[2024-01-24 14:05:16,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference
[2024-01-24 14:05:17,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,571] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg1329d86a-eda2-4875-b2d6-5529b566b71c/GCF_000308475.2_ASM30847v2_genomic.fna.gz | prodigal -d GCF_000308475.2_ASM30847v2_genomic.fna/cds.fna -a GCF_000308475.2_ASM30847v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:50,399] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:50,399] [INFO] Task started: HMMsearch
[2024-01-24 14:05:50,399] [INFO] Running command: hmmsearch --tblout GCF_000308475.2_ASM30847v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/reference_markers.hmm GCF_000308475.2_ASM30847v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:50,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:50,773] [INFO] Found 6/6 markers.
[2024-01-24 14:05:50,849] [INFO] Query marker FASTA was written to GCF_000308475.2_ASM30847v2_genomic.fna/markers.fasta
[2024-01-24 14:05:50,849] [INFO] Task started: Blastn
[2024-01-24 14:05:50,849] [INFO] Running command: blastn -query GCF_000308475.2_ASM30847v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/reference_markers.fasta -out GCF_000308475.2_ASM30847v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:52,108] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:52,112] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:52,113] [INFO] Target genome list was writen to GCF_000308475.2_ASM30847v2_genomic.fna/target_genomes.txt
[2024-01-24 14:05:52,120] [INFO] Task started: fastANI
[2024-01-24 14:05:52,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg1329d86a-eda2-4875-b2d6-5529b566b71c/GCF_000308475.2_ASM30847v2_genomic.fna.gz --refList GCF_000308475.2_ASM30847v2_genomic.fna/target_genomes.txt --output GCF_000308475.2_ASM30847v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:15,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:15,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:15,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:15,193] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:06:15,193] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:15,193] [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 brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	100.0	2904	2910	95	inconclusive
Nocardia brasiliensis	strain=NCTC11294	GCA_900454265.1	37326	37326	suspected-type	True	99.9928	2902	2910	95	inconclusive
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	95.8419	2660	2910	95	inconclusive
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	95.8238	2713	2910	95	inconclusive
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	85.2238	2084	2910	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	84.9731	2034	2910	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	84.8149	1814	2910	95	below_threshold
Nocardia tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	84.7198	2005	2910	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	84.3918	1911	2910	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	82.5809	1363	2910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:15,195] [INFO] DFAST Taxonomy check result was written to GCF_000308475.2_ASM30847v2_genomic.fna/tc_result.tsv
[2024-01-24 14:06:15,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:15,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:15,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/checkm_data
[2024-01-24 14:06:15,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:15,294] [INFO] Task started: CheckM
[2024-01-24 14:06:15,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308475.2_ASM30847v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308475.2_ASM30847v2_genomic.fna/checkm_input GCF_000308475.2_ASM30847v2_genomic.fna/checkm_result
[2024-01-24 14:07:47,405] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:47,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2024-01-24 14:07:47,446] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:47,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:47,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308475.2_ASM30847v2_genomic.fna/markers.fasta)
[2024-01-24 14:07:47,447] [INFO] Task started: Blastn
[2024-01-24 14:07:47,447] [INFO] Running command: blastn -query GCF_000308475.2_ASM30847v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa800c50-89cf-472c-9fea-703cc489034e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308475.2_ASM30847v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:49,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:49,351] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:49,352] [INFO] Target genome list was writen to GCF_000308475.2_ASM30847v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:49,360] [INFO] Task started: fastANI
[2024-01-24 14:07:49,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg1329d86a-eda2-4875-b2d6-5529b566b71c/GCF_000308475.2_ASM30847v2_genomic.fna.gz --refList GCF_000308475.2_ASM30847v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000308475.2_ASM30847v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:07,680] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:07,694] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:07,694] [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_000308475.2	s__Nocardia brasiliensis	100.0	2904	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	conclusive
GCF_001613425.1	s__Nocardia vulneris	95.8238	2713	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	conclusive
GCF_000710915.1	s__Nocardia brasiliensis_A	95.1663	2569	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_000250675.2	s__Nocardia brasiliensis_B	95.0587	2699	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_011801125.1	s__Nocardia brasiliensis_C	89.7365	2246	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308715.1	s__Nocardia tenerifensis	84.8231	1813	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613365.1	s__Nocardia xishanensis	81.9217	1380	2910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	80.8046	1120	2910	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 14:08:07,696] [INFO] GTDB search result was written to GCF_000308475.2_ASM30847v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:07,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:07,700] [INFO] DFAST_QC result json was written to GCF_000308475.2_ASM30847v2_genomic.fna/dqc_result.json
[2024-01-24 14:08:07,700] [INFO] DFAST_QC completed!
[2024-01-24 14:08:07,700] [INFO] Total running time: 0h2m51s