[2024-01-24 14:53:50,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference
[2024-01-24 14:53:51,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,636] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg0895747d-96fa-47d3-b2be-fd0b19d00ff3/GCF_003945385.1_ASM394538v1_genomic.fna.gz | prodigal -d GCF_003945385.1_ASM394538v1_genomic.fna/cds.fna -a GCF_003945385.1_ASM394538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:18,678] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:18,679] [INFO] Task started: HMMsearch
[2024-01-24 14:54:18,679] [INFO] Running command: hmmsearch --tblout GCF_003945385.1_ASM394538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/reference_markers.hmm GCF_003945385.1_ASM394538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:19,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:19,027] [INFO] Found 6/6 markers.
[2024-01-24 14:54:19,085] [INFO] Query marker FASTA was written to GCF_003945385.1_ASM394538v1_genomic.fna/markers.fasta
[2024-01-24 14:54:19,085] [INFO] Task started: Blastn
[2024-01-24 14:54:19,085] [INFO] Running command: blastn -query GCF_003945385.1_ASM394538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/reference_markers.fasta -out GCF_003945385.1_ASM394538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:20,438] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:20,442] [INFO] Selected 6 target genomes.
[2024-01-24 14:54:20,442] [INFO] Target genome list was writen to GCF_003945385.1_ASM394538v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:20,446] [INFO] Task started: fastANI
[2024-01-24 14:54:20,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg0895747d-96fa-47d3-b2be-fd0b19d00ff3/GCF_003945385.1_ASM394538v1_genomic.fna.gz --refList GCF_003945385.1_ASM394538v1_genomic.fna/target_genomes.txt --output GCF_003945385.1_ASM394538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:35,056] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:35,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:35,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:35,063] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:54:35,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:35,064] [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 autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	100.0	2510	2511	95	conclusive
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	99.9952	2508	2511	95	conclusive
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	99.9489	2392	2511	95	conclusive
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	84.8343	1535	2511	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	84.7072	1509	2511	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	84.2575	1425	2511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:35,065] [INFO] DFAST Taxonomy check result was written to GCF_003945385.1_ASM394538v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:35,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:35,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:35,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/checkm_data
[2024-01-24 14:54:35,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:35,140] [INFO] Task started: CheckM
[2024-01-24 14:54:35,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003945385.1_ASM394538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003945385.1_ASM394538v1_genomic.fna/checkm_input GCF_003945385.1_ASM394538v1_genomic.fna/checkm_result
[2024-01-24 14:57:10,589] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:10,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:10,610] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:10,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:10,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003945385.1_ASM394538v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:10,612] [INFO] Task started: Blastn
[2024-01-24 14:57:10,612] [INFO] Running command: blastn -query GCF_003945385.1_ASM394538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg536026bc-4d26-48c8-be66-ce0dd4c6042c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003945385.1_ASM394538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:12,715] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:12,718] [INFO] Selected 8 target genomes.
[2024-01-24 14:57:12,718] [INFO] Target genome list was writen to GCF_003945385.1_ASM394538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:12,726] [INFO] Task started: fastANI
[2024-01-24 14:57:12,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg0895747d-96fa-47d3-b2be-fd0b19d00ff3/GCF_003945385.1_ASM394538v1_genomic.fna.gz --refList GCF_003945385.1_ASM394538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003945385.1_ASM394538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:32,318] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:32,326] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:32,326] [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_003945385.1	s__Pseudonocardia autotrophica	100.0	2510	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_017876315.1	s__Pseudonocardia parietis	84.8225	1537	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	84.6247	1522	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420995.1	s__Pseudonocardia sp001420995	84.3734	1495	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_014267175.1	s__Pseudonocardia sp014267175	84.1815	1314	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813375.1	s__Pseudonocardia alni	83.9809	1447	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001294645.1	s__Pseudonocardia sp001294645	83.7421	1397	2511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
GCF_001698125.1	s__Pseudonocardia sp001698125	83.6856	1355	2511	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 14:57:32,328] [INFO] GTDB search result was written to GCF_003945385.1_ASM394538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:32,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:32,331] [INFO] DFAST_QC result json was written to GCF_003945385.1_ASM394538v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:32,332] [INFO] DFAST_QC completed!
[2024-01-24 14:57:32,332] [INFO] Total running time: 0h3m42s