[2024-01-24 13:49:40,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference
[2024-01-24 13:49:42,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,044] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,044] [INFO] Running command: gunzip -c /var/lib/cwl/stga687bb83-ff12-4dca-be57-1f49fd35545e/GCF_012396035.1_ASM1239603v1_genomic.fna.gz | prodigal -d GCF_012396035.1_ASM1239603v1_genomic.fna/cds.fna -a GCF_012396035.1_ASM1239603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:09,966] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:09,966] [INFO] Task started: HMMsearch
[2024-01-24 13:50:09,966] [INFO] Running command: hmmsearch --tblout GCF_012396035.1_ASM1239603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/reference_markers.hmm GCF_012396035.1_ASM1239603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:10,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:10,315] [INFO] Found 6/6 markers.
[2024-01-24 13:50:11,632] [INFO] Query marker FASTA was written to GCF_012396035.1_ASM1239603v1_genomic.fna/markers.fasta
[2024-01-24 13:50:11,633] [INFO] Task started: Blastn
[2024-01-24 13:50:11,633] [INFO] Running command: blastn -query GCF_012396035.1_ASM1239603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/reference_markers.fasta -out GCF_012396035.1_ASM1239603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:12,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:12,592] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:12,593] [INFO] Target genome list was writen to GCF_012396035.1_ASM1239603v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:12,613] [INFO] Task started: fastANI
[2024-01-24 13:50:12,614] [INFO] Running command: fastANI --query /var/lib/cwl/stga687bb83-ff12-4dca-be57-1f49fd35545e/GCF_012396035.1_ASM1239603v1_genomic.fna.gz --refList GCF_012396035.1_ASM1239603v1_genomic.fna/target_genomes.txt --output GCF_012396035.1_ASM1239603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:26,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:26,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:26,421] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:26,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:26,421] [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 flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	100.0	2454	2457	95	conclusive
Nocardia flavorosea	strain=NBRC 108225	GCA_001613385.1	53429	53429	type	True	99.9891	2429	2457	95	conclusive
Nocardia carnea	strain=NBRC 14403	GCA_000308515.1	37328	37328	type	True	92.6568	1903	2457	95	below_threshold
Nocardia speluncae	strain=NBRC 108251	GCA_001613245.1	419477	419477	type	True	89.879	1791	2457	95	below_threshold
Nocardia speluncae	strain=DSM 45078	GCA_012395985.1	419477	419477	type	True	89.8308	1805	2457	95	below_threshold
Nocardia grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	82.8786	1352	2457	95	below_threshold
Nocardia brevicatena	strain=NBRC 12119	GCA_000308495.1	37327	37327	type	True	80.102	977	2457	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	78.6056	763	2457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,423] [INFO] DFAST Taxonomy check result was written to GCF_012396035.1_ASM1239603v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:26,423] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:26,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:26,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/checkm_data
[2024-01-24 13:50:26,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:26,505] [INFO] Task started: CheckM
[2024-01-24 13:50:26,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396035.1_ASM1239603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396035.1_ASM1239603v1_genomic.fna/checkm_input GCF_012396035.1_ASM1239603v1_genomic.fna/checkm_result
[2024-01-24 13:51:34,968] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:34,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:34,997] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:34,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:34,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396035.1_ASM1239603v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:34,998] [INFO] Task started: Blastn
[2024-01-24 13:51:34,998] [INFO] Running command: blastn -query GCF_012396035.1_ASM1239603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb17fd98-9256-4dec-a946-a42c43811dba/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396035.1_ASM1239603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:36,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:36,280] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:36,280] [INFO] Target genome list was writen to GCF_012396035.1_ASM1239603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:36,305] [INFO] Task started: fastANI
[2024-01-24 13:51:36,306] [INFO] Running command: fastANI --query /var/lib/cwl/stga687bb83-ff12-4dca-be57-1f49fd35545e/GCF_012396035.1_ASM1239603v1_genomic.fna.gz --refList GCF_012396035.1_ASM1239603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396035.1_ASM1239603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:50,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:50,272] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:50,273] [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_001613385.1	s__Nocardia flavorosea	99.9891	2429	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000308515.1	s__Nocardia carnea	92.648	1905	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613245.1	s__Nocardia speluncae	89.8704	1792	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015477805.1	s__Nocardia flavorosea_A	88.7099	1746	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308775.1	s__Nocardia testacea	83.062	1407	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613445.1	s__Nocardia grenadensis	82.8858	1352	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361595.1	s__Nocardia sp013361595	82.583	895	2457	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	78.6044	765	2457	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 13:51:50,275] [INFO] GTDB search result was written to GCF_012396035.1_ASM1239603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:50,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:50,280] [INFO] DFAST_QC result json was written to GCF_012396035.1_ASM1239603v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:50,281] [INFO] DFAST_QC completed!
[2024-01-24 13:51:50,281] [INFO] Total running time: 0h2m10s