[2023-06-29 03:20:45,865] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:20:45,867] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:20:45,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference
[2023-06-29 03:20:47,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:20:47,132] [INFO] Task started: Prodigal
[2023-06-29 03:20:47,133] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc870ebd-0b60-4843-8e10-d716b8bdff5f/GCA_005776565.1_ASM577656v1_genomic.fna.gz | prodigal -d GCA_005776565.1_ASM577656v1_genomic.fna/cds.fna -a GCA_005776565.1_ASM577656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:20:52,514] [INFO] Task succeeded: Prodigal
[2023-06-29 03:20:52,514] [INFO] Task started: HMMsearch
[2023-06-29 03:20:52,514] [INFO] Running command: hmmsearch --tblout GCA_005776565.1_ASM577656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/reference_markers.hmm GCA_005776565.1_ASM577656v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:20:52,682] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:20:52,684] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdc870ebd-0b60-4843-8e10-d716b8bdff5f/GCA_005776565.1_ASM577656v1_genomic.fna.gz]
[2023-06-29 03:20:52,709] [INFO] Query marker FASTA was written to GCA_005776565.1_ASM577656v1_genomic.fna/markers.fasta
[2023-06-29 03:20:52,710] [INFO] Task started: Blastn
[2023-06-29 03:20:52,710] [INFO] Running command: blastn -query GCA_005776565.1_ASM577656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/reference_markers.fasta -out GCA_005776565.1_ASM577656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:20:53,222] [INFO] Task succeeded: Blastn
[2023-06-29 03:20:53,229] [INFO] Selected 5 target genomes.
[2023-06-29 03:20:53,229] [INFO] Target genome list was writen to GCA_005776565.1_ASM577656v1_genomic.fna/target_genomes.txt
[2023-06-29 03:20:53,230] [INFO] Task started: fastANI
[2023-06-29 03:20:53,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc870ebd-0b60-4843-8e10-d716b8bdff5f/GCA_005776565.1_ASM577656v1_genomic.fna.gz --refList GCA_005776565.1_ASM577656v1_genomic.fna/target_genomes.txt --output GCA_005776565.1_ASM577656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:20:56,923] [INFO] Task succeeded: fastANI
[2023-06-29 03:20:56,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:20:56,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:20:56,930] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:20:56,930] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:20:56,930] [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
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	80.2723	248	429	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	79.8881	229	429	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	79.8171	238	429	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	79.7761	231	429	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	79.2775	208	429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:20:56,932] [INFO] DFAST Taxonomy check result was written to GCA_005776565.1_ASM577656v1_genomic.fna/tc_result.tsv
[2023-06-29 03:20:56,933] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:20:56,933] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:20:56,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/checkm_data
[2023-06-29 03:20:56,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:20:56,958] [INFO] Task started: CheckM
[2023-06-29 03:20:56,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005776565.1_ASM577656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005776565.1_ASM577656v1_genomic.fna/checkm_input GCA_005776565.1_ASM577656v1_genomic.fna/checkm_result
[2023-06-29 03:21:19,165] [INFO] Task succeeded: CheckM
[2023-06-29 03:21:19,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 15.48%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:21:19,191] [INFO] ===== Completeness check finished =====
[2023-06-29 03:21:19,191] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:21:19,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005776565.1_ASM577656v1_genomic.fna/markers.fasta)
[2023-06-29 03:21:19,192] [INFO] Task started: Blastn
[2023-06-29 03:21:19,192] [INFO] Running command: blastn -query GCA_005776565.1_ASM577656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b0b644-7a6b-4c7a-b1da-91e343f94a6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_005776565.1_ASM577656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:21:19,660] [INFO] Task succeeded: Blastn
[2023-06-29 03:21:19,664] [INFO] Selected 5 target genomes.
[2023-06-29 03:21:19,664] [INFO] Target genome list was writen to GCA_005776565.1_ASM577656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:21:19,723] [INFO] Task started: fastANI
[2023-06-29 03:21:19,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc870ebd-0b60-4843-8e10-d716b8bdff5f/GCA_005776565.1_ASM577656v1_genomic.fna.gz --refList GCA_005776565.1_ASM577656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005776565.1_ASM577656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:21:24,275] [INFO] Task succeeded: fastANI
[2023-06-29 03:21:24,282] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:21:24,282] [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_002127265.1	s__Hydrogenophaga sp002127265	85.5574	330	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592305.1	s__Hydrogenophaga taeniospiralis	80.2723	248	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723405.1	s__Hydrogenophaga intermedia	79.7735	240	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.52	98.31	0.93	0.83	5	-
GCA_017302505.1	s__Rubrivivax sp017302505	76.4606	78	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069755.1	s__Ideonella sp018069755	75.9313	83	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:21:24,284] [INFO] GTDB search result was written to GCA_005776565.1_ASM577656v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:21:24,285] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:21:24,289] [INFO] DFAST_QC result json was written to GCA_005776565.1_ASM577656v1_genomic.fna/dqc_result.json
[2023-06-29 03:21:24,289] [INFO] DFAST_QC completed!
[2023-06-29 03:21:24,289] [INFO] Total running time: 0h0m38s