[2024-01-25 20:18:05,927] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:05,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:05,928] [INFO] DQC Reference Directory: /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference
[2024-01-25 20:18:07,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:07,077] [INFO] Task started: Prodigal
[2024-01-25 20:18:07,078] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb60845b-1625-4d8b-a879-ed346ea28b1b/GCF_027922425.1_ASM2792242v1_genomic.fna.gz | prodigal -d GCF_027922425.1_ASM2792242v1_genomic.fna/cds.fna -a GCF_027922425.1_ASM2792242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:26,081] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:26,081] [INFO] Task started: HMMsearch
[2024-01-25 20:18:26,082] [INFO] Running command: hmmsearch --tblout GCF_027922425.1_ASM2792242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/reference_markers.hmm GCF_027922425.1_ASM2792242v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:26,410] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:26,411] [INFO] Found 6/6 markers.
[2024-01-25 20:18:26,475] [INFO] Query marker FASTA was written to GCF_027922425.1_ASM2792242v1_genomic.fna/markers.fasta
[2024-01-25 20:18:26,475] [INFO] Task started: Blastn
[2024-01-25 20:18:26,475] [INFO] Running command: blastn -query GCF_027922425.1_ASM2792242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/reference_markers.fasta -out GCF_027922425.1_ASM2792242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:27,752] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:27,755] [INFO] Selected 13 target genomes.
[2024-01-25 20:18:27,755] [INFO] Target genome list was writen to GCF_027922425.1_ASM2792242v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:27,762] [INFO] Task started: fastANI
[2024-01-25 20:18:27,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb60845b-1625-4d8b-a879-ed346ea28b1b/GCF_027922425.1_ASM2792242v1_genomic.fna.gz --refList GCF_027922425.1_ASM2792242v1_genomic.fna/target_genomes.txt --output GCF_027922425.1_ASM2792242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:52,810] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:52,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:52,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:52,819] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:52,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:52,819] [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 kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	90.8805	1814	2572	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	90.8616	1891	2572	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	83.8213	920	2572	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	83.448	1312	2572	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	80.2923	1209	2572	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	80.2123	1117	2572	95	below_threshold
Pseudonocardia sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	80.1887	1190	2572	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.1548	1221	2572	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	79.9575	1104	2572	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	79.5418	1248	2572	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.5371	1137	2572	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	79.3331	1185	2572	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	79.2333	1064	2572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:52,821] [INFO] DFAST Taxonomy check result was written to GCF_027922425.1_ASM2792242v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:52,821] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:52,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:52,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/checkm_data
[2024-01-25 20:18:52,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:52,895] [INFO] Task started: CheckM
[2024-01-25 20:18:52,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922425.1_ASM2792242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922425.1_ASM2792242v1_genomic.fna/checkm_input GCF_027922425.1_ASM2792242v1_genomic.fna/checkm_result
[2024-01-25 20:20:40,774] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:40,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:40,823] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:40,823] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:40,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922425.1_ASM2792242v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:40,824] [INFO] Task started: Blastn
[2024-01-25 20:20:40,824] [INFO] Running command: blastn -query GCF_027922425.1_ASM2792242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefa6209-4c21-44e5-b1ff-87fd6fea4ff5/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922425.1_ASM2792242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:42,764] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:42,768] [INFO] Selected 19 target genomes.
[2024-01-25 20:20:42,768] [INFO] Target genome list was writen to GCF_027922425.1_ASM2792242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:42,781] [INFO] Task started: fastANI
[2024-01-25 20:20:42,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb60845b-1625-4d8b-a879-ed346ea28b1b/GCF_027922425.1_ASM2792242v1_genomic.fna.gz --refList GCF_027922425.1_ASM2792242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922425.1_ASM2792242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:16,850] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:16,861] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:16,861] [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	99.9825	2566	2572	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_900102195.1	s__Pseudonocardia oroxyli	83.376	1324	2572	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	80.5465	1025	2572	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	80.2408	1215	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCA_019263595.1	s__Pseudonocardia sp019263595	80.2348	1041	2572	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	80.1758	1216	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCF_002583555.1	s__Pseudonocardia sp002583555	80.1703	1128	2572	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	80.1346	1134	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725415.1	s__Pseudonocardia sp001725415	80.0675	1213	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCF_014267175.1	s__Pseudonocardia sp014267175	79.9052	1059	2572	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	79.652	1182	2572	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	79.6395	1093	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
GCA_001942415.1	s__Pseudonocardia sp001942415	79.6276	1101	2572	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	79.4943	1260	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698125.1	s__Pseudonocardia sp001698125	79.4666	1066	2572	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	79.3607	1181	2572	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	79.3458	1164	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	79.3319	1161	2572	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	79.2867	1199	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:16,863] [INFO] GTDB search result was written to GCF_027922425.1_ASM2792242v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:16,863] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:16,868] [INFO] DFAST_QC result json was written to GCF_027922425.1_ASM2792242v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:16,869] [INFO] DFAST_QC completed!
[2024-01-25 20:21:16,869] [INFO] Total running time: 0h3m11s