[2023-06-28 05:38:06,466] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:06,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:06,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference
[2023-06-28 05:38:07,982] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:07,983] [INFO] Task started: Prodigal
[2023-06-28 05:38:07,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e32086f-31c2-49cd-9294-4d0483d52d32/GCA_019455265.1_ASM1945526v1_genomic.fna.gz | prodigal -d GCA_019455265.1_ASM1945526v1_genomic.fna/cds.fna -a GCA_019455265.1_ASM1945526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:21,394] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:21,395] [INFO] Task started: HMMsearch
[2023-06-28 05:38:21,395] [INFO] Running command: hmmsearch --tblout GCA_019455265.1_ASM1945526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/reference_markers.hmm GCA_019455265.1_ASM1945526v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:21,692] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:21,694] [INFO] Found 6/6 markers.
[2023-06-28 05:38:21,734] [INFO] Query marker FASTA was written to GCA_019455265.1_ASM1945526v1_genomic.fna/markers.fasta
[2023-06-28 05:38:21,735] [INFO] Task started: Blastn
[2023-06-28 05:38:21,735] [INFO] Running command: blastn -query GCA_019455265.1_ASM1945526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/reference_markers.fasta -out GCA_019455265.1_ASM1945526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:22,754] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:22,760] [INFO] Selected 18 target genomes.
[2023-06-28 05:38:22,760] [INFO] Target genome list was writen to GCA_019455265.1_ASM1945526v1_genomic.fna/target_genomes.txt
[2023-06-28 05:38:22,763] [INFO] Task started: fastANI
[2023-06-28 05:38:22,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e32086f-31c2-49cd-9294-4d0483d52d32/GCA_019455265.1_ASM1945526v1_genomic.fna.gz --refList GCA_019455265.1_ASM1945526v1_genomic.fna/target_genomes.txt --output GCA_019455265.1_ASM1945526v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:38:39,592] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:39,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:38:39,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:38:39,619] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 05:38:39,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 05:38:39,620] [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
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	98.5579	1180	1230	95	conclusive
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	84.6795	901	1230	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.7239	637	1230	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.364	640	1230	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.2706	661	1230	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	80.2161	535	1230	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	80.172	544	1230	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.9662	634	1230	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.9119	603	1230	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	79.56	519	1230	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	79.4198	357	1230	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0969	459	1230	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	79.0726	554	1230	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	79.071	560	1230	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	78.7781	454	1230	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6979	441	1230	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.3047	418	1230	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.2176	458	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:38:39,621] [INFO] DFAST Taxonomy check result was written to GCA_019455265.1_ASM1945526v1_genomic.fna/tc_result.tsv
[2023-06-28 05:38:39,622] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:38:39,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:38:39,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/checkm_data
[2023-06-28 05:38:39,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:38:39,670] [INFO] Task started: CheckM
[2023-06-28 05:38:39,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019455265.1_ASM1945526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019455265.1_ASM1945526v1_genomic.fna/checkm_input GCA_019455265.1_ASM1945526v1_genomic.fna/checkm_result
[2023-06-28 05:39:23,519] [INFO] Task succeeded: CheckM
[2023-06-28 05:39:23,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:39:23,542] [INFO] ===== Completeness check finished =====
[2023-06-28 05:39:23,542] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:39:23,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019455265.1_ASM1945526v1_genomic.fna/markers.fasta)
[2023-06-28 05:39:23,543] [INFO] Task started: Blastn
[2023-06-28 05:39:23,543] [INFO] Running command: blastn -query GCA_019455265.1_ASM1945526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32b8e1c8-5fff-4e99-bda0-0882a782fdae/dqc_reference/reference_markers_gtdb.fasta -out GCA_019455265.1_ASM1945526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:39:25,390] [INFO] Task succeeded: Blastn
[2023-06-28 05:39:25,395] [INFO] Selected 14 target genomes.
[2023-06-28 05:39:25,395] [INFO] Target genome list was writen to GCA_019455265.1_ASM1945526v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:39:25,400] [INFO] Task started: fastANI
[2023-06-28 05:39:25,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e32086f-31c2-49cd-9294-4d0483d52d32/GCA_019455265.1_ASM1945526v1_genomic.fna.gz --refList GCA_019455265.1_ASM1945526v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019455265.1_ASM1945526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:39:38,089] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:38,104] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:39:38,105] [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_003008595.1	s__Giesbergeria suum	98.5579	1180	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017985015.1	s__Giesbergeria sp017985015	88.2388	892	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.01	95.86	0.92	0.90	6	-
GCF_003570885.1	s__Giesbergeria hankyongi	84.6948	899	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	82.5636	577	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	81.5814	716	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_003604195.1	s__Giesbergeria lacusdiani	81.3043	712	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.1067	657	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_000739995.1	s__Giesbergeria granuli	80.8465	654	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCA_001770955.1	s__Giesbergeria sp001770955	80.7298	652	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_010020825.1	s__Giesbergeria sp010020825	80.7223	662	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCF_014207955.1	s__Acidovorax soli_A	80.0476	697	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	79.802	572	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCA_018240985.1	s__Alicycliphilus sp018240985	79.7009	503	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCF_000282995.1	s__Melaminivora alkalimesophila	79.4259	357	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-28 05:39:38,107] [INFO] GTDB search result was written to GCA_019455265.1_ASM1945526v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:39:38,107] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:39:38,112] [INFO] DFAST_QC result json was written to GCA_019455265.1_ASM1945526v1_genomic.fna/dqc_result.json
[2023-06-28 05:39:38,112] [INFO] DFAST_QC completed!
[2023-06-28 05:39:38,112] [INFO] Total running time: 0h1m32s