[2024-01-24 14:22:33,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference
[2024-01-24 14:22:34,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,902] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,903] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3bceaaf-474b-4377-9a56-a47b991cfba7/GCF_901764995.1_5970_8_10_v2_genomic.fna.gz | prodigal -d GCF_901764995.1_5970_8_10_v2_genomic.fna/cds.fna -a GCF_901764995.1_5970_8_10_v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:40,330] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:40,330] [INFO] Task started: HMMsearch
[2024-01-24 14:22:40,330] [INFO] Running command: hmmsearch --tblout GCF_901764995.1_5970_8_10_v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/reference_markers.hmm GCF_901764995.1_5970_8_10_v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:40,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:40,585] [INFO] Found 6/6 markers.
[2024-01-24 14:22:40,610] [INFO] Query marker FASTA was written to GCF_901764995.1_5970_8_10_v2_genomic.fna/markers.fasta
[2024-01-24 14:22:40,611] [INFO] Task started: Blastn
[2024-01-24 14:22:40,611] [INFO] Running command: blastn -query GCF_901764995.1_5970_8_10_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/reference_markers.fasta -out GCF_901764995.1_5970_8_10_v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:41,258] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:41,262] [INFO] Selected 20 target genomes.
[2024-01-24 14:22:41,263] [INFO] Target genome list was writen to GCF_901764995.1_5970_8_10_v2_genomic.fna/target_genomes.txt
[2024-01-24 14:22:41,272] [INFO] Task started: fastANI
[2024-01-24 14:22:41,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3bceaaf-474b-4377-9a56-a47b991cfba7/GCF_901764995.1_5970_8_10_v2_genomic.fna.gz --refList GCF_901764995.1_5970_8_10_v2_genomic.fna/target_genomes.txt --output GCF_901764995.1_5970_8_10_v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:51,529] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:51,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:51,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:51,557] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:51,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:51,558] [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	100.0	740	743	95	conclusive
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	100.0	740	743	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	78.6516	196	743	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.6349	198	743	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	78.5495	199	743	95	below_threshold
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	78.3238	245	743	95	below_threshold
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	78.3157	245	743	95	below_threshold
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	78.2368	223	743	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.2312	228	743	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	78.1268	221	743	95	below_threshold
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	78.0728	228	743	95	below_threshold
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	78.0606	212	743	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	77.9728	226	743	95	below_threshold
Basfia succiniciproducens	strain=DSM 22022	GCA_900101275.1	653940	653940	suspected-type	True	77.9067	222	743	95	below_threshold
Mesocricetibacter intestinalis	strain=DSM 28403	GCA_004363295.1	1521930	1521930	type	True	77.6029	104	743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,560] [INFO] DFAST Taxonomy check result was written to GCF_901764995.1_5970_8_10_v2_genomic.fna/tc_result.tsv
[2024-01-24 14:22:51,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:51,561] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:51,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/checkm_data
[2024-01-24 14:22:51,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:51,590] [INFO] Task started: CheckM
[2024-01-24 14:22:51,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_901764995.1_5970_8_10_v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_901764995.1_5970_8_10_v2_genomic.fna/checkm_input GCF_901764995.1_5970_8_10_v2_genomic.fna/checkm_result
[2024-01-24 14:23:14,719] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:14,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:14,770] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:14,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:14,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_901764995.1_5970_8_10_v2_genomic.fna/markers.fasta)
[2024-01-24 14:23:14,772] [INFO] Task started: Blastn
[2024-01-24 14:23:14,772] [INFO] Running command: blastn -query GCF_901764995.1_5970_8_10_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdd4c20b-b3c4-4a2b-9ab8-d9cc9149c7f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_901764995.1_5970_8_10_v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:15,635] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:15,639] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:15,639] [INFO] Target genome list was writen to GCF_901764995.1_5970_8_10_v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:15,657] [INFO] Task started: fastANI
[2024-01-24 14:23:15,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3bceaaf-474b-4377-9a56-a47b991cfba7/GCF_901764995.1_5970_8_10_v2_genomic.fna.gz --refList GCF_901764995.1_5970_8_10_v2_genomic.fna/target_genomes_gtdb.txt --output GCF_901764995.1_5970_8_10_v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:24,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:24,425] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:24,425] [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_901764995.1	s__Basfia_A porcinus	100.0	740	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_900444965.1	s__Basfia_A rossii	84.2991	497	743	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_003096995.1	s__Basfia_A langaaensis	79.9723	390	743	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_014843355.1	s__Basfia_A sp014843355	79.1086	257	743	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_003253005.1	s__Haemophilus_D parainfluenzae_M	78.5519	189	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_900756875.1	s__Haemophilus_D sp900756875	78.4535	181	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
GCF_004565475.1	s__Lonepinella koalarum	78.3549	243	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	-
GCA_000017245.1	s__Basfia_A succinogenes	78.1881	226	743	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_002921135.1	s__Avibacterium gallinarum	78.1102	222	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_011455875.1	s__Basfia succiniciproducens	78.0889	227	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	99.17	98.70	0.95	0.93	4	-
GCF_000185305.1	s__Aggregatibacter segnis	78.0859	195	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.84	95.38	0.95	0.88	6	-
GCF_900636915.1	s__Aggregatibacter aphrophilus	77.9751	181	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.58	96.00	0.94	0.87	19	-
GCF_900454535.1	s__Avibacterium avium	77.9679	227	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_002795405.1	s__Caviibacterium pharyngocola	77.9364	228	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363295.1	s__Mesocricetibacter intestinalis	77.5735	105	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:24,427] [INFO] GTDB search result was written to GCF_901764995.1_5970_8_10_v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:24,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:24,431] [INFO] DFAST_QC result json was written to GCF_901764995.1_5970_8_10_v2_genomic.fna/dqc_result.json
[2024-01-24 14:23:24,432] [INFO] DFAST_QC completed!
[2024-01-24 14:23:24,432] [INFO] Total running time: 0h0m51s