[2024-01-24 12:06:50,951] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference
[2024-01-24 12:06:52,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,136] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ca4c6aa-3910-4c87-96ba-d2292520f2ea/GCF_000746485.1_ASM74648v1_genomic.fna.gz | prodigal -d GCF_000746485.1_ASM74648v1_genomic.fna/cds.fna -a GCF_000746485.1_ASM74648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:56,835] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:56,835] [INFO] Task started: HMMsearch
[2024-01-24 12:06:56,835] [INFO] Running command: hmmsearch --tblout GCF_000746485.1_ASM74648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/reference_markers.hmm GCF_000746485.1_ASM74648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:57,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:57,074] [INFO] Found 6/6 markers.
[2024-01-24 12:06:57,098] [INFO] Query marker FASTA was written to GCF_000746485.1_ASM74648v1_genomic.fna/markers.fasta
[2024-01-24 12:06:57,098] [INFO] Task started: Blastn
[2024-01-24 12:06:57,099] [INFO] Running command: blastn -query GCF_000746485.1_ASM74648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/reference_markers.fasta -out GCF_000746485.1_ASM74648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:57,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:57,818] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:57,818] [INFO] Target genome list was writen to GCF_000746485.1_ASM74648v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:57,823] [INFO] Task started: fastANI
[2024-01-24 12:06:57,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca4c6aa-3910-4c87-96ba-d2292520f2ea/GCF_000746485.1_ASM74648v1_genomic.fna.gz --refList GCF_000746485.1_ASM74648v1_genomic.fna/target_genomes.txt --output GCF_000746485.1_ASM74648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:04,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:04,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:04,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:04,453] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:07:04,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:04,453] [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 parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	100.0	702	703	95	conclusive
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	99.9913	700	703	95	conclusive
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	99.99	700	703	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	99.9641	696	703	95	conclusive
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	83.1923	344	703	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	81.1852	312	703	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.5614	306	703	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	78.9563	289	703	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	78.5732	51	703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:04,455] [INFO] DFAST Taxonomy check result was written to GCF_000746485.1_ASM74648v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:04,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:04,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:04,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/checkm_data
[2024-01-24 12:07:04,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:04,479] [INFO] Task started: CheckM
[2024-01-24 12:07:04,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000746485.1_ASM74648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000746485.1_ASM74648v1_genomic.fna/checkm_input GCF_000746485.1_ASM74648v1_genomic.fna/checkm_result
[2024-01-24 12:07:25,712] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:25,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:25,734] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:25,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:25,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000746485.1_ASM74648v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:25,735] [INFO] Task started: Blastn
[2024-01-24 12:07:25,735] [INFO] Running command: blastn -query GCF_000746485.1_ASM74648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9355ded9-661e-4c83-8b19-dae7b3b1c00b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000746485.1_ASM74648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:26,899] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:26,903] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:26,903] [INFO] Target genome list was writen to GCF_000746485.1_ASM74648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:26,929] [INFO] Task started: fastANI
[2024-01-24 12:07:26,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca4c6aa-3910-4c87-96ba-d2292520f2ea/GCF_000746485.1_ASM74648v1_genomic.fna.gz --refList GCF_000746485.1_ASM74648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000746485.1_ASM74648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:33,408] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:33,422] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:33,423] [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_000191405.1	s__Haemophilus_D parainfluenzae	99.9641	696	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	conclusive
GCF_003252755.1	s__Haemophilus_D parainfluenzae_N	94.5815	593	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.46	95.02	0.94	0.93	5	-
GCA_905214375.1	s__Haemophilus_D sp905214375	94.5135	494	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCF_014931395.1	s__Haemophilus_D sp900764435	94.3382	605	703	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_003252795.1	s__Haemophilus_D parainfluenzae_K	94.1919	584	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCF_001815355.1	s__Haemophilus_D sp001815355	93.9702	570	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.35	95.20	0.94	0.91	8	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	93.8969	599	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCA_900756155.1	s__Haemophilus_D sp900756155	93.8825	567	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCA_015255025.1	s__Haemophilus_D sp015255025	93.7446	437	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCA_905215245.1	s__Haemophilus_D sp905215245	93.6985	416	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCA_905207935.1	s__Haemophilus_D sp905207935	93.6691	480	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	93.4871	585	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.33	95.18	0.90	0.88	7	-
GCF_014931275.1	s__Haemophilus_D sp900755445	93.076	592	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	92.9726	572	703	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_905205995.1	s__Haemophilus_D sp905205995	92.8568	547	703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,425] [INFO] GTDB search result was written to GCF_000746485.1_ASM74648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:33,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:33,428] [INFO] DFAST_QC result json was written to GCF_000746485.1_ASM74648v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:33,428] [INFO] DFAST_QC completed!
[2024-01-24 12:07:33,429] [INFO] Total running time: 0h0m42s