[2024-01-24 13:37:28,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:28,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:28,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference
[2024-01-24 13:37:29,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,297] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg20f16135-cb38-4d4c-bb21-582d030f91d0/GCF_000238795.1_ASM23879v2_genomic.fna.gz | prodigal -d GCF_000238795.1_ASM23879v2_genomic.fna/cds.fna -a GCF_000238795.1_ASM23879v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:33,846] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:33,846] [INFO] Task started: HMMsearch
[2024-01-24 13:37:33,846] [INFO] Running command: hmmsearch --tblout GCF_000238795.1_ASM23879v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/reference_markers.hmm GCF_000238795.1_ASM23879v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:34,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:34,103] [INFO] Found 6/6 markers.
[2024-01-24 13:37:34,128] [INFO] Query marker FASTA was written to GCF_000238795.1_ASM23879v2_genomic.fna/markers.fasta
[2024-01-24 13:37:34,128] [INFO] Task started: Blastn
[2024-01-24 13:37:34,128] [INFO] Running command: blastn -query GCF_000238795.1_ASM23879v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/reference_markers.fasta -out GCF_000238795.1_ASM23879v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,803] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:34,804] [INFO] Target genome list was writen to GCF_000238795.1_ASM23879v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:34,906] [INFO] Task started: fastANI
[2024-01-24 13:37:34,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg20f16135-cb38-4d4c-bb21-582d030f91d0/GCF_000238795.1_ASM23879v2_genomic.fna.gz --refList GCF_000238795.1_ASM23879v2_genomic.fna/target_genomes.txt --output GCF_000238795.1_ASM23879v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:43,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:43,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:43,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:43,974] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:43,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:43,974] [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
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	100.0	686	688	95	conclusive
Haemophilus parahaemolyticus	strain=NCTC 8479	GCA_900450675.1	735	735	type	True	81.5032	275	688	95	below_threshold
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	81.4403	273	688	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	81.3595	282	688	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	81.186	287	688	95	below_threshold
Haemophilus parahaemolyticus	strain=HK385	GCA_000262265.1	735	735	type	True	81.1857	268	688	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	79.6399	250	688	95	below_threshold
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	79.4712	259	688	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	79.4226	264	688	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	79.1808	253	688	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	79.0236	221	688	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	78.8327	248	688	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	78.8311	244	688	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	78.633	223	688	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.5475	193	688	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.4914	191	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:43,976] [INFO] DFAST Taxonomy check result was written to GCF_000238795.1_ASM23879v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:43,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:43,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:43,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/checkm_data
[2024-01-24 13:37:43,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:44,003] [INFO] Task started: CheckM
[2024-01-24 13:37:44,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000238795.1_ASM23879v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000238795.1_ASM23879v2_genomic.fna/checkm_input GCF_000238795.1_ASM23879v2_genomic.fna/checkm_result
[2024-01-24 13:38:05,080] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:05,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:05,101] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:05,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:05,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000238795.1_ASM23879v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:05,102] [INFO] Task started: Blastn
[2024-01-24 13:38:05,102] [INFO] Running command: blastn -query GCF_000238795.1_ASM23879v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b121647-0a8e-4ec4-8ab8-29b24ceb00b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000238795.1_ASM23879v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:06,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:06,131] [INFO] Selected 16 target genomes.
[2024-01-24 13:38:06,131] [INFO] Target genome list was writen to GCF_000238795.1_ASM23879v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:06,287] [INFO] Task started: fastANI
[2024-01-24 13:38:06,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg20f16135-cb38-4d4c-bb21-582d030f91d0/GCF_000238795.1_ASM23879v2_genomic.fna.gz --refList GCF_000238795.1_ASM23879v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000238795.1_ASM23879v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:13,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:13,390] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:13,390] [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_000238795.1	s__Haemophilus_A sputorum	100.0	686	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	conclusive
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	81.3763	281	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	81.1853	285	688	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	80.7426	230	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188255.1	s__Actinobacillus ureae	79.652	249	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900636745.1	s__Actinobacillus equuli	79.5492	252	688	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	79.5081	263	688	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_000739435.1	s__Actinobacillus suis	79.4346	261	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_000175195.1	s__Actinobacillus_A minor	79.4189	241	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	79.2142	252	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	79.0866	218	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_901687125.1	s__Actinobacillus vicugnae	79.0755	282	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377255.1	s__Mannheimia granulomatis	78.8368	220	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_000521605.1	s__Mannheimia sp000521605	78.7479	235	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.6306	211	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.4659	223	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,392] [INFO] GTDB search result was written to GCF_000238795.1_ASM23879v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:13,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:13,398] [INFO] DFAST_QC result json was written to GCF_000238795.1_ASM23879v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:13,399] [INFO] DFAST_QC completed!
[2024-01-24 13:38:13,399] [INFO] Total running time: 0h0m45s