[2024-01-24 14:30:30,202] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,205] [INFO] DQC Reference Directory: /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference
[2024-01-24 14:30:31,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,598] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,598] [INFO] Running command: gunzip -c /var/lib/cwl/stga8e414df-7707-4f61-af47-5017319a606f/GCF_007994075.1_ASM799407v1_genomic.fna.gz | prodigal -d GCF_007994075.1_ASM799407v1_genomic.fna/cds.fna -a GCF_007994075.1_ASM799407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:02,293] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:02,293] [INFO] Task started: HMMsearch
[2024-01-24 14:31:02,293] [INFO] Running command: hmmsearch --tblout GCF_007994075.1_ASM799407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/reference_markers.hmm GCF_007994075.1_ASM799407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:02,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:02,724] [INFO] Found 6/6 markers.
[2024-01-24 14:31:02,795] [INFO] Query marker FASTA was written to GCF_007994075.1_ASM799407v1_genomic.fna/markers.fasta
[2024-01-24 14:31:02,796] [INFO] Task started: Blastn
[2024-01-24 14:31:02,796] [INFO] Running command: blastn -query GCF_007994075.1_ASM799407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/reference_markers.fasta -out GCF_007994075.1_ASM799407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:04,310] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:04,313] [INFO] Selected 8 target genomes.
[2024-01-24 14:31:04,314] [INFO] Target genome list was writen to GCF_007994075.1_ASM799407v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:04,320] [INFO] Task started: fastANI
[2024-01-24 14:31:04,320] [INFO] Running command: fastANI --query /var/lib/cwl/stga8e414df-7707-4f61-af47-5017319a606f/GCF_007994075.1_ASM799407v1_genomic.fna.gz --refList GCF_007994075.1_ASM799407v1_genomic.fna/target_genomes.txt --output GCF_007994075.1_ASM799407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:23,987] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:23,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:23,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:23,996] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:23,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:23,996] [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 hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	100.0	2952	2952	95	conclusive
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	89.0471	2184	2952	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	84.1427	1780	2952	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	81.7703	1368	2952	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	81.431	1324	2952	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	80.7346	1412	2952	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	80.4344	1209	2952	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.2701	1253	2952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:23,998] [INFO] DFAST Taxonomy check result was written to GCF_007994075.1_ASM799407v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:23,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:23,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:23,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/checkm_data
[2024-01-24 14:31:24,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:24,089] [INFO] Task started: CheckM
[2024-01-24 14:31:24,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007994075.1_ASM799407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007994075.1_ASM799407v1_genomic.fna/checkm_input GCF_007994075.1_ASM799407v1_genomic.fna/checkm_result
[2024-01-24 14:33:37,441] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:37,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:37,463] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:37,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:37,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007994075.1_ASM799407v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:37,464] [INFO] Task started: Blastn
[2024-01-24 14:33:37,464] [INFO] Running command: blastn -query GCF_007994075.1_ASM799407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd25217-d2ad-4146-85bf-e0bc987db7ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_007994075.1_ASM799407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:39,586] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:39,596] [INFO] Selected 8 target genomes.
[2024-01-24 14:33:39,596] [INFO] Target genome list was writen to GCF_007994075.1_ASM799407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:39,615] [INFO] Task started: fastANI
[2024-01-24 14:33:39,616] [INFO] Running command: fastANI --query /var/lib/cwl/stga8e414df-7707-4f61-af47-5017319a606f/GCF_007994075.1_ASM799407v1_genomic.fna.gz --refList GCF_007994075.1_ASM799407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007994075.1_ASM799407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:58,527] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:58,535] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:58,535] [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_007994075.1	s__Pseudonocardia hierapolitana	100.0	2951	2952	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_006717045.1	s__Pseudonocardia cypriaca	89.0479	2184	2952	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	87.0525	2000	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	84.14	1779	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262885.1	s__Pseudonocardia sp002262885	83.7689	1830	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911925.1	s__Pseudonocardia xinjiangensis	81.4395	1323	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	80.5025	1107	2952	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	80.2494	1258	2952	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 14:33:58,537] [INFO] GTDB search result was written to GCF_007994075.1_ASM799407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:58,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:58,543] [INFO] DFAST_QC result json was written to GCF_007994075.1_ASM799407v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:58,543] [INFO] DFAST_QC completed!
[2024-01-24 14:33:58,543] [INFO] Total running time: 0h3m28s