[2023-06-05 23:03:07,833] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:03:07,857] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:03:07,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference
[2023-06-05 23:03:09,612] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:03:09,613] [INFO] Task started: Prodigal
[2023-06-05 23:03:09,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgb19b591a-b5c9-4cb9-80f5-50611d9a88b3/GCA_004560675.1_ASM456067v1_genomic.fna.gz | prodigal -d GCA_004560675.1_ASM456067v1_genomic.fna/cds.fna -a GCA_004560675.1_ASM456067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:03:25,232] [INFO] Task succeeded: Prodigal
[2023-06-05 23:03:25,233] [INFO] Task started: HMMsearch
[2023-06-05 23:03:25,233] [INFO] Running command: hmmsearch --tblout GCA_004560675.1_ASM456067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/reference_markers.hmm GCA_004560675.1_ASM456067v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:03:25,513] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:03:25,514] [INFO] Found 6/6 markers.
[2023-06-05 23:03:25,537] [INFO] Query marker FASTA was written to GCA_004560675.1_ASM456067v1_genomic.fna/markers.fasta
[2023-06-05 23:03:25,537] [INFO] Task started: Blastn
[2023-06-05 23:03:25,537] [INFO] Running command: blastn -query GCA_004560675.1_ASM456067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/reference_markers.fasta -out GCA_004560675.1_ASM456067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:03:26,287] [INFO] Task succeeded: Blastn
[2023-06-05 23:03:26,296] [INFO] Selected 32 target genomes.
[2023-06-05 23:03:26,299] [INFO] Target genome list was writen to GCA_004560675.1_ASM456067v1_genomic.fna/target_genomes.txt
[2023-06-05 23:03:26,329] [INFO] Task started: fastANI
[2023-06-05 23:03:26,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19b591a-b5c9-4cb9-80f5-50611d9a88b3/GCA_004560675.1_ASM456067v1_genomic.fna.gz --refList GCA_004560675.1_ASM456067v1_genomic.fna/target_genomes.txt --output GCA_004560675.1_ASM456067v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:03:46,607] [INFO] Task succeeded: fastANI
[2023-06-05 23:03:46,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:03:46,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:03:46,615] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:03:46,615] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 23:03:46,615] [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	76.0049	60	562	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	76.002	60	562	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 23:03:46,617] [INFO] DFAST Taxonomy check result was written to GCA_004560675.1_ASM456067v1_genomic.fna/tc_result.tsv
[2023-06-05 23:03:46,618] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:03:46,618] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:03:46,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/checkm_data
[2023-06-05 23:03:46,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:03:46,655] [INFO] Task started: CheckM
[2023-06-05 23:03:46,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004560675.1_ASM456067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004560675.1_ASM456067v1_genomic.fna/checkm_input GCA_004560675.1_ASM456067v1_genomic.fna/checkm_result
[2023-06-05 23:04:31,745] [INFO] Task succeeded: CheckM
[2023-06-05 23:04:31,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:04:31,764] [INFO] ===== Completeness check finished =====
[2023-06-05 23:04:31,764] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:04:31,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004560675.1_ASM456067v1_genomic.fna/markers.fasta)
[2023-06-05 23:04:31,764] [INFO] Task started: Blastn
[2023-06-05 23:04:31,765] [INFO] Running command: blastn -query GCA_004560675.1_ASM456067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6376628-61a0-41c4-aa92-58e4e479b0d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_004560675.1_ASM456067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:04:32,714] [INFO] Task succeeded: Blastn
[2023-06-05 23:04:32,718] [INFO] Selected 19 target genomes.
[2023-06-05 23:04:32,718] [INFO] Target genome list was writen to GCA_004560675.1_ASM456067v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:04:32,727] [INFO] Task started: fastANI
[2023-06-05 23:04:32,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19b591a-b5c9-4cb9-80f5-50611d9a88b3/GCA_004560675.1_ASM456067v1_genomic.fna.gz --refList GCA_004560675.1_ASM456067v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004560675.1_ASM456067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:04:40,850] [INFO] Task succeeded: fastANI
[2023-06-05 23:04:40,857] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:04:40,858] [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_004557385.1	s__SFTJ01 sp004557385	99.7582	519	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	97.97	96.18	0.87	0.82	3	conclusive
GCA_900769345.1	s__SFTJ01 sp900769345	78.9316	171	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563195.1	s__SFTJ01 sp004563195	78.6452	223	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210415.1	s__SFTJ01 sp905210415	78.5067	216	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292745.1	s__SFRY01 sp004562065	77.3161	64	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFRY01	95.0	98.75	98.75	0.84	0.84	2	-
GCA_004557565.1	s__Sodaliphilus sp004557565	77.0315	74	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.84	96.54	0.87	0.65	13	-
GCA_900314215.1	s__Sodaliphilus sp900314215	76.7466	64	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900770215.1	s__Sodaliphilus sp900770215	75.9942	68	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:04:40,860] [INFO] GTDB search result was written to GCA_004560675.1_ASM456067v1_genomic.fna/result_gtdb.tsv
[2023-06-05 23:04:40,860] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:04:40,863] [INFO] DFAST_QC result json was written to GCA_004560675.1_ASM456067v1_genomic.fna/dqc_result.json
[2023-06-05 23:04:40,863] [INFO] DFAST_QC completed!
[2023-06-05 23:04:40,864] [INFO] Total running time: 0h1m33s