[2024-01-24 11:43:42,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference
[2024-01-24 11:43:43,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,562] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,562] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe9ed577-660d-4575-b0f5-d20e136fd42e/GCF_030160315.1_ASM3016031v1_genomic.fna.gz | prodigal -d GCF_030160315.1_ASM3016031v1_genomic.fna/cds.fna -a GCF_030160315.1_ASM3016031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:07,144] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:07,144] [INFO] Task started: HMMsearch
[2024-01-24 11:44:07,145] [INFO] Running command: hmmsearch --tblout GCF_030160315.1_ASM3016031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/reference_markers.hmm GCF_030160315.1_ASM3016031v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:07,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:07,511] [INFO] Found 6/6 markers.
[2024-01-24 11:44:07,557] [INFO] Query marker FASTA was written to GCF_030160315.1_ASM3016031v1_genomic.fna/markers.fasta
[2024-01-24 11:44:07,557] [INFO] Task started: Blastn
[2024-01-24 11:44:07,558] [INFO] Running command: blastn -query GCF_030160315.1_ASM3016031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/reference_markers.fasta -out GCF_030160315.1_ASM3016031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:08,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:08,560] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:08,560] [INFO] Target genome list was writen to GCF_030160315.1_ASM3016031v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:08,564] [INFO] Task started: fastANI
[2024-01-24 11:44:08,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9ed577-660d-4575-b0f5-d20e136fd42e/GCF_030160315.1_ASM3016031v1_genomic.fna.gz --refList GCF_030160315.1_ASM3016031v1_genomic.fna/target_genomes.txt --output GCF_030160315.1_ASM3016031v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:20,069] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:20,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:20,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:20,080] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:20,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:20,080] [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 mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	99.9867	1710	1717	95	conclusive
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	83.3091	1036	1717	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	82.9378	917	1717	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	82.2028	949	1717	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	82.1888	953	1717	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	81.1926	867	1717	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.4879	540	1717	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.1264	675	1717	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	79.9493	564	1717	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.8844	556	1717	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.7513	290	1717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:20,084] [INFO] DFAST Taxonomy check result was written to GCF_030160315.1_ASM3016031v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:20,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:20,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:20,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/checkm_data
[2024-01-24 11:44:20,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:20,142] [INFO] Task started: CheckM
[2024-01-24 11:44:20,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160315.1_ASM3016031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160315.1_ASM3016031v1_genomic.fna/checkm_input GCF_030160315.1_ASM3016031v1_genomic.fna/checkm_result
[2024-01-24 11:45:24,729] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:24,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.87%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:24,838] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:24,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:24,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160315.1_ASM3016031v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:24,839] [INFO] Task started: Blastn
[2024-01-24 11:45:24,839] [INFO] Running command: blastn -query GCF_030160315.1_ASM3016031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eac5a71-3124-416a-aa5d-f642b0a8d918/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160315.1_ASM3016031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:26,696] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:26,700] [INFO] Selected 10 target genomes.
[2024-01-24 11:45:26,700] [INFO] Target genome list was writen to GCF_030160315.1_ASM3016031v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:26,708] [INFO] Task started: fastANI
[2024-01-24 11:45:26,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9ed577-660d-4575-b0f5-d20e136fd42e/GCF_030160315.1_ASM3016031v1_genomic.fna.gz --refList GCF_030160315.1_ASM3016031v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160315.1_ASM3016031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:37,498] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:37,514] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:37,514] [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_016904945.1	s__Dyella_B mobilis	99.9867	1710	1717	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_014863405.1	s__Dyella_B sp014863405	83.2967	1038	1717	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	82.9394	917	1717	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_016865235.1	s__Dyella_B caseinilytica	82.181	952	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003363265.1	s__Dyella_B psychrodurans	81.9314	887	1717	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	81.8956	643	1717	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	81.5366	881	1717	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_003977665.1	s__Dyella_B choica	81.1799	869	1717	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	81.0378	733	1717	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_900112865.1	s__Dyella marensis	80.7079	729	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:37,516] [INFO] GTDB search result was written to GCF_030160315.1_ASM3016031v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:37,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:37,519] [INFO] DFAST_QC result json was written to GCF_030160315.1_ASM3016031v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:37,520] [INFO] DFAST_QC completed!
[2024-01-24 11:45:37,520] [INFO] Total running time: 0h1m55s