[2024-01-24 12:31:17,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:17,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:17,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference
[2024-01-24 12:31:18,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:18,995] [INFO] Task started: Prodigal
[2024-01-24 12:31:18,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg220b105f-17c8-4742-b4c4-2ed3da9407cd/GCF_007558725.1_ASM755872v1_genomic.fna.gz | prodigal -d GCF_007558725.1_ASM755872v1_genomic.fna/cds.fna -a GCF_007558725.1_ASM755872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,644] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,644] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,644] [INFO] Running command: hmmsearch --tblout GCF_007558725.1_ASM755872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/reference_markers.hmm GCF_007558725.1_ASM755872v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,872] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,909] [INFO] Query marker FASTA was written to GCF_007558725.1_ASM755872v1_genomic.fna/markers.fasta
[2024-01-24 12:31:36,909] [INFO] Task started: Blastn
[2024-01-24 12:31:36,909] [INFO] Running command: blastn -query GCF_007558725.1_ASM755872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/reference_markers.fasta -out GCF_007558725.1_ASM755872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,458] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,462] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:37,462] [INFO] Target genome list was writen to GCF_007558725.1_ASM755872v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,471] [INFO] Task started: fastANI
[2024-01-24 12:31:37,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg220b105f-17c8-4742-b4c4-2ed3da9407cd/GCF_007558725.1_ASM755872v1_genomic.fna.gz --refList GCF_007558725.1_ASM755872v1_genomic.fna/target_genomes.txt --output GCF_007558725.1_ASM755872v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:53,988] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:53,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:53,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:53,994] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:53,994] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:53,994] [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
Fluviicola chungangensis	strain=MAH-3	GCA_007558725.1	2597671	2597671	type	True	100.0	1414	1414	95	conclusive
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	79.3956	547	1414	95	below_threshold
Taishania pollutisoli	strain=CZZ-1	GCA_014518315.1	2766479	2766479	type	True	76.942	76	1414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:53,995] [INFO] DFAST Taxonomy check result was written to GCF_007558725.1_ASM755872v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:53,996] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:53,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:53,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/checkm_data
[2024-01-24 12:31:53,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:54,037] [INFO] Task started: CheckM
[2024-01-24 12:31:54,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007558725.1_ASM755872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007558725.1_ASM755872v1_genomic.fna/checkm_input GCF_007558725.1_ASM755872v1_genomic.fna/checkm_result
[2024-01-24 12:32:45,419] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:45,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:45,435] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:45,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:45,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007558725.1_ASM755872v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:45,436] [INFO] Task started: Blastn
[2024-01-24 12:32:45,436] [INFO] Running command: blastn -query GCF_007558725.1_ASM755872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeac5a10-5ae7-4a59-9843-e96476616094/dqc_reference/reference_markers_gtdb.fasta -out GCF_007558725.1_ASM755872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:46,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:46,189] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:46,189] [INFO] Target genome list was writen to GCF_007558725.1_ASM755872v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:46,196] [INFO] Task started: fastANI
[2024-01-24 12:32:46,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg220b105f-17c8-4742-b4c4-2ed3da9407cd/GCF_007558725.1_ASM755872v1_genomic.fna.gz --refList GCF_007558725.1_ASM755872v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007558725.1_ASM755872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:54,970] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:54,976] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:54,976] [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
GCF_007558725.1	s__Fluviicola chungangensis	100.0	1414	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902168135.1	s__Fluviicola sp902168135	81.7652	908	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483265.1	s__Fluviicola sp002483265	81.5419	929	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432565.1	s__Fluviicola sp002432565	81.3475	764	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856375.1	s__Fluviicola amylolytica	79.5701	692	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	79.4133	545	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002243285.1	s__Fluviicola riflensis	77.4969	205	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:54,977] [INFO] GTDB search result was written to GCF_007558725.1_ASM755872v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:54,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:54,980] [INFO] DFAST_QC result json was written to GCF_007558725.1_ASM755872v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:54,980] [INFO] DFAST_QC completed!
[2024-01-24 12:32:54,981] [INFO] Total running time: 0h1m37s