[2024-01-24 14:05:00,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference
[2024-01-24 14:05:02,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:02,096] [INFO] Task started: Prodigal
[2024-01-24 14:05:02,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg66d26606-df65-4f1c-b47e-a1eac38c753f/GCF_001613345.1_ASM161334v1_genomic.fna.gz | prodigal -d GCF_001613345.1_ASM161334v1_genomic.fna/cds.fna -a GCF_001613345.1_ASM161334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:37,214] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:37,214] [INFO] Task started: HMMsearch
[2024-01-24 14:05:37,214] [INFO] Running command: hmmsearch --tblout GCF_001613345.1_ASM161334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/reference_markers.hmm GCF_001613345.1_ASM161334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:37,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:37,573] [INFO] Found 6/6 markers.
[2024-01-24 14:05:37,641] [INFO] Query marker FASTA was written to GCF_001613345.1_ASM161334v1_genomic.fna/markers.fasta
[2024-01-24 14:05:37,642] [INFO] Task started: Blastn
[2024-01-24 14:05:37,642] [INFO] Running command: blastn -query GCF_001613345.1_ASM161334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/reference_markers.fasta -out GCF_001613345.1_ASM161334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:38,832] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:38,835] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:38,836] [INFO] Target genome list was writen to GCF_001613345.1_ASM161334v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:38,853] [INFO] Task started: fastANI
[2024-01-24 14:05:38,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d26606-df65-4f1c-b47e-a1eac38c753f/GCF_001613345.1_ASM161334v1_genomic.fna.gz --refList GCF_001613345.1_ASM161334v1_genomic.fna/target_genomes.txt --output GCF_001613345.1_ASM161334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:02,848] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:02,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:02,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:02,859] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:02,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:02,859] [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 uniformis	strain=NBRC 13702	GCA_001613345.1	53432	53432	type	True	100.0	2842	2849	95	conclusive
Nocardia uniformis	strain=JCM 3224	GCA_013004475.1	53432	53432	type	True	99.9957	2844	2849	95	conclusive
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	83.0377	1606	2849	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	82.9816	1653	2849	95	below_threshold
Nocardia acididurans	strain=LPG 2	GCA_016741815.1	2802282	2802282	type	True	81.3905	1437	2849	95	below_threshold
Nocardia acidivorans	strain=NBRC 108247	GCA_001625085.1	404580	404580	type	True	81.334	1336	2849	95	below_threshold
Nocardia huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	81.3213	1480	2849	95	below_threshold
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	81.0558	1290	2849	95	below_threshold
Nocardia jejuensis	strain=NBRC 103114	GCA_001613145.1	328049	328049	type	True	81.0191	1342	2849	95	below_threshold
Nocardia inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	81.018	1417	2849	95	below_threshold
Nocardia terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	80.78	1386	2849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:02,860] [INFO] DFAST Taxonomy check result was written to GCF_001613345.1_ASM161334v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:02,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:02,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:02,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/checkm_data
[2024-01-24 14:06:02,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:02,940] [INFO] Task started: CheckM
[2024-01-24 14:06:02,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613345.1_ASM161334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613345.1_ASM161334v1_genomic.fna/checkm_input GCF_001613345.1_ASM161334v1_genomic.fna/checkm_result
[2024-01-24 14:07:37,109] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:37,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:37,130] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:37,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:37,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613345.1_ASM161334v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:37,131] [INFO] Task started: Blastn
[2024-01-24 14:07:37,131] [INFO] Running command: blastn -query GCF_001613345.1_ASM161334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd06f248-e629-4828-87f9-d1db7f7d334e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613345.1_ASM161334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:38,777] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:38,780] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:38,781] [INFO] Target genome list was writen to GCF_001613345.1_ASM161334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:38,792] [INFO] Task started: fastANI
[2024-01-24 14:07:38,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d26606-df65-4f1c-b47e-a1eac38c753f/GCF_001613345.1_ASM161334v1_genomic.fna.gz --refList GCF_001613345.1_ASM161334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613345.1_ASM161334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:05,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:05,350] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:05,350] [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_001613345.1	s__Nocardia uniformis	100.0	2842	2849	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_000308635.1	s__Nocardia otitidiscaviarum	83.0684	1600	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
GCF_001613405.1	s__Nocardia crassostreae	81.4613	1448	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741815.1	s__Nocardia sp016741815	81.4015	1435	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625085.1	s__Nocardia acidivorans	81.3327	1336	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013744875.1	s__Nocardia sp013744875	81.3315	1476	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649815.1	s__Nocardia sp009649815	81.2163	1341	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990715.1	s__Nocardia seriolae	81.0376	1295	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.94	99.87	0.97	0.93	20	-
GCF_001613145.1	s__Nocardia jejuensis	81.0353	1338	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612945.1	s__Nocardia inohanensis	81.0184	1416	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308655.1	s__Nocardia niigatensis	80.863	1283	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760405.1	s__Nocardia terrae	80.8031	1381	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	79.5671	954	2849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:05,353] [INFO] GTDB search result was written to GCF_001613345.1_ASM161334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:05,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:05,356] [INFO] DFAST_QC result json was written to GCF_001613345.1_ASM161334v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:05,357] [INFO] DFAST_QC completed!
[2024-01-24 14:08:05,357] [INFO] Total running time: 0h3m4s