[2024-01-24 14:39:59,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:59,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:59,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference
[2024-01-24 14:40:01,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:01,361] [INFO] Task started: Prodigal
[2024-01-24 14:40:01,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c438f91-2dd9-42b8-8047-19d9b63e4e92/GCF_014203315.1_ASM1420331v1_genomic.fna.gz | prodigal -d GCF_014203315.1_ASM1420331v1_genomic.fna/cds.fna -a GCF_014203315.1_ASM1420331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:35,051] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:35,052] [INFO] Task started: HMMsearch
[2024-01-24 14:40:35,052] [INFO] Running command: hmmsearch --tblout GCF_014203315.1_ASM1420331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/reference_markers.hmm GCF_014203315.1_ASM1420331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:35,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:35,434] [INFO] Found 6/6 markers.
[2024-01-24 14:40:35,506] [INFO] Query marker FASTA was written to GCF_014203315.1_ASM1420331v1_genomic.fna/markers.fasta
[2024-01-24 14:40:35,507] [INFO] Task started: Blastn
[2024-01-24 14:40:35,507] [INFO] Running command: blastn -query GCF_014203315.1_ASM1420331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/reference_markers.fasta -out GCF_014203315.1_ASM1420331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:36,812] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:36,815] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:36,816] [INFO] Target genome list was writen to GCF_014203315.1_ASM1420331v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:36,827] [INFO] Task started: fastANI
[2024-01-24 14:40:36,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c438f91-2dd9-42b8-8047-19d9b63e4e92/GCF_014203315.1_ASM1420331v1_genomic.fna.gz --refList GCF_014203315.1_ASM1420331v1_genomic.fna/target_genomes.txt --output GCF_014203315.1_ASM1420331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:58,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:58,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:58,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:58,594] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:58,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:58,594] [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 transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	100.0	2795	2798	95	conclusive
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	99.9721	2733	2798	95	conclusive
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	84.9444	1875	2798	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	84.8457	1816	2798	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	82.9622	1451	2798	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	80.9777	1372	2798	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	80.6922	1150	2798	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	80.5013	1198	2798	95	below_threshold
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	80.2985	1084	2798	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	80.124	1213	2798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:58,596] [INFO] DFAST Taxonomy check result was written to GCF_014203315.1_ASM1420331v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:58,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:58,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:58,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/checkm_data
[2024-01-24 14:40:58,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:58,672] [INFO] Task started: CheckM
[2024-01-24 14:40:58,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203315.1_ASM1420331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203315.1_ASM1420331v1_genomic.fna/checkm_input GCF_014203315.1_ASM1420331v1_genomic.fna/checkm_result
[2024-01-24 14:42:36,136] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:36,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.64%
Strain heterogeneity: 22.22%
--------------------------------------------------------------------------------
[2024-01-24 14:42:36,168] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:36,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:36,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203315.1_ASM1420331v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:36,169] [INFO] Task started: Blastn
[2024-01-24 14:42:36,169] [INFO] Running command: blastn -query GCF_014203315.1_ASM1420331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ad1d04-9fe3-4df2-b7b8-686631302d84/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203315.1_ASM1420331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:38,194] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:38,197] [INFO] Selected 9 target genomes.
[2024-01-24 14:42:38,197] [INFO] Target genome list was writen to GCF_014203315.1_ASM1420331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:38,208] [INFO] Task started: fastANI
[2024-01-24 14:42:38,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c438f91-2dd9-42b8-8047-19d9b63e4e92/GCF_014203315.1_ASM1420331v1_genomic.fna.gz --refList GCF_014203315.1_ASM1420331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203315.1_ASM1420331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:58,439] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:58,454] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:58,455] [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_000308875.1	s__Nocardia transvalensis	99.9721	2733	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_015477355.1	s__Nocardia blacklockiae	85.5419	1908	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014466955.1	s__Nocardia wallacei	85.0012	1791	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613165.1	s__Nocardia mexicana	84.8142	1822	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000526215.1	s__Nocardia sp000526215	84.5242	1715	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	80.6355	1154	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_003315035.1	s__Nocardia puris	80.5116	1197	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_011801125.1	s__Nocardia brasiliensis_C	80.369	1241	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250675.2	s__Nocardia brasiliensis_B	80.1523	1298	2798	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:58,457] [INFO] GTDB search result was written to GCF_014203315.1_ASM1420331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:58,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:58,461] [INFO] DFAST_QC result json was written to GCF_014203315.1_ASM1420331v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:58,461] [INFO] DFAST_QC completed!
[2024-01-24 14:42:58,461] [INFO] Total running time: 0h2m59s