[2024-01-24 13:43:26,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference
[2024-01-24 13:43:28,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,079] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg15198427-4dc1-4daa-9cf3-59f6f186c168/GCF_002081715.1_ASM208171v1_genomic.fna.gz | prodigal -d GCF_002081715.1_ASM208171v1_genomic.fna/cds.fna -a GCF_002081715.1_ASM208171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:51,989] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:51,990] [INFO] Task started: HMMsearch
[2024-01-24 13:43:51,990] [INFO] Running command: hmmsearch --tblout GCF_002081715.1_ASM208171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/reference_markers.hmm GCF_002081715.1_ASM208171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:52,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:52,217] [INFO] Found 6/6 markers.
[2024-01-24 13:43:52,260] [INFO] Query marker FASTA was written to GCF_002081715.1_ASM208171v1_genomic.fna/markers.fasta
[2024-01-24 13:43:52,261] [INFO] Task started: Blastn
[2024-01-24 13:43:52,261] [INFO] Running command: blastn -query GCF_002081715.1_ASM208171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/reference_markers.fasta -out GCF_002081715.1_ASM208171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:53,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:53,313] [INFO] Selected 20 target genomes.
[2024-01-24 13:43:53,313] [INFO] Target genome list was writen to GCF_002081715.1_ASM208171v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:53,324] [INFO] Task started: fastANI
[2024-01-24 13:43:53,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg15198427-4dc1-4daa-9cf3-59f6f186c168/GCF_002081715.1_ASM208171v1_genomic.fna.gz --refList GCF_002081715.1_ASM208171v1_genomic.fna/target_genomes.txt --output GCF_002081715.1_ASM208171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:44:19,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:19,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:44:19,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:44:19,736] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:44:19,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:44:19,737] [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 donostiensis	strain=X1654	GCA_002081715.1	1538463	1538463	type	True	100.0	1860	1864	95	conclusive
Nocardia brevicatena	strain=NBRC 12119	GCA_000308495.1	37327	37327	type	True	81.2368	987	1864	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	80.7078	922	1864	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	80.6695	954	1864	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	80.6216	943	1864	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	80.4482	905	1864	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	80.4255	956	1864	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	80.4135	926	1864	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	80.3914	936	1864	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	80.3547	908	1864	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	80.3524	933	1864	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	80.3394	918	1864	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	80.2341	901	1864	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	80.1997	895	1864	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	80.0671	900	1864	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	80.0372	915	1864	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	79.964	885	1864	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	79.9626	884	1864	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	79.9434	882	1864	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	79.8075	864	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:44:19,739] [INFO] DFAST Taxonomy check result was written to GCF_002081715.1_ASM208171v1_genomic.fna/tc_result.tsv
[2024-01-24 13:44:19,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:44:19,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:44:19,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/checkm_data
[2024-01-24 13:44:19,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:44:19,794] [INFO] Task started: CheckM
[2024-01-24 13:44:19,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002081715.1_ASM208171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002081715.1_ASM208171v1_genomic.fna/checkm_input GCF_002081715.1_ASM208171v1_genomic.fna/checkm_result
[2024-01-24 13:45:23,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:45:23,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:45:23,391] [INFO] ===== Completeness check finished =====
[2024-01-24 13:45:23,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:45:23,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002081715.1_ASM208171v1_genomic.fna/markers.fasta)
[2024-01-24 13:45:23,392] [INFO] Task started: Blastn
[2024-01-24 13:45:23,392] [INFO] Running command: blastn -query GCF_002081715.1_ASM208171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4362177d-30d2-4705-9b0f-e31c49742c9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002081715.1_ASM208171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:24,870] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:24,873] [INFO] Selected 21 target genomes.
[2024-01-24 13:45:24,873] [INFO] Target genome list was writen to GCF_002081715.1_ASM208171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:45:24,890] [INFO] Task started: fastANI
[2024-01-24 13:45:24,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg15198427-4dc1-4daa-9cf3-59f6f186c168/GCF_002081715.1_ASM208171v1_genomic.fna.gz --refList GCF_002081715.1_ASM208171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002081715.1_ASM208171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:45:53,653] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:53,669] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:45:53,669] [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_002081715.1	s__Nocardia donostiensis	100.0	1860	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.79	99.59	0.98	0.98	3	conclusive
GCF_000308495.1	s__Nocardia brevicatena	81.241	986	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308675.1	s__Nocardia paucivorans	80.741	931	1864	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	80.7063	949	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_000308755.1	s__Nocardia pneumoniae	80.4337	955	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	80.4178	959	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612615.1	s__Nocardia amikacinitolerans	80.4109	910	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001612785.1	s__Nocardia beijingensis	80.3968	935	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_013315795.1	s__Nocardia barduliensis	80.3642	930	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315035.1	s__Nocardia puris	80.3433	919	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_000308435.1	s__Nocardia araoensis	80.3404	911	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477775.1	s__Nocardia abscessus_A	80.2951	940	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	80.2637	896	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829295.1	s__Nocardia sp009829295	80.2481	914	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	-
GCF_001613365.1	s__Nocardia xishanensis	80.243	899	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308415.1	s__Nocardia asiatica	80.1998	895	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308595.1	s__Nocardia higoensis	80.1698	836	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710915.1	s__Nocardia brasiliensis_A	80.1063	907	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_007990755.1	s__Nocardia ninae	80.0378	917	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_900637185.1	s__Nocardia asteroides	79.9333	893	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_015674855.1	s__Nocardia bovistercoris	79.7901	867	1864	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 13:45:53,671] [INFO] GTDB search result was written to GCF_002081715.1_ASM208171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:45:53,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:45:53,676] [INFO] DFAST_QC result json was written to GCF_002081715.1_ASM208171v1_genomic.fna/dqc_result.json
[2024-01-24 13:45:53,676] [INFO] DFAST_QC completed!
[2024-01-24 13:45:53,676] [INFO] Total running time: 0h2m27s