[2024-01-24 13:32:42,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference
[2024-01-24 13:32:43,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,727] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg13669dd2-2031-4270-b526-dfa658937f56/GCF_006539565.1_ASM653956v1_genomic.fna.gz | prodigal -d GCF_006539565.1_ASM653956v1_genomic.fna/cds.fna -a GCF_006539565.1_ASM653956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:58,395] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:58,396] [INFO] Task started: HMMsearch
[2024-01-24 13:32:58,396] [INFO] Running command: hmmsearch --tblout GCF_006539565.1_ASM653956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/reference_markers.hmm GCF_006539565.1_ASM653956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:58,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:58,672] [INFO] Found 6/6 markers.
[2024-01-24 13:32:58,722] [INFO] Query marker FASTA was written to GCF_006539565.1_ASM653956v1_genomic.fna/markers.fasta
[2024-01-24 13:32:58,723] [INFO] Task started: Blastn
[2024-01-24 13:32:58,723] [INFO] Running command: blastn -query GCF_006539565.1_ASM653956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/reference_markers.fasta -out GCF_006539565.1_ASM653956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:00,214] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:00,217] [INFO] Selected 5 target genomes.
[2024-01-24 13:33:00,217] [INFO] Target genome list was writen to GCF_006539565.1_ASM653956v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:00,220] [INFO] Task started: fastANI
[2024-01-24 13:33:00,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg13669dd2-2031-4270-b526-dfa658937f56/GCF_006539565.1_ASM653956v1_genomic.fna.gz --refList GCF_006539565.1_ASM653956v1_genomic.fna/target_genomes.txt --output GCF_006539565.1_ASM653956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:10,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:10,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:10,551] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:10,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:10,551] [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 hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	100.0	1716	1723	95	conclusive
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	88.9929	1361	1723	95	below_threshold
Pseudonocardia abyssalis	strain=KRD168	GCA_019263705.2	2792008	2792008	type	True	88.2309	1363	1723	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	87.2024	1345	1723	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	87.0231	1344	1723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,555] [INFO] DFAST Taxonomy check result was written to GCF_006539565.1_ASM653956v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:10,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:10,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:10,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/checkm_data
[2024-01-24 13:33:10,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:10,618] [INFO] Task started: CheckM
[2024-01-24 13:33:10,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539565.1_ASM653956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539565.1_ASM653956v1_genomic.fna/checkm_input GCF_006539565.1_ASM653956v1_genomic.fna/checkm_result
[2024-01-24 13:34:16,960] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:16,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:16,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:16,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:16,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539565.1_ASM653956v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:16,986] [INFO] Task started: Blastn
[2024-01-24 13:34:16,986] [INFO] Running command: blastn -query GCF_006539565.1_ASM653956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc91d926c-f9fa-4f94-a223-ae55c3aa666c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539565.1_ASM653956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:19,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:19,145] [INFO] Selected 5 target genomes.
[2024-01-24 13:34:19,145] [INFO] Target genome list was writen to GCF_006539565.1_ASM653956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:19,156] [INFO] Task started: fastANI
[2024-01-24 13:34:19,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg13669dd2-2031-4270-b526-dfa658937f56/GCF_006539565.1_ASM653956v1_genomic.fna.gz --refList GCF_006539565.1_ASM653956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539565.1_ASM653956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:29,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:29,130] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:29,130] [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_006539565.1	s__Pseudonocardia hydrocarbonoxydans	100.0	1716	1723	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_014235185.1	s__Pseudonocardia sp014235185	88.9729	1363	1723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263705.1	s__Pseudonocardia sp019263705	88.2306	1363	1723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013155125.1	s__Pseudonocardia broussonetiae	87.1747	1348	1723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263585.1	s__Pseudonocardia sp019263585	87.0187	1344	1723	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 13:34:29,132] [INFO] GTDB search result was written to GCF_006539565.1_ASM653956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:29,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:29,135] [INFO] DFAST_QC result json was written to GCF_006539565.1_ASM653956v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:29,135] [INFO] DFAST_QC completed!
[2024-01-24 13:34:29,135] [INFO] Total running time: 0h1m47s