[2024-01-24 13:58:40,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:40,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:40,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference
[2024-01-24 13:58:41,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:41,888] [INFO] Task started: Prodigal
[2024-01-24 13:58:41,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg8acf34fc-59d0-4ee7-aa22-87d053d15301/GCF_013377995.1_ASM1337799v1_genomic.fna.gz | prodigal -d GCF_013377995.1_ASM1337799v1_genomic.fna/cds.fna -a GCF_013377995.1_ASM1337799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:46,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:46,743] [INFO] Task started: HMMsearch
[2024-01-24 13:58:46,743] [INFO] Running command: hmmsearch --tblout GCF_013377995.1_ASM1337799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/reference_markers.hmm GCF_013377995.1_ASM1337799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:47,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:47,060] [INFO] Found 6/6 markers.
[2024-01-24 13:58:47,083] [INFO] Query marker FASTA was written to GCF_013377995.1_ASM1337799v1_genomic.fna/markers.fasta
[2024-01-24 13:58:47,083] [INFO] Task started: Blastn
[2024-01-24 13:58:47,083] [INFO] Running command: blastn -query GCF_013377995.1_ASM1337799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/reference_markers.fasta -out GCF_013377995.1_ASM1337799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,767] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:47,768] [INFO] Target genome list was writen to GCF_013377995.1_ASM1337799v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:47,774] [INFO] Task started: fastANI
[2024-01-24 13:58:47,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg8acf34fc-59d0-4ee7-aa22-87d053d15301/GCF_013377995.1_ASM1337799v1_genomic.fna.gz --refList GCF_013377995.1_ASM1337799v1_genomic.fna/target_genomes.txt --output GCF_013377995.1_ASM1337799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:56,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:56,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:56,725] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:56,726] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:56,726] [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
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	100.0	720	723	95	inconclusive
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	97.5961	619	723	95	inconclusive
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	84.369	522	723	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	83.8591	506	723	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	82.594	485	723	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	82.2863	472	723	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	80.6015	462	723	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.2497	251	723	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	78.6241	195	723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,728] [INFO] DFAST Taxonomy check result was written to GCF_013377995.1_ASM1337799v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:56,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:56,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:56,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/checkm_data
[2024-01-24 13:58:56,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:56,754] [INFO] Task started: CheckM
[2024-01-24 13:58:56,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377995.1_ASM1337799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377995.1_ASM1337799v1_genomic.fna/checkm_input GCF_013377995.1_ASM1337799v1_genomic.fna/checkm_result
[2024-01-24 13:59:18,997] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:18,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,018] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:19,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:19,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377995.1_ASM1337799v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:19,019] [INFO] Task started: Blastn
[2024-01-24 13:59:19,020] [INFO] Running command: blastn -query GCF_013377995.1_ASM1337799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg028524d8-d9c3-4737-913c-154cd99140ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377995.1_ASM1337799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:20,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:20,096] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:20,097] [INFO] Target genome list was writen to GCF_013377995.1_ASM1337799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:20,104] [INFO] Task started: fastANI
[2024-01-24 13:59:20,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg8acf34fc-59d0-4ee7-aa22-87d053d15301/GCF_013377995.1_ASM1337799v1_genomic.fna.gz --refList GCF_013377995.1_ASM1337799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377995.1_ASM1337799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:25,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:25,488] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:25,488] [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_013377995.1	s__Mannheimia pernigra	100.0	720	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	conclusive
GCF_000521605.1	s__Mannheimia sp000521605	84.8602	527	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014541205.1	s__Mannheimia bovis	84.4042	522	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	83.9601	506	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_004342115.1	s__Mannheimia haemolytica	82.3111	471	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_013377255.1	s__Mannheimia granulomatis	81.0759	468	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_011455695.1	s__Mannheimia granulomatis_A	80.9117	460	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636745.1	s__Actinobacillus equuli	79.3334	248	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.8441	240	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	78.6241	195	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCA_018373095.1	s__Haemophilus_A parahaemolyticus_A	77.9993	190	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,490] [INFO] GTDB search result was written to GCF_013377995.1_ASM1337799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:25,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:25,495] [INFO] DFAST_QC result json was written to GCF_013377995.1_ASM1337799v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:25,496] [INFO] DFAST_QC completed!
[2024-01-24 13:59:25,496] [INFO] Total running time: 0h0m45s