[2024-01-24 15:02:18,202] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference
[2024-01-24 15:02:22,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:22,120] [INFO] Task started: Prodigal
[2024-01-24 15:02:22,121] [INFO] Running command: gunzip -c /var/lib/cwl/stgf81c4d38-8b17-4a63-b43a-2cfa97352cbc/GCF_003096995.1_ASM309699v1_genomic.fna.gz | prodigal -d GCF_003096995.1_ASM309699v1_genomic.fna/cds.fna -a GCF_003096995.1_ASM309699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:26,894] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:26,894] [INFO] Task started: HMMsearch
[2024-01-24 15:02:26,895] [INFO] Running command: hmmsearch --tblout GCF_003096995.1_ASM309699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/reference_markers.hmm GCF_003096995.1_ASM309699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:27,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:27,144] [INFO] Found 6/6 markers.
[2024-01-24 15:02:27,218] [INFO] Query marker FASTA was written to GCF_003096995.1_ASM309699v1_genomic.fna/markers.fasta
[2024-01-24 15:02:27,219] [INFO] Task started: Blastn
[2024-01-24 15:02:27,219] [INFO] Running command: blastn -query GCF_003096995.1_ASM309699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/reference_markers.fasta -out GCF_003096995.1_ASM309699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:29,636] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:29,641] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:29,641] [INFO] Target genome list was writen to GCF_003096995.1_ASM309699v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:29,796] [INFO] Task started: fastANI
[2024-01-24 15:02:29,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81c4d38-8b17-4a63-b43a-2cfa97352cbc/GCF_003096995.1_ASM309699v1_genomic.fna.gz --refList GCF_003096995.1_ASM309699v1_genomic.fna/target_genomes.txt --output GCF_003096995.1_ASM309699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:37,635] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:37,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:37,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:37,655] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:37,655] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:37,655] [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
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	80.0514	379	648	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	80.0191	381	648	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.6849	231	648	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	78.6394	213	648	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.5042	189	648	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	78.504	188	648	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	78.5034	189	648	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	78.5033	230	648	95	below_threshold
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	78.4697	227	648	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	78.3912	210	648	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	78.3891	171	648	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	78.2291	175	648	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	78.1282	200	648	95	below_threshold
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	78.0759	219	648	95	below_threshold
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	78.0256	223	648	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	77.9211	149	648	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	77.7672	170	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:37,657] [INFO] DFAST Taxonomy check result was written to GCF_003096995.1_ASM309699v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:37,658] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:37,658] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:37,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/checkm_data
[2024-01-24 15:02:37,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:37,687] [INFO] Task started: CheckM
[2024-01-24 15:02:37,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096995.1_ASM309699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096995.1_ASM309699v1_genomic.fna/checkm_input GCF_003096995.1_ASM309699v1_genomic.fna/checkm_result
[2024-01-24 15:02:59,709] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:59,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:59,727] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:59,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:59,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096995.1_ASM309699v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:59,729] [INFO] Task started: Blastn
[2024-01-24 15:02:59,729] [INFO] Running command: blastn -query GCF_003096995.1_ASM309699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1707a0a8-e679-4b87-9cc2-0e30e6576e3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096995.1_ASM309699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:00,887] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:00,890] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:00,891] [INFO] Target genome list was writen to GCF_003096995.1_ASM309699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:00,903] [INFO] Task started: fastANI
[2024-01-24 15:03:00,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81c4d38-8b17-4a63-b43a-2cfa97352cbc/GCF_003096995.1_ASM309699v1_genomic.fna.gz --refList GCF_003096995.1_ASM309699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096995.1_ASM309699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:07,804] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:07,822] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:07,822] [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_003096995.1	s__Basfia_A langaaensis	100.0	645	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900444965.1	s__Basfia_A rossii	80.1842	400	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901764995.1	s__Basfia_A porcinus	80.0293	380	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014843355.1	s__Basfia_A sp014843355	78.852	219	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931395.1	s__Haemophilus_D sp900764435	78.6063	189	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.55	95.23	0.94	0.91	6	-
GCF_900454535.1	s__Avibacterium avium	78.5119	230	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_002921145.1	s__Avibacterium endocarditidis	78.4933	225	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_000262245.1	s__Basfia bettyae	78.4566	208	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
GCA_000017245.1	s__Basfia_A succinogenes	78.364	213	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900475755.1	s__Haemophilus influenzae_D	78.3198	169	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.4263	96.90	95.46	0.91	0.81	69	-
GCF_004565475.1	s__Lonepinella koalarum	78.0759	219	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	-
GCF_001999335.1	s__Rodentibacter sp001999335	77.8388	146	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795405.1	s__Caviibacterium pharyngocola	77.7228	197	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:07,824] [INFO] GTDB search result was written to GCF_003096995.1_ASM309699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:07,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:07,830] [INFO] DFAST_QC result json was written to GCF_003096995.1_ASM309699v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:07,830] [INFO] DFAST_QC completed!
[2024-01-24 15:03:07,831] [INFO] Total running time: 0h0m50s