[2024-01-24 14:14:02,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:02,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:02,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference
[2024-01-24 14:14:03,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:03,753] [INFO] Task started: Prodigal
[2024-01-24 14:14:03,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f3e1d8e-dc23-49ff-b977-b5ec24fe1c73/GCF_014191445.1_ASM1419144v1_genomic.fna.gz | prodigal -d GCF_014191445.1_ASM1419144v1_genomic.fna/cds.fna -a GCF_014191445.1_ASM1419144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:10,532] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:10,532] [INFO] Task started: HMMsearch
[2024-01-24 14:14:10,532] [INFO] Running command: hmmsearch --tblout GCF_014191445.1_ASM1419144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/reference_markers.hmm GCF_014191445.1_ASM1419144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:10,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:10,777] [INFO] Found 6/6 markers.
[2024-01-24 14:14:10,799] [INFO] Query marker FASTA was written to GCF_014191445.1_ASM1419144v1_genomic.fna/markers.fasta
[2024-01-24 14:14:10,799] [INFO] Task started: Blastn
[2024-01-24 14:14:10,799] [INFO] Running command: blastn -query GCF_014191445.1_ASM1419144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/reference_markers.fasta -out GCF_014191445.1_ASM1419144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:11,718] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:11,722] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:11,722] [INFO] Target genome list was writen to GCF_014191445.1_ASM1419144v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:11,756] [INFO] Task started: fastANI
[2024-01-24 14:14:11,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f3e1d8e-dc23-49ff-b977-b5ec24fe1c73/GCF_014191445.1_ASM1419144v1_genomic.fna.gz --refList GCF_014191445.1_ASM1419144v1_genomic.fna/target_genomes.txt --output GCF_014191445.1_ASM1419144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:22,295] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:22,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:22,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:22,309] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:22,309] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:22,309] [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
Trueperella pyogenes	strain=DSM 20630	GCA_014191445.1	1661	1661	type	True	100.0	708	715	95	conclusive
Trueperella pyogenes	strain=NCTC5224	GCA_900460345.1	1661	1661	type	True	99.9997	699	715	95	conclusive
Trueperella pecoris	strain=19M2397	GCA_014926385.1	2733571	2733571	type	True	81.1643	326	715	95	below_threshold
Trueperella bernardiae	strain=LCDC 89-0504	GCA_001469025.1	59561	59561	type	True	79.5715	307	715	95	below_threshold
Trueperella bialowiezensis	strain=NCTC13354	GCA_900637955.1	312285	312285	type	True	77.8741	129	715	95	below_threshold
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	77.4381	77	715	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	76.7469	65	715	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	76.7337	63	715	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.6156	73	715	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	76.4847	67	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:22,311] [INFO] DFAST Taxonomy check result was written to GCF_014191445.1_ASM1419144v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:22,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:22,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:22,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/checkm_data
[2024-01-24 14:14:22,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:22,340] [INFO] Task started: CheckM
[2024-01-24 14:14:22,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191445.1_ASM1419144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191445.1_ASM1419144v1_genomic.fna/checkm_input GCF_014191445.1_ASM1419144v1_genomic.fna/checkm_result
[2024-01-24 14:14:47,433] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:47,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,455] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:47,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:47,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191445.1_ASM1419144v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:47,456] [INFO] Task started: Blastn
[2024-01-24 14:14:47,456] [INFO] Running command: blastn -query GCF_014191445.1_ASM1419144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fab81a4-3802-41c7-af4f-adf74d455d34/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191445.1_ASM1419144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:48,674] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:48,678] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:48,679] [INFO] Target genome list was writen to GCF_014191445.1_ASM1419144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:48,719] [INFO] Task started: fastANI
[2024-01-24 14:14:48,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f3e1d8e-dc23-49ff-b977-b5ec24fe1c73/GCF_014191445.1_ASM1419144v1_genomic.fna.gz --refList GCF_014191445.1_ASM1419144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191445.1_ASM1419144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:58,870] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:58,879] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:58,879] [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_900460345.1	s__Trueperella pyogenes	99.9997	699	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	98.61	97.91	0.94	0.87	20	conclusive
GCF_014926385.1	s__Trueperella pecoris	81.1381	325	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	97.88	95.38	0.92	0.88	4	-
GCF_001469025.1	s__Trueperella bernardiae	79.5882	306	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCF_900637955.1	s__Trueperella bialowiezensis	77.9582	131	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814705.1	s__Georgenia muralis	77.4957	73	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	77.4284	77	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595995.2	s__Actinomyces sp011751985	77.0558	67	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_003991205.1	s__Georgenia sp003991205	76.6029	64	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193155.1	s__Georgenia subflava	76.5096	67	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	76.4598	69	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:58,882] [INFO] GTDB search result was written to GCF_014191445.1_ASM1419144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:58,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:58,888] [INFO] DFAST_QC result json was written to GCF_014191445.1_ASM1419144v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:58,888] [INFO] DFAST_QC completed!
[2024-01-24 14:14:58,889] [INFO] Total running time: 0h0m56s