[2024-01-24 13:01:53,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference
[2024-01-24 13:01:54,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,541] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg84936e17-6787-4341-8b65-c0fa572f6352/GCF_017948305.1_ASM1794830v1_genomic.fna.gz | prodigal -d GCF_017948305.1_ASM1794830v1_genomic.fna/cds.fna -a GCF_017948305.1_ASM1794830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:03,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:03,102] [INFO] Task started: HMMsearch
[2024-01-24 13:02:03,102] [INFO] Running command: hmmsearch --tblout GCF_017948305.1_ASM1794830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/reference_markers.hmm GCF_017948305.1_ASM1794830v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:03,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:03,430] [INFO] Found 6/6 markers.
[2024-01-24 13:02:03,485] [INFO] Query marker FASTA was written to GCF_017948305.1_ASM1794830v1_genomic.fna/markers.fasta
[2024-01-24 13:02:03,485] [INFO] Task started: Blastn
[2024-01-24 13:02:03,486] [INFO] Running command: blastn -query GCF_017948305.1_ASM1794830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/reference_markers.fasta -out GCF_017948305.1_ASM1794830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:04,236] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:04,241] [INFO] Selected 8 target genomes.
[2024-01-24 13:02:04,242] [INFO] Target genome list was writen to GCF_017948305.1_ASM1794830v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:04,245] [INFO] Task started: fastANI
[2024-01-24 13:02:04,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg84936e17-6787-4341-8b65-c0fa572f6352/GCF_017948305.1_ASM1794830v1_genomic.fna.gz --refList GCF_017948305.1_ASM1794830v1_genomic.fna/target_genomes.txt --output GCF_017948305.1_ASM1794830v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:09,761] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:09,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:09,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:09,769] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:09,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:09,769] [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
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	100.0	944	945	95	conclusive
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	86.6205	747	945	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	82.2835	595	945	95	below_threshold
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	79.8441	466	945	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	79.3514	434	945	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	79.309	429	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,772] [INFO] DFAST Taxonomy check result was written to GCF_017948305.1_ASM1794830v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:09,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:09,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:09,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/checkm_data
[2024-01-24 13:02:09,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:09,808] [INFO] Task started: CheckM
[2024-01-24 13:02:09,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017948305.1_ASM1794830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017948305.1_ASM1794830v1_genomic.fna/checkm_input GCF_017948305.1_ASM1794830v1_genomic.fna/checkm_result
[2024-01-24 13:02:40,229] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:40,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:40,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:40,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017948305.1_ASM1794830v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:40,254] [INFO] Task started: Blastn
[2024-01-24 13:02:40,254] [INFO] Running command: blastn -query GCF_017948305.1_ASM1794830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7dc822-adbd-4488-ab83-f8ee03c530ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_017948305.1_ASM1794830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:41,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:41,146] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:41,146] [INFO] Target genome list was writen to GCF_017948305.1_ASM1794830v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:41,158] [INFO] Task started: fastANI
[2024-01-24 13:02:41,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg84936e17-6787-4341-8b65-c0fa572f6352/GCF_017948305.1_ASM1794830v1_genomic.fna.gz --refList GCF_017948305.1_ASM1794830v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017948305.1_ASM1794830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:47,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:47,202] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:47,202] [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_017948305.1	s__Faecalibacter bovis	100.0	944	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	98.04	98.04	0.91	0.91	2	conclusive
GCA_003687725.1	s__Faecalibacter macacae	86.6251	746	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234135.1	s__Faecalibacter rhinopitheci	82.2531	595	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	98.99	98.99	0.97	0.97	2	-
GCA_900770875.1	s__Faecalibacter sp900770875	81.5093	483	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785645.1	s__Empedobacter tilapiae	79.8207	468	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115015.1	s__Algoriella xinjiangensis	79.6888	470	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCA_002430925.1	s__Chishuiella sp002430925	79.6474	339	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013116755.1	s__Empedobacter stercoris	79.5062	420	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_900142565.1	s__Chishuiella changwenlii	79.3412	436	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:47,204] [INFO] GTDB search result was written to GCF_017948305.1_ASM1794830v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:47,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:47,207] [INFO] DFAST_QC result json was written to GCF_017948305.1_ASM1794830v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:47,207] [INFO] DFAST_QC completed!
[2024-01-24 13:02:47,207] [INFO] Total running time: 0h0m54s