[2023-06-19 11:13:15,909] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:13:15,911] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:13:15,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference
[2023-06-19 11:13:17,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:13:17,654] [INFO] Task started: Prodigal
[2023-06-19 11:13:17,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd829b8c-a460-46da-bfb5-b347b373de9d/GCA_018366115.1_ASM1836611v1_genomic.fna.gz | prodigal -d GCA_018366115.1_ASM1836611v1_genomic.fna/cds.fna -a GCA_018366115.1_ASM1836611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:13:21,926] [INFO] Task succeeded: Prodigal
[2023-06-19 11:13:21,926] [INFO] Task started: HMMsearch
[2023-06-19 11:13:21,927] [INFO] Running command: hmmsearch --tblout GCA_018366115.1_ASM1836611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/reference_markers.hmm GCA_018366115.1_ASM1836611v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:13:22,103] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:13:22,105] [INFO] Found 6/6 markers.
[2023-06-19 11:13:22,127] [INFO] Query marker FASTA was written to GCA_018366115.1_ASM1836611v1_genomic.fna/markers.fasta
[2023-06-19 11:13:22,127] [INFO] Task started: Blastn
[2023-06-19 11:13:22,128] [INFO] Running command: blastn -query GCA_018366115.1_ASM1836611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/reference_markers.fasta -out GCA_018366115.1_ASM1836611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:13:22,822] [INFO] Task succeeded: Blastn
[2023-06-19 11:13:22,827] [INFO] Selected 17 target genomes.
[2023-06-19 11:13:22,827] [INFO] Target genome list was writen to GCA_018366115.1_ASM1836611v1_genomic.fna/target_genomes.txt
[2023-06-19 11:13:22,828] [INFO] Task started: fastANI
[2023-06-19 11:13:22,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd829b8c-a460-46da-bfb5-b347b373de9d/GCA_018366115.1_ASM1836611v1_genomic.fna.gz --refList GCA_018366115.1_ASM1836611v1_genomic.fna/target_genomes.txt --output GCA_018366115.1_ASM1836611v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:13:31,047] [INFO] Task succeeded: fastANI
[2023-06-19 11:13:31,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:13:31,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:13:31,059] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:13:31,059] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 11:13:31,059] [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=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	94.3685	573	648	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	94.348	574	648	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	94.3478	568	648	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	94.3366	577	648	95	below_threshold
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	83.4152	324	648	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	82.0611	342	648	95	below_threshold
Haemophilus haemolyticus	strain=ATCC 33390	GCA_004368535.1	726	726	type	True	81.9605	340	648	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	81.892	343	648	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	81.0706	306	648	95	below_threshold
Haemophilus aegyptius	strain=FDAARGOS_1478	GCA_019930905.1	197575	197575	type	True	81.0377	306	648	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.8752	313	648	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	78.802	286	648	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	78.2048	227	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 11:13:31,061] [INFO] DFAST Taxonomy check result was written to GCA_018366115.1_ASM1836611v1_genomic.fna/tc_result.tsv
[2023-06-19 11:13:31,061] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:13:31,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:13:31,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/checkm_data
[2023-06-19 11:13:31,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:13:31,084] [INFO] Task started: CheckM
[2023-06-19 11:13:31,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018366115.1_ASM1836611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018366115.1_ASM1836611v1_genomic.fna/checkm_input GCA_018366115.1_ASM1836611v1_genomic.fna/checkm_result
[2023-06-19 11:13:50,135] [INFO] Task succeeded: CheckM
[2023-06-19 11:13:50,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:13:50,154] [INFO] ===== Completeness check finished =====
[2023-06-19 11:13:50,154] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:13:50,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018366115.1_ASM1836611v1_genomic.fna/markers.fasta)
[2023-06-19 11:13:50,155] [INFO] Task started: Blastn
[2023-06-19 11:13:50,155] [INFO] Running command: blastn -query GCA_018366115.1_ASM1836611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea370c46-c880-4dfa-b29f-e7fa8085258b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018366115.1_ASM1836611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:13:51,231] [INFO] Task succeeded: Blastn
[2023-06-19 11:13:51,237] [INFO] Selected 14 target genomes.
[2023-06-19 11:13:51,237] [INFO] Target genome list was writen to GCA_018366115.1_ASM1836611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:13:51,238] [INFO] Task started: fastANI
[2023-06-19 11:13:51,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd829b8c-a460-46da-bfb5-b347b373de9d/GCA_018366115.1_ASM1836611v1_genomic.fna.gz --refList GCA_018366115.1_ASM1836611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018366115.1_ASM1836611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:13:57,316] [INFO] Task succeeded: fastANI
[2023-06-19 11:13:57,327] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 11:13:57,328] [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_001815355.1	s__Haemophilus_D sp001815355	94.9484	568	648	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_003252755.1	s__Haemophilus_D parainfluenzae_N	94.9463	601	648	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_900756155.1	s__Haemophilus_D sp900756155	94.6984	569	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	94.6944	568	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCA_015255025.1	s__Haemophilus_D sp015255025	94.4576	444	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	94.4148	565	648	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_014931395.1	s__Haemophilus_D sp900764435	94.352	576	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_000191405.1	s__Haemophilus_D parainfluenzae	94.348	574	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCA_905214375.1	s__Haemophilus_D sp905214375	94.2174	486	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCA_905207935.1	s__Haemophilus_D sp905207935	94.132	470	648	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_001679485.1	s__Haemophilus_D sp001679485	93.9473	567	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	93.9293	578	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCF_014931275.1	s__Haemophilus_D sp900755445	93.8219	585	648	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	93.4012	555	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
--------------------------------------------------------------------------------
[2023-06-19 11:13:57,331] [INFO] GTDB search result was written to GCA_018366115.1_ASM1836611v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:13:57,331] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:13:57,335] [INFO] DFAST_QC result json was written to GCA_018366115.1_ASM1836611v1_genomic.fna/dqc_result.json
[2023-06-19 11:13:57,335] [INFO] DFAST_QC completed!
[2023-06-19 11:13:57,335] [INFO] Total running time: 0h0m41s