[2024-01-24 11:59:22,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference
[2024-01-24 11:59:25,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,642] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgadc3f4b4-2822-447a-954f-d4859648c028/GCF_001613305.1_ASM161330v1_genomic.fna.gz | prodigal -d GCF_001613305.1_ASM161330v1_genomic.fna/cds.fna -a GCF_001613305.1_ASM161330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:00,533] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:00,534] [INFO] Task started: HMMsearch
[2024-01-24 12:00:00,534] [INFO] Running command: hmmsearch --tblout GCF_001613305.1_ASM161330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/reference_markers.hmm GCF_001613305.1_ASM161330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:00,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:00,900] [INFO] Found 6/6 markers.
[2024-01-24 12:00:00,972] [INFO] Query marker FASTA was written to GCF_001613305.1_ASM161330v1_genomic.fna/markers.fasta
[2024-01-24 12:00:00,973] [INFO] Task started: Blastn
[2024-01-24 12:00:00,973] [INFO] Running command: blastn -query GCF_001613305.1_ASM161330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/reference_markers.fasta -out GCF_001613305.1_ASM161330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:02,158] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:02,161] [INFO] Selected 6 target genomes.
[2024-01-24 12:00:02,162] [INFO] Target genome list was writen to GCF_001613305.1_ASM161330v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:02,169] [INFO] Task started: fastANI
[2024-01-24 12:00:02,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgadc3f4b4-2822-447a-954f-d4859648c028/GCF_001613305.1_ASM161330v1_genomic.fna.gz --refList GCF_001613305.1_ASM161330v1_genomic.fna/target_genomes.txt --output GCF_001613305.1_ASM161330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:17,111] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:17,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:17,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:17,122] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:17,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:17,122] [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
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	100.0	3002	3007	95	conclusive
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	89.2733	2133	3007	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	89.0232	2207	3007	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	88.6667	2042	3007	95	below_threshold
Nocardia macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	87.1531	1946	3007	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	82.4212	1525	3007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:17,124] [INFO] DFAST Taxonomy check result was written to GCF_001613305.1_ASM161330v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:17,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:17,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:17,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/checkm_data
[2024-01-24 12:00:17,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:17,211] [INFO] Task started: CheckM
[2024-01-24 12:00:17,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613305.1_ASM161330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613305.1_ASM161330v1_genomic.fna/checkm_input GCF_001613305.1_ASM161330v1_genomic.fna/checkm_result
[2024-01-24 12:01:55,587] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:55,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:55,656] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:55,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:55,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613305.1_ASM161330v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:55,657] [INFO] Task started: Blastn
[2024-01-24 12:01:55,657] [INFO] Running command: blastn -query GCF_001613305.1_ASM161330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cc0faac-f72b-460f-9ec9-ae5ebfeacdc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613305.1_ASM161330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:57,473] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:57,477] [INFO] Selected 9 target genomes.
[2024-01-24 12:01:57,477] [INFO] Target genome list was writen to GCF_001613305.1_ASM161330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:57,485] [INFO] Task started: fastANI
[2024-01-24 12:01:57,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgadc3f4b4-2822-447a-954f-d4859648c028/GCF_001613305.1_ASM161330v1_genomic.fna.gz --refList GCF_001613305.1_ASM161330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613305.1_ASM161330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:16,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:16,722] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:16,722] [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_001613305.1	s__Nocardia vaccinii	100.0	3002	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000308615.1	s__Nocardia jiangxiensis	89.274	2133	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	88.6843	2038	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604405.1	s__Nocardia sp009604405	87.1534	1947	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860155.1	s__Nocardia sp018860155	82.4004	1527	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013186535.1	s__Nocardia terpenica	81.0744	1248	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
GCF_000526215.1	s__Nocardia sp000526215	80.7429	1319	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523235.1	s__Nocardia nova_A	80.5408	1242	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354405.1	s__Nocardia sp015354405	80.4748	1193	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:16,724] [INFO] GTDB search result was written to GCF_001613305.1_ASM161330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:16,724] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:16,727] [INFO] DFAST_QC result json was written to GCF_001613305.1_ASM161330v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:16,727] [INFO] DFAST_QC completed!
[2024-01-24 12:02:16,727] [INFO] Total running time: 0h2m54s