[2024-01-24 14:19:14,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:14,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:14,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference
[2024-01-24 14:19:15,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:15,994] [INFO] Task started: Prodigal
[2024-01-24 14:19:15,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg6df9974c-5966-46ec-a54b-c3952dbdc239/GCF_006539585.1_ASM653958v1_genomic.fna.gz | prodigal -d GCF_006539585.1_ASM653958v1_genomic.fna/cds.fna -a GCF_006539585.1_ASM653958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:35,402] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:35,402] [INFO] Task started: HMMsearch
[2024-01-24 14:19:35,402] [INFO] Running command: hmmsearch --tblout GCF_006539585.1_ASM653958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/reference_markers.hmm GCF_006539585.1_ASM653958v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:35,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:35,683] [INFO] Found 6/6 markers.
[2024-01-24 14:19:35,737] [INFO] Query marker FASTA was written to GCF_006539585.1_ASM653958v1_genomic.fna/markers.fasta
[2024-01-24 14:19:35,738] [INFO] Task started: Blastn
[2024-01-24 14:19:35,738] [INFO] Running command: blastn -query GCF_006539585.1_ASM653958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/reference_markers.fasta -out GCF_006539585.1_ASM653958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:36,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:36,976] [INFO] Selected 6 target genomes.
[2024-01-24 14:19:36,976] [INFO] Target genome list was writen to GCF_006539585.1_ASM653958v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:36,993] [INFO] Task started: fastANI
[2024-01-24 14:19:36,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df9974c-5966-46ec-a54b-c3952dbdc239/GCF_006539585.1_ASM653958v1_genomic.fna.gz --refList GCF_006539585.1_ASM653958v1_genomic.fna/target_genomes.txt --output GCF_006539585.1_ASM653958v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:49,959] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:49,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:49,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:49,968] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:49,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:49,969] [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	99.9977	2354	2355	95	conclusive
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	99.9961	2355	2355	95	conclusive
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	99.9918	2340	2355	95	conclusive
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	84.8645	1469	2355	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	84.664	1473	2355	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	84.278	1400	2355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:49,971] [INFO] DFAST Taxonomy check result was written to GCF_006539585.1_ASM653958v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:49,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:49,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:49,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/checkm_data
[2024-01-24 14:19:49,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:50,046] [INFO] Task started: CheckM
[2024-01-24 14:19:50,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539585.1_ASM653958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539585.1_ASM653958v1_genomic.fna/checkm_input GCF_006539585.1_ASM653958v1_genomic.fna/checkm_result
[2024-01-24 14:21:22,057] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:22,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:22,080] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:22,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:22,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539585.1_ASM653958v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:22,081] [INFO] Task started: Blastn
[2024-01-24 14:21:22,081] [INFO] Running command: blastn -query GCF_006539585.1_ASM653958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bcb5d35-baef-4a85-ae71-62805654f198/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539585.1_ASM653958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:23,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:23,901] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:23,902] [INFO] Target genome list was writen to GCF_006539585.1_ASM653958v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:23,912] [INFO] Task started: fastANI
[2024-01-24 14:21:23,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df9974c-5966-46ec-a54b-c3952dbdc239/GCF_006539585.1_ASM653958v1_genomic.fna.gz --refList GCF_006539585.1_ASM653958v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539585.1_ASM653958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:40,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:40,082] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:40,082] [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	99.9977	2354	2355	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	84.8277	1474	2355	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	84.662	1473	2355	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	84.258	1460	2355	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	84.133	1279	2355	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	84.1094	1377	2355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001698125.1	s__Pseudonocardia sp001698125	83.5548	1331	2355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294645.1	s__Pseudonocardia sp001294645	83.5235	1363	2355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:40,084] [INFO] GTDB search result was written to GCF_006539585.1_ASM653958v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:40,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:40,087] [INFO] DFAST_QC result json was written to GCF_006539585.1_ASM653958v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:40,087] [INFO] DFAST_QC completed!
[2024-01-24 14:21:40,087] [INFO] Total running time: 0h2m25s