[2023-06-27 11:31:29,004] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:31:29,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:31:29,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference
[2023-06-27 11:31:30,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:31:30,492] [INFO] Task started: Prodigal
[2023-06-27 11:31:30,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c6abd0b-5180-4e85-a3eb-2ee4cdd11413/GCA_026391375.1_ASM2639137v1_genomic.fna.gz | prodigal -d GCA_026391375.1_ASM2639137v1_genomic.fna/cds.fna -a GCA_026391375.1_ASM2639137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:31:39,924] [INFO] Task succeeded: Prodigal
[2023-06-27 11:31:39,924] [INFO] Task started: HMMsearch
[2023-06-27 11:31:39,924] [INFO] Running command: hmmsearch --tblout GCA_026391375.1_ASM2639137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/reference_markers.hmm GCA_026391375.1_ASM2639137v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:31:40,188] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:31:40,190] [INFO] Found 6/6 markers.
[2023-06-27 11:31:40,219] [INFO] Query marker FASTA was written to GCA_026391375.1_ASM2639137v1_genomic.fna/markers.fasta
[2023-06-27 11:31:40,219] [INFO] Task started: Blastn
[2023-06-27 11:31:40,220] [INFO] Running command: blastn -query GCA_026391375.1_ASM2639137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/reference_markers.fasta -out GCA_026391375.1_ASM2639137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:31:40,810] [INFO] Task succeeded: Blastn
[2023-06-27 11:31:40,826] [INFO] Selected 18 target genomes.
[2023-06-27 11:31:40,827] [INFO] Target genome list was writen to GCA_026391375.1_ASM2639137v1_genomic.fna/target_genomes.txt
[2023-06-27 11:31:40,830] [INFO] Task started: fastANI
[2023-06-27 11:31:40,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c6abd0b-5180-4e85-a3eb-2ee4cdd11413/GCA_026391375.1_ASM2639137v1_genomic.fna.gz --refList GCA_026391375.1_ASM2639137v1_genomic.fna/target_genomes.txt --output GCA_026391375.1_ASM2639137v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:31:54,518] [INFO] Task succeeded: fastANI
[2023-06-27 11:31:54,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:31:54,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:31:54,530] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:31:54,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:31:54,530] [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
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.064	72	744	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.9035	63	744	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	75.8546	57	744	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.8511	54	744	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.6354	62	744	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:31:54,539] [INFO] DFAST Taxonomy check result was written to GCA_026391375.1_ASM2639137v1_genomic.fna/tc_result.tsv
[2023-06-27 11:31:54,540] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:31:54,540] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:31:54,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/checkm_data
[2023-06-27 11:31:54,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:31:54,577] [INFO] Task started: CheckM
[2023-06-27 11:31:54,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026391375.1_ASM2639137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026391375.1_ASM2639137v1_genomic.fna/checkm_input GCA_026391375.1_ASM2639137v1_genomic.fna/checkm_result
[2023-06-27 11:32:28,313] [INFO] Task succeeded: CheckM
[2023-06-27 11:32:28,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:32:28,351] [INFO] ===== Completeness check finished =====
[2023-06-27 11:32:28,352] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:32:28,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026391375.1_ASM2639137v1_genomic.fna/markers.fasta)
[2023-06-27 11:32:28,353] [INFO] Task started: Blastn
[2023-06-27 11:32:28,353] [INFO] Running command: blastn -query GCA_026391375.1_ASM2639137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02b16df0-47f0-499f-b295-25862ad94191/dqc_reference/reference_markers_gtdb.fasta -out GCA_026391375.1_ASM2639137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:32:29,175] [INFO] Task succeeded: Blastn
[2023-06-27 11:32:29,191] [INFO] Selected 7 target genomes.
[2023-06-27 11:32:29,191] [INFO] Target genome list was writen to GCA_026391375.1_ASM2639137v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:32:29,222] [INFO] Task started: fastANI
[2023-06-27 11:32:29,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c6abd0b-5180-4e85-a3eb-2ee4cdd11413/GCA_026391375.1_ASM2639137v1_genomic.fna.gz --refList GCA_026391375.1_ASM2639137v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026391375.1_ASM2639137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:32:32,844] [INFO] Task succeeded: fastANI
[2023-06-27 11:32:32,854] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:32:32,855] [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_903910765.1	s__Sediminibacterium sp903910765	96.4727	494	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009920495.1	s__Sediminibacterium sp009920495	92.5075	501	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005800655.1	s__Sediminibacterium sp005800655	90.8758	505	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953815.1	s__Sediminibacterium sp903953815	90.8517	551	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.40	99.39	0.85	0.84	4	-
GCA_003509845.1	s__Sediminibacterium sp003509845	90.5969	408	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693715.1	s__Sediminibacterium sp009693715	89.6778	479	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824725.1	s__Sediminibacterium sp903824725	81.1474	462	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:32:32,857] [INFO] GTDB search result was written to GCA_026391375.1_ASM2639137v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:32:32,858] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:32:32,861] [INFO] DFAST_QC result json was written to GCA_026391375.1_ASM2639137v1_genomic.fna/dqc_result.json
[2023-06-27 11:32:32,861] [INFO] DFAST_QC completed!
[2023-06-27 11:32:32,862] [INFO] Total running time: 0h1m4s