[2024-01-24 12:52:25,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference
[2024-01-24 12:52:26,403] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,403] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a550d1a-a90d-4a02-836d-9310c77dbfab/GCF_024172045.1_ASM2417204v1_genomic.fna.gz | prodigal -d GCF_024172045.1_ASM2417204v1_genomic.fna/cds.fna -a GCF_024172045.1_ASM2417204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:03,171] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:03,171] [INFO] Task started: HMMsearch
[2024-01-24 12:53:03,171] [INFO] Running command: hmmsearch --tblout GCF_024172045.1_ASM2417204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/reference_markers.hmm GCF_024172045.1_ASM2417204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:03,512] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:03,514] [INFO] Found 6/6 markers.
[2024-01-24 12:53:03,576] [INFO] Query marker FASTA was written to GCF_024172045.1_ASM2417204v1_genomic.fna/markers.fasta
[2024-01-24 12:53:03,576] [INFO] Task started: Blastn
[2024-01-24 12:53:03,576] [INFO] Running command: blastn -query GCF_024172045.1_ASM2417204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/reference_markers.fasta -out GCF_024172045.1_ASM2417204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:04,831] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:04,835] [INFO] Selected 8 target genomes.
[2024-01-24 12:53:04,835] [INFO] Target genome list was writen to GCF_024172045.1_ASM2417204v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:04,852] [INFO] Task started: fastANI
[2024-01-24 12:53:04,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a550d1a-a90d-4a02-836d-9310c77dbfab/GCF_024172045.1_ASM2417204v1_genomic.fna.gz --refList GCF_024172045.1_ASM2417204v1_genomic.fna/target_genomes.txt --output GCF_024172045.1_ASM2417204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:20,870] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:20,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:20,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:20,879] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:53:20,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:20,880] [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 amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	100.0	2521	2527	95	conclusive
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	99.9758	2478	2527	95	conclusive
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	93.3539	2062	2527	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	89.6885	1869	2527	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	89.0107	1874	2527	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	83.7218	1538	2527	95	below_threshold
Nocardia cyriacigeorgica	strain=NBRC 100375	GCA_000308555.1	135487	135487	type	True	81.9321	1124	2527	95	below_threshold
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	81.9095	1186	2527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:20,882] [INFO] DFAST Taxonomy check result was written to GCF_024172045.1_ASM2417204v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:20,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:20,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:20,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/checkm_data
[2024-01-24 12:53:20,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:20,958] [INFO] Task started: CheckM
[2024-01-24 12:53:20,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172045.1_ASM2417204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172045.1_ASM2417204v1_genomic.fna/checkm_input GCF_024172045.1_ASM2417204v1_genomic.fna/checkm_result
[2024-01-24 12:54:55,903] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:55,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:55,931] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:55,931] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:55,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172045.1_ASM2417204v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:55,932] [INFO] Task started: Blastn
[2024-01-24 12:54:55,932] [INFO] Running command: blastn -query GCF_024172045.1_ASM2417204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a55541-fd24-4400-a83c-aa21e328a3c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172045.1_ASM2417204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:57,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:57,964] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:57,964] [INFO] Target genome list was writen to GCF_024172045.1_ASM2417204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:57,973] [INFO] Task started: fastANI
[2024-01-24 12:54:57,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a550d1a-a90d-4a02-836d-9310c77dbfab/GCF_024172045.1_ASM2417204v1_genomic.fna.gz --refList GCF_024172045.1_ASM2417204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172045.1_ASM2417204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:21,019] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:21,036] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:21,036] [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_001612615.1	s__Nocardia amikacinitolerans	99.9758	2478	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	conclusive
GCF_006716565.1	s__Nocardia bhagyanarayanae	93.3449	2063	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	89.6711	1873	2527	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	89.012	1874	2527	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	83.7241	1538	2527	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	82.4388	1406	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	82.3778	1387	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_000710915.1	s__Nocardia brasiliensis_A	82.2079	1331	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_000308555.1	s__Nocardia cyriacigeorgica	81.9405	1121	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	-
GCF_900637185.1	s__Nocardia asteroides	81.8114	1314	2527	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	81.7246	1322	2527	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 12:55:21,038] [INFO] GTDB search result was written to GCF_024172045.1_ASM2417204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:21,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:21,042] [INFO] DFAST_QC result json was written to GCF_024172045.1_ASM2417204v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:21,043] [INFO] DFAST_QC completed!
[2024-01-24 12:55:21,043] [INFO] Total running time: 0h2m56s