[2024-01-24 13:56:26,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:26,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:26,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference
[2024-01-24 13:56:27,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:27,878] [INFO] Task started: Prodigal
[2024-01-24 13:56:27,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdbd710d-2db1-424a-aa07-168e917fd1ae/GCF_008704205.1_ASM870420v1_genomic.fna.gz | prodigal -d GCF_008704205.1_ASM870420v1_genomic.fna/cds.fna -a GCF_008704205.1_ASM870420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:13,327] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:13,327] [INFO] Task started: HMMsearch
[2024-01-24 13:57:13,327] [INFO] Running command: hmmsearch --tblout GCF_008704205.1_ASM870420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/reference_markers.hmm GCF_008704205.1_ASM870420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:13,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:13,736] [INFO] Found 6/6 markers.
[2024-01-24 13:57:13,832] [INFO] Query marker FASTA was written to GCF_008704205.1_ASM870420v1_genomic.fna/markers.fasta
[2024-01-24 13:57:13,833] [INFO] Task started: Blastn
[2024-01-24 13:57:13,833] [INFO] Running command: blastn -query GCF_008704205.1_ASM870420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/reference_markers.fasta -out GCF_008704205.1_ASM870420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:15,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:15,281] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:15,281] [INFO] Target genome list was writen to GCF_008704205.1_ASM870420v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:15,294] [INFO] Task started: fastANI
[2024-01-24 13:57:15,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbd710d-2db1-424a-aa07-168e917fd1ae/GCF_008704205.1_ASM870420v1_genomic.fna.gz --refList GCF_008704205.1_ASM870420v1_genomic.fna/target_genomes.txt --output GCF_008704205.1_ASM870420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:38,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:38,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:38,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:38,832] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:38,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:38,833] [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 colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	100.0	3304	3307	95	conclusive
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	87.3716	2259	3307	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	87.3026	2213	3307	95	below_threshold
Nocardia tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	87.0631	2287	3307	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	87.007	2060	3307	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	86.5324	2058	3307	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	85.1567	2105	3307	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	85.1024	2149	3307	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	82.1881	1418	3307	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	80.6897	1118	3307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:38,834] [INFO] DFAST Taxonomy check result was written to GCF_008704205.1_ASM870420v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:38,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:38,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:38,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/checkm_data
[2024-01-24 13:57:38,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:38,945] [INFO] Task started: CheckM
[2024-01-24 13:57:38,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704205.1_ASM870420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704205.1_ASM870420v1_genomic.fna/checkm_input GCF_008704205.1_ASM870420v1_genomic.fna/checkm_result
[2024-01-24 13:59:41,085] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:41,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:59:41,122] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:41,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:41,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704205.1_ASM870420v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:41,124] [INFO] Task started: Blastn
[2024-01-24 13:59:41,124] [INFO] Running command: blastn -query GCF_008704205.1_ASM870420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da1b741-f75f-4b50-9cfd-a86cb4a1cfd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704205.1_ASM870420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:43,100] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:43,104] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:43,104] [INFO] Target genome list was writen to GCF_008704205.1_ASM870420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:43,128] [INFO] Task started: fastANI
[2024-01-24 13:59:43,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbd710d-2db1-424a-aa07-168e917fd1ae/GCF_008704205.1_ASM870420v1_genomic.fna.gz --refList GCF_008704205.1_ASM870420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704205.1_ASM870420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:07,534] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:07,548] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:07,549] [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_008704205.1	s__Nocardia colli	100.0	3304	3307	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_900269665.1	s__Nocardia suismassiliense	87.3729	2259	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_007990755.1	s__Nocardia ninae	87.2954	2214	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_000308715.1	s__Nocardia tenerifensis	87.022	2059	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_019222765.1	s__Nocardia iowensis	86.519	2061	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	85.0963	2150	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_000710915.1	s__Nocardia brasiliensis_A	85.0319	2068	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_001612685.1	s__Nocardia altamirensis	85.03	2053	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	82.2134	1413	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612825.1	s__Nocardia caishijiensis	80.6767	1098	3307	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:07,566] [INFO] GTDB search result was written to GCF_008704205.1_ASM870420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:07,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:07,570] [INFO] DFAST_QC result json was written to GCF_008704205.1_ASM870420v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:07,570] [INFO] DFAST_QC completed!
[2024-01-24 14:00:07,570] [INFO] Total running time: 0h3m41s