[2024-01-25 18:56:05,662] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference
[2024-01-25 18:56:06,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,804] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,804] [INFO] Running command: gunzip -c /var/lib/cwl/stgdaab7d20-1154-4e24-8ff6-c08177a3c50d/GCF_014642835.1_ASM1464283v1_genomic.fna.gz | prodigal -d GCF_014642835.1_ASM1464283v1_genomic.fna/cds.fna -a GCF_014642835.1_ASM1464283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:38,902] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:38,902] [INFO] Task started: HMMsearch
[2024-01-25 18:56:38,902] [INFO] Running command: hmmsearch --tblout GCF_014642835.1_ASM1464283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/reference_markers.hmm GCF_014642835.1_ASM1464283v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:39,170] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:39,171] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdaab7d20-1154-4e24-8ff6-c08177a3c50d/GCF_014642835.1_ASM1464283v1_genomic.fna.gz]
[2024-01-25 18:56:39,219] [INFO] Query marker FASTA was written to GCF_014642835.1_ASM1464283v1_genomic.fna/markers.fasta
[2024-01-25 18:56:39,219] [INFO] Task started: Blastn
[2024-01-25 18:56:39,219] [INFO] Running command: blastn -query GCF_014642835.1_ASM1464283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/reference_markers.fasta -out GCF_014642835.1_ASM1464283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:39,965] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:39,967] [INFO] Selected 12 target genomes.
[2024-01-25 18:56:39,968] [INFO] Target genome list was writen to GCF_014642835.1_ASM1464283v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:39,977] [INFO] Task started: fastANI
[2024-01-25 18:56:39,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaab7d20-1154-4e24-8ff6-c08177a3c50d/GCF_014642835.1_ASM1464283v1_genomic.fna.gz --refList GCF_014642835.1_ASM1464283v1_genomic.fna/target_genomes.txt --output GCF_014642835.1_ASM1464283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:52,933] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:52,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:52,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:52,944] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:52,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:52,945] [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
Dyella nitratireducens	strain=CGMCC 1.15439	GCA_014642835.1	1849580	1849580	type	True	100.0	1887	1887	95	conclusive
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	83.0058	1126	1887	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.6748	1003	1887	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	81.6233	960	1887	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.2874	882	1887	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	81.21	844	1887	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	80.9495	911	1887	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	80.7352	868	1887	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.7634	513	1887	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.5815	632	1887	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1398	485	1887	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.5058	186	1887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:52,946] [INFO] DFAST Taxonomy check result was written to GCF_014642835.1_ASM1464283v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:52,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:52,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:52,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/checkm_data
[2024-01-25 18:56:52,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:53,003] [INFO] Task started: CheckM
[2024-01-25 18:56:53,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642835.1_ASM1464283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642835.1_ASM1464283v1_genomic.fna/checkm_input GCF_014642835.1_ASM1464283v1_genomic.fna/checkm_result
[2024-01-25 18:58:21,901] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:21,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:21,920] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:21,920] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:21,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642835.1_ASM1464283v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:21,922] [INFO] Task started: Blastn
[2024-01-25 18:58:21,922] [INFO] Running command: blastn -query GCF_014642835.1_ASM1464283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca353f4-eb1d-4dea-9e8d-46341b948a21/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642835.1_ASM1464283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:23,286] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:23,290] [INFO] Selected 9 target genomes.
[2024-01-25 18:58:23,290] [INFO] Target genome list was writen to GCF_014642835.1_ASM1464283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:23,300] [INFO] Task started: fastANI
[2024-01-25 18:58:23,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaab7d20-1154-4e24-8ff6-c08177a3c50d/GCF_014642835.1_ASM1464283v1_genomic.fna.gz --refList GCF_014642835.1_ASM1464283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642835.1_ASM1464283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:34,100] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:34,107] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:34,107] [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_014642835.1	s__Dyella_B nitratireducens	100.0	1887	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003977665.1	s__Dyella_B choica	83.019	1124	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873315.1	s__Dyella_B sp014873315	82.7056	1134	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863405.1	s__Dyella_B sp014863405	81.6667	1003	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363155.1	s__Dyella_B monticola	81.6279	959	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904955.1	s__Dyella_B flava	81.2029	844	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	80.9497	911	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114615.1	s__Dyella_B sp004114615	80.5233	594	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970555.1	s__Dyella_B sp903970555	80.3101	731	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:34,109] [INFO] GTDB search result was written to GCF_014642835.1_ASM1464283v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:34,110] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:34,112] [INFO] DFAST_QC result json was written to GCF_014642835.1_ASM1464283v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:34,113] [INFO] DFAST_QC completed!
[2024-01-25 18:58:34,113] [INFO] Total running time: 0h2m28s