [INFO] Task started: Blastn
[2023-06-13 17:13:26,523] [INFO] Running command: blastn -query GCA_022778865.1_ASM2277886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ee13e3-d696-4ff3-bb85-f52e20b48500/dqc_reference/reference_markers_gtdb.fasta -out GCA_022778865.1_ASM2277886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:13:27,336] [INFO] Task succeeded: Blastn
[2023-06-13 17:13:27,340] [INFO] Selected 21 target genomes.
[2023-06-13 17:13:27,340] [INFO] Target genome list was writen to GCA_022778865.1_ASM2277886v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:13:27,346] [INFO] Task started: fastANI
[2023-06-13 17:13:27,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg74af364c-9265-48c5-8f19-230e6f93a2f0/GCA_022778865.1_ASM2277886v1_genomic.fna.gz --refList GCA_022778865.1_ASM2277886v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022778865.1_ASM2277886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:37,568] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:37,584] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:13:37,584] [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_004557565.1	s__Sodaliphilus sp004557565	98.0985	645	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.84	96.54	0.87	0.65	13	conclusive
GCA_002476625.1	s__Sodaliphilus sp002476625	80.2813	336	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004559845.1	s__Sodaliphilus sp004559845	79.9434	236	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.70	97.51	0.74	0.68	3	-
GCA_004557385.1	s__SFTJ01 sp004557385	78.0764	89	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	97.97	96.18	0.87	0.82	3	-
GCA_900770215.1	s__Sodaliphilus sp900770215	77.2173	126	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287065.1	s__Sodaliphilus sp016287065	77.1897	91	718	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	77.1428	121	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065815.1	s__Sodaliphilus sp018065815	77.052	92	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762385.1	s__Sodaliphilus sp902762385	77.0274	73	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.01	95.72	0.89	0.77	6	-
GCA_017483645.1	s__Sodaliphilus sp017483645	76.9557	63	718	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	76.9533	139	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017619355.1	s__Sodaliphilus sp017619355	76.9248	124	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769345.1	s__SFTJ01 sp900769345	76.8846	69	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233845.1	s__Sodaliphilus sp905233845	76.8001	62	718	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	76.4465	106	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_902782465.1	s__Sodaliphilus sp902782465	76.4436	62	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.05	98.05	0.87	0.87	2	-
GCA_017477555.1	s__Sodaliphilus sp017477555	76.4306	64	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.74	97.72	0.83	0.78	3	-
GCA_018065165.1	s__Sodaliphilus sp018065165	76.3494	67	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318535.1	s__Sodaliphilus sp900318535	75.9689	58	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.25	96.02	0.89	0.86	17	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:37,586] [INFO] GTDB search result was written to GCA_022778865.1_ASM2277886v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:37,587] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:37,590] [INFO] DFAST_QC result json was written to GCA_022778865.1_ASM2277886v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:37,591] [INFO] DFAST_QC completed!
[2023-06-13 17:13:37,591] [INFO] Total running time: 0h1m29s