[2024-01-24 11:51:10,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference
[2024-01-24 11:51:12,023] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,024] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,024] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7871105-eaf9-454c-a27c-5521d15a0ed6/GCF_021343995.1_ASM2134399v1_genomic.fna.gz | prodigal -d GCF_021343995.1_ASM2134399v1_genomic.fna/cds.fna -a GCF_021343995.1_ASM2134399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:31,146] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:31,146] [INFO] Task started: HMMsearch
[2024-01-24 11:51:31,146] [INFO] Running command: hmmsearch --tblout GCF_021343995.1_ASM2134399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/reference_markers.hmm GCF_021343995.1_ASM2134399v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:31,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:31,493] [INFO] Found 6/6 markers.
[2024-01-24 11:51:31,550] [INFO] Query marker FASTA was written to GCF_021343995.1_ASM2134399v1_genomic.fna/markers.fasta
[2024-01-24 11:51:31,551] [INFO] Task started: Blastn
[2024-01-24 11:51:31,551] [INFO] Running command: blastn -query GCF_021343995.1_ASM2134399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/reference_markers.fasta -out GCF_021343995.1_ASM2134399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:32,823] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:32,826] [INFO] Selected 7 target genomes.
[2024-01-24 11:51:32,826] [INFO] Target genome list was writen to GCF_021343995.1_ASM2134399v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:32,836] [INFO] Task started: fastANI
[2024-01-24 11:51:32,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7871105-eaf9-454c-a27c-5521d15a0ed6/GCF_021343995.1_ASM2134399v1_genomic.fna.gz --refList GCF_021343995.1_ASM2134399v1_genomic.fna/target_genomes.txt --output GCF_021343995.1_ASM2134399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,295] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,304] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:46,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:46,304] [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 terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	100.0	2401	2412	95	conclusive
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	92.3434	1781	2412	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	83.7514	870	2412	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	83.0202	1274	2412	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	80.1301	1208	2412	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	79.711	1144	2412	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.6113	1072	2412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,307] [INFO] DFAST Taxonomy check result was written to GCF_021343995.1_ASM2134399v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/checkm_data
[2024-01-24 11:51:46,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,375] [INFO] Task started: CheckM
[2024-01-24 11:51:46,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021343995.1_ASM2134399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021343995.1_ASM2134399v1_genomic.fna/checkm_input GCF_021343995.1_ASM2134399v1_genomic.fna/checkm_result
[2024-01-24 11:53:17,141] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:17,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:17,162] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:17,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:17,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021343995.1_ASM2134399v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:17,163] [INFO] Task started: Blastn
[2024-01-24 11:53:17,163] [INFO] Running command: blastn -query GCF_021343995.1_ASM2134399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d0d13a4-fdc0-41eb-b026-579776ceecfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_021343995.1_ASM2134399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:19,018] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:19,021] [INFO] Selected 15 target genomes.
[2024-01-24 11:53:19,022] [INFO] Target genome list was writen to GCF_021343995.1_ASM2134399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:19,047] [INFO] Task started: fastANI
[2024-01-24 11:53:19,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7871105-eaf9-454c-a27c-5521d15a0ed6/GCF_021343995.1_ASM2134399v1_genomic.fna.gz --refList GCF_021343995.1_ASM2134399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021343995.1_ASM2134399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:44,106] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:44,118] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:44,118] [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_000717175.1	s__Pseudonocardia autotrophica_A	90.8231	1901	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102195.1	s__Pseudonocardia oroxyli	83.0153	1277	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	80.5057	1019	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	80.3028	1084	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263595.1	s__Pseudonocardia sp019263595	80.1526	1027	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	80.1521	1202	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCA_001725415.1	s__Pseudonocardia sp001725415	80.0377	1176	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCA_002813375.1	s__Pseudonocardia alni	79.9272	1075	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001420995.1	s__Pseudonocardia sp001420995	79.8265	1160	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_001294645.1	s__Pseudonocardia sp001294645	79.7606	1057	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	79.6903	1148	2412	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	79.5211	988	2412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	79.4509	1099	2412	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	79.3537	1192	2412	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	79.3206	1152	2412	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 11:53:44,120] [INFO] GTDB search result was written to GCF_021343995.1_ASM2134399v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:44,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:44,123] [INFO] DFAST_QC result json was written to GCF_021343995.1_ASM2134399v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:44,124] [INFO] DFAST_QC completed!
[2024-01-24 11:53:44,124] [INFO] Total running time: 0h2m33s