[2023-06-30 21:40:51,526] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:40:51,528] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:40:51,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference
[2023-06-30 21:40:52,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:40:52,859] [INFO] Task started: Prodigal
[2023-06-30 21:40:52,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c71a833-a6c1-496f-b647-b4232ec7b98c/GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:41:09,570] [INFO] Task succeeded: Prodigal
[2023-06-30 21:41:09,570] [INFO] Task started: HMMsearch
[2023-06-30 21:41:09,570] [INFO] Running command: hmmsearch --tblout GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/reference_markers.hmm GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:41:09,823] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:41:09,825] [INFO] Found 6/6 markers.
[2023-06-30 21:41:09,861] [INFO] Query marker FASTA was written to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 21:41:09,862] [INFO] Task started: Blastn
[2023-06-30 21:41:09,862] [INFO] Running command: blastn -query GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/reference_markers.fasta -out GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:41:10,487] [INFO] Task succeeded: Blastn
[2023-06-30 21:41:10,491] [INFO] Selected 23 target genomes.
[2023-06-30 21:41:10,491] [INFO] Target genome list was writen to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 21:41:10,504] [INFO] Task started: fastANI
[2023-06-30 21:41:10,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c71a833-a6c1-496f-b647-b4232ec7b98c/GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:41:23,285] [INFO] Task succeeded: fastANI
[2023-06-30 21:41:23,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:41:23,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:41:23,290] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:41:23,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:41:23,290] [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	76.8353	117	921	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.7696	115	921	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:41:23,292] [INFO] DFAST Taxonomy check result was written to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 21:41:23,293] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:41:23,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:41:23,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/checkm_data
[2023-06-30 21:41:23,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:41:23,329] [INFO] Task started: CheckM
[2023-06-30 21:41:23,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 21:42:13,345] [INFO] Task succeeded: CheckM
[2023-06-30 21:42:13,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:42:13,369] [INFO] ===== Completeness check finished =====
[2023-06-30 21:42:13,369] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:42:13,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 21:42:13,370] [INFO] Task started: Blastn
[2023-06-30 21:42:13,370] [INFO] Running command: blastn -query GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg00b5e8ea-1f77-414c-a370-cdc9936cbc1c/dqc_reference/reference_markers_gtdb.fasta -out GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:42:14,263] [INFO] Task succeeded: Blastn
[2023-06-30 21:42:14,268] [INFO] Selected 9 target genomes.
[2023-06-30 21:42:14,269] [INFO] Target genome list was writen to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:42:14,270] [INFO] Task started: fastANI
[2023-06-30 21:42:14,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c71a833-a6c1-496f-b647-b4232ec7b98c/GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:42:20,115] [INFO] Task succeeded: fastANI
[2023-06-30 21:42:20,129] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:42:20,129] [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
GCA_900316835.1	s__Sodaliphilus sp900316835	97.4668	815	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.09	97.35	0.92	0.87	12	conclusive
GCA_002396125.1	s__Sodaliphilus sp002396125	82.7085	455	921	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	80.4414	440	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_900318255.1	s__Sodaliphilus sp900318255	80.0366	448	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_902762385.1	s__Sodaliphilus sp902762385	79.8732	394	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.01	95.72	0.89	0.77	6	-
GCA_902792435.1	s__Sodaliphilus sp902792435	79.8125	375	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.75	96.43	0.87	0.84	5	-
GCA_902785925.1	s__Sodaliphilus sp902785925	79.3987	374	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.61	97.00	0.89	0.87	5	-
GCA_902777835.1	s__Sodaliphilus sp902777835	79.0514	356	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.18	97.18	0.83	0.83	2	-
GCA_017557625.1	s__Sodaliphilus sp017557625	78.64	358	921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:42:20,131] [INFO] GTDB search result was written to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 21:42:20,132] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:42:20,135] [INFO] DFAST_QC result json was written to GCA_946415035.1_SRR12081300_bin.5_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 21:42:20,135] [INFO] DFAST_QC completed!
[2023-06-30 21:42:20,135] [INFO] Total running time: 0h1m29s