[2024-01-24 12:37:08,351] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:08,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:08,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference
[2024-01-24 12:37:09,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:09,659] [INFO] Task started: Prodigal
[2024-01-24 12:37:09,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg631d3d80-df1f-4c41-8ebd-8752e28f2ec8/GCF_006716445.1_ASM671644v1_genomic.fna.gz | prodigal -d GCF_006716445.1_ASM671644v1_genomic.fna/cds.fna -a GCF_006716445.1_ASM671644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:36,986] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:36,987] [INFO] Task started: HMMsearch
[2024-01-24 12:37:36,987] [INFO] Running command: hmmsearch --tblout GCF_006716445.1_ASM671644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/reference_markers.hmm GCF_006716445.1_ASM671644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:37,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:37,360] [INFO] Found 6/6 markers.
[2024-01-24 12:37:37,431] [INFO] Query marker FASTA was written to GCF_006716445.1_ASM671644v1_genomic.fna/markers.fasta
[2024-01-24 12:37:37,431] [INFO] Task started: Blastn
[2024-01-24 12:37:37,431] [INFO] Running command: blastn -query GCF_006716445.1_ASM671644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/reference_markers.fasta -out GCF_006716445.1_ASM671644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:38,844] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:38,847] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:38,848] [INFO] Target genome list was writen to GCF_006716445.1_ASM671644v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:38,854] [INFO] Task started: fastANI
[2024-01-24 12:37:38,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg631d3d80-df1f-4c41-8ebd-8752e28f2ec8/GCF_006716445.1_ASM671644v1_genomic.fna.gz --refList GCF_006716445.1_ASM671644v1_genomic.fna/target_genomes.txt --output GCF_006716445.1_ASM671644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:58,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:58,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:58,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:58,176] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:58,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:58,176] [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
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	100.0	3040	3042	95	conclusive
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	84.0249	1799	3042	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	83.769	1716	3042	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	82.5164	1479	3042	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	81.3973	1322	3042	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	81.0582	1167	3042	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	80.8349	1397	3042	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.8339	1288	3042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:58,178] [INFO] DFAST Taxonomy check result was written to GCF_006716445.1_ASM671644v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:58,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:58,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:58,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/checkm_data
[2024-01-24 12:37:58,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:58,266] [INFO] Task started: CheckM
[2024-01-24 12:37:58,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716445.1_ASM671644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716445.1_ASM671644v1_genomic.fna/checkm_input GCF_006716445.1_ASM671644v1_genomic.fna/checkm_result
[2024-01-24 12:40:37,333] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:37,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:37,366] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:37,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:37,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716445.1_ASM671644v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:37,367] [INFO] Task started: Blastn
[2024-01-24 12:40:37,367] [INFO] Running command: blastn -query GCF_006716445.1_ASM671644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a16bd11-5059-422b-b50a-c0b7de9aeb44/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716445.1_ASM671644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:39,619] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:39,623] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:39,623] [INFO] Target genome list was writen to GCF_006716445.1_ASM671644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:39,628] [INFO] Task started: fastANI
[2024-01-24 12:40:39,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg631d3d80-df1f-4c41-8ebd-8752e28f2ec8/GCF_006716445.1_ASM671644v1_genomic.fna.gz --refList GCF_006716445.1_ASM671644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716445.1_ASM671644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:58,390] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:58,400] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:58,400] [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_006716445.1	s__Pseudonocardia kunmingensis	100.0	3040	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002262885.1	s__Pseudonocardia sp002262885	89.8756	2203	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942185.1	s__Pseudonocardia sp001942185	84.1639	1781	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	84.0414	1796	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	83.7558	1719	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899645.1	s__Pseudonocardia sp001899645	80.8068	1202	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.47	99.47	0.91	0.91	2	-
GCA_019263585.1	s__Pseudonocardia sp019263585	80.7929	1299	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,402] [INFO] GTDB search result was written to GCF_006716445.1_ASM671644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:58,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:58,406] [INFO] DFAST_QC result json was written to GCF_006716445.1_ASM671644v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:58,406] [INFO] DFAST_QC completed!
[2024-01-24 12:40:58,407] [INFO] Total running time: 0h3m50s