[2024-01-24 12:31:34,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference
[2024-01-24 12:31:35,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,806] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg51edbbba-09d5-41aa-b5a8-4ca2cc3c7079/GCF_021283305.1_ASM2128330v1_genomic.fna.gz | prodigal -d GCF_021283305.1_ASM2128330v1_genomic.fna/cds.fna -a GCF_021283305.1_ASM2128330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:56,897] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:56,897] [INFO] Task started: HMMsearch
[2024-01-24 12:31:56,897] [INFO] Running command: hmmsearch --tblout GCF_021283305.1_ASM2128330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/reference_markers.hmm GCF_021283305.1_ASM2128330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:57,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:57,310] [INFO] Found 6/6 markers.
[2024-01-24 12:31:57,377] [INFO] Query marker FASTA was written to GCF_021283305.1_ASM2128330v1_genomic.fna/markers.fasta
[2024-01-24 12:31:57,378] [INFO] Task started: Blastn
[2024-01-24 12:31:57,378] [INFO] Running command: blastn -query GCF_021283305.1_ASM2128330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/reference_markers.fasta -out GCF_021283305.1_ASM2128330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:58,716] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:58,720] [INFO] Selected 9 target genomes.
[2024-01-24 12:31:58,720] [INFO] Target genome list was writen to GCF_021283305.1_ASM2128330v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:58,732] [INFO] Task started: fastANI
[2024-01-24 12:31:58,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg51edbbba-09d5-41aa-b5a8-4ca2cc3c7079/GCF_021283305.1_ASM2128330v1_genomic.fna.gz --refList GCF_021283305.1_ASM2128330v1_genomic.fna/target_genomes.txt --output GCF_021283305.1_ASM2128330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:16,046] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:16,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:16,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:16,058] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:16,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:16,059] [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	100.0	2625	2630	95	conclusive
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	92.3849	1790	2630	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	83.429	891	2630	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	83.1366	1355	2630	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	80.2379	1243	2630	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	79.9929	1100	2630	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.5602	1072	2630	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	79.4682	1225	2630	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	79.4455	1034	2630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:16,063] [INFO] DFAST Taxonomy check result was written to GCF_021283305.1_ASM2128330v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:16,064] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:16,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:16,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/checkm_data
[2024-01-24 12:32:16,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:16,143] [INFO] Task started: CheckM
[2024-01-24 12:32:16,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021283305.1_ASM2128330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021283305.1_ASM2128330v1_genomic.fna/checkm_input GCF_021283305.1_ASM2128330v1_genomic.fna/checkm_result
[2024-01-24 12:33:59,353] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:59,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:59,384] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:59,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:59,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021283305.1_ASM2128330v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:59,385] [INFO] Task started: Blastn
[2024-01-24 12:33:59,385] [INFO] Running command: blastn -query GCF_021283305.1_ASM2128330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b3d636-72ea-4d08-b23d-0233c8f9451d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021283305.1_ASM2128330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:01,332] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:01,336] [INFO] Selected 18 target genomes.
[2024-01-24 12:34:01,337] [INFO] Target genome list was writen to GCF_021283305.1_ASM2128330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:01,350] [INFO] Task started: fastANI
[2024-01-24 12:34:01,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg51edbbba-09d5-41aa-b5a8-4ca2cc3c7079/GCF_021283305.1_ASM2128330v1_genomic.fna.gz --refList GCF_021283305.1_ASM2128330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021283305.1_ASM2128330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:31,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:31,200] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:34:31,200] [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	90.9131	1861	2630	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	83.1074	1360	2630	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	80.41	1055	2630	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	80.2727	1236	2630	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	80.0785	1027	2630	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	80.0322	1092	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583555.1	s__Pseudonocardia sp002583555	80.0292	1073	2630	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	79.9535	1168	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCA_001899645.1	s__Pseudonocardia sp001899645	79.7753	1104	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.47	99.47	0.91	0.91	2	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	79.699	1132	2630	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	79.4646	1224	2630	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	79.3998	1045	2630	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	79.3907	1019	2630	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	79.2138	1160	2630	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	79.19	1197	2630	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	79.1446	1153	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	77.5328	755	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.5355	590	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:31,202] [INFO] GTDB search result was written to GCF_021283305.1_ASM2128330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:31,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:31,206] [INFO] DFAST_QC result json was written to GCF_021283305.1_ASM2128330v1_genomic.fna/dqc_result.json
[2024-01-24 12:34:31,206] [INFO] DFAST_QC completed!
[2024-01-24 12:34:31,207] [INFO] Total running time: 0h2m57s