[2024-01-24 12:09:05,773] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference
[2024-01-24 12:09:06,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,996] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg4db226fb-64ef-4d7f-bfad-77840e746591/GCF_019263585.2_ASM1926358v2_genomic.fna.gz | prodigal -d GCF_019263585.2_ASM1926358v2_genomic.fna/cds.fna -a GCF_019263585.2_ASM1926358v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:25,435] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:25,436] [INFO] Task started: HMMsearch
[2024-01-24 12:09:25,436] [INFO] Running command: hmmsearch --tblout GCF_019263585.2_ASM1926358v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/reference_markers.hmm GCF_019263585.2_ASM1926358v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:25,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:25,756] [INFO] Found 6/6 markers.
[2024-01-24 12:09:25,809] [INFO] Query marker FASTA was written to GCF_019263585.2_ASM1926358v2_genomic.fna/markers.fasta
[2024-01-24 12:09:25,809] [INFO] Task started: Blastn
[2024-01-24 12:09:25,809] [INFO] Running command: blastn -query GCF_019263585.2_ASM1926358v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/reference_markers.fasta -out GCF_019263585.2_ASM1926358v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:27,157] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:27,161] [INFO] Selected 6 target genomes.
[2024-01-24 12:09:27,162] [INFO] Target genome list was writen to GCF_019263585.2_ASM1926358v2_genomic.fna/target_genomes.txt
[2024-01-24 12:09:27,165] [INFO] Task started: fastANI
[2024-01-24 12:09:27,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db226fb-64ef-4d7f-bfad-77840e746591/GCF_019263585.2_ASM1926358v2_genomic.fna.gz --refList GCF_019263585.2_ASM1926358v2_genomic.fna/target_genomes.txt --output GCF_019263585.2_ASM1926358v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:40,723] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:40,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:40,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:40,733] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:40,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:40,733] [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 oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	100.0	2262	2273	95	conclusive
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	93.7376	1810	2273	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	87.9127	1576	2273	95	below_threshold
Pseudonocardia abyssalis	strain=KRD168	GCA_019263705.2	2792008	2792008	type	True	87.4345	1550	2273	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	86.93	1365	2273	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	80.5079	1216	2273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:40,734] [INFO] DFAST Taxonomy check result was written to GCF_019263585.2_ASM1926358v2_genomic.fna/tc_result.tsv
[2024-01-24 12:09:40,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:40,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:40,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/checkm_data
[2024-01-24 12:09:40,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:40,798] [INFO] Task started: CheckM
[2024-01-24 12:09:40,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019263585.2_ASM1926358v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019263585.2_ASM1926358v2_genomic.fna/checkm_input GCF_019263585.2_ASM1926358v2_genomic.fna/checkm_result
[2024-01-24 12:11:29,057] [INFO] Task succeeded: CheckM
[2024-01-24 12:11:29,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:11:29,087] [INFO] ===== Completeness check finished =====
[2024-01-24 12:11:29,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:11:29,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019263585.2_ASM1926358v2_genomic.fna/markers.fasta)
[2024-01-24 12:11:29,089] [INFO] Task started: Blastn
[2024-01-24 12:11:29,089] [INFO] Running command: blastn -query GCF_019263585.2_ASM1926358v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg312fa1c3-f940-419e-84ad-9f14f98ef0fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_019263585.2_ASM1926358v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:11:31,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:11:31,195] [INFO] Selected 6 target genomes.
[2024-01-24 12:11:31,195] [INFO] Target genome list was writen to GCF_019263585.2_ASM1926358v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:11:31,243] [INFO] Task started: fastANI
[2024-01-24 12:11:31,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db226fb-64ef-4d7f-bfad-77840e746591/GCF_019263585.2_ASM1926358v2_genomic.fna.gz --refList GCF_019263585.2_ASM1926358v2_genomic.fna/target_genomes_gtdb.txt --output GCF_019263585.2_ASM1926358v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:11:44,477] [INFO] Task succeeded: fastANI
[2024-01-24 12:11:44,489] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:11:44,489] [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
GCA_019263585.1	s__Pseudonocardia sp019263585	100.0	2265	2273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	conclusive
GCF_013155125.1	s__Pseudonocardia broussonetiae	93.7058	1813	2273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235185.1	s__Pseudonocardia sp014235185	87.9511	1570	2273	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	87.5035	1544	2273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	86.8678	1372	2273	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	80.4575	1227	2273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:11:44,491] [INFO] GTDB search result was written to GCF_019263585.2_ASM1926358v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:11:44,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:11:44,494] [INFO] DFAST_QC result json was written to GCF_019263585.2_ASM1926358v2_genomic.fna/dqc_result.json
[2024-01-24 12:11:44,494] [INFO] DFAST_QC completed!
[2024-01-24 12:11:44,494] [INFO] Total running time: 0h2m39s