[2024-01-25 20:21:35,777] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference
[2024-01-25 20:21:36,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,908] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgc112886a-3518-42cf-839c-994db6fb2d18/GCF_003123685.1_ASM312368v1_genomic.fna.gz | prodigal -d GCF_003123685.1_ASM312368v1_genomic.fna/cds.fna -a GCF_003123685.1_ASM312368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:19,419] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:19,420] [INFO] Task started: HMMsearch
[2024-01-25 20:22:19,420] [INFO] Running command: hmmsearch --tblout GCF_003123685.1_ASM312368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/reference_markers.hmm GCF_003123685.1_ASM312368v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:19,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:19,797] [INFO] Found 6/6 markers.
[2024-01-25 20:22:19,870] [INFO] Query marker FASTA was written to GCF_003123685.1_ASM312368v1_genomic.fna/markers.fasta
[2024-01-25 20:22:19,870] [INFO] Task started: Blastn
[2024-01-25 20:22:19,871] [INFO] Running command: blastn -query GCF_003123685.1_ASM312368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/reference_markers.fasta -out GCF_003123685.1_ASM312368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:21,012] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:21,015] [INFO] Selected 13 target genomes.
[2024-01-25 20:22:21,015] [INFO] Target genome list was writen to GCF_003123685.1_ASM312368v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:21,031] [INFO] Task started: fastANI
[2024-01-25 20:22:21,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgc112886a-3518-42cf-839c-994db6fb2d18/GCF_003123685.1_ASM312368v1_genomic.fna.gz --refList GCF_003123685.1_ASM312368v1_genomic.fna/target_genomes.txt --output GCF_003123685.1_ASM312368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:46,138] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:46,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:46,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:46,148] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:22:46,148] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:22:46,148] [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 aurea	strain=SYSU K10002	GCA_003123685.1	2144174	2144174	type	True	100.0	3028	3034	95	inconclusive
Nocardia noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	95.2003	2129	3034	95	inconclusive
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	82.4509	1426	3034	95	below_threshold
Nocardia arizonensis	strain=NBRC 108935	GCA_001618405.1	1141647	1141647	type	True	82.4323	1452	3034	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	82.403	1647	3034	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	81.7413	1397	3034	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	81.5803	1341	3034	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.5585	1343	3034	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	80.9614	1265	3034	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	80.9397	1281	3034	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	80.8988	1282	3034	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	80.7324	1194	3034	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	80.5426	1170	3034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:46,149] [INFO] DFAST Taxonomy check result was written to GCF_003123685.1_ASM312368v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:46,150] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:46,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:46,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/checkm_data
[2024-01-25 20:22:46,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:46,233] [INFO] Task started: CheckM
[2024-01-25 20:22:46,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003123685.1_ASM312368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003123685.1_ASM312368v1_genomic.fna/checkm_input GCF_003123685.1_ASM312368v1_genomic.fna/checkm_result
[2024-01-25 20:24:54,585] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:54,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:54,608] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:54,608] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:54,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003123685.1_ASM312368v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:54,610] [INFO] Task started: Blastn
[2024-01-25 20:24:54,610] [INFO] Running command: blastn -query GCF_003123685.1_ASM312368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09fe454f-4285-49a1-8e2e-af74f5d63982/dqc_reference/reference_markers_gtdb.fasta -out GCF_003123685.1_ASM312368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:56,232] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:56,235] [INFO] Selected 16 target genomes.
[2024-01-25 20:24:56,235] [INFO] Target genome list was writen to GCF_003123685.1_ASM312368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:56,264] [INFO] Task started: fastANI
[2024-01-25 20:24:56,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgc112886a-3518-42cf-839c-994db6fb2d18/GCF_003123685.1_ASM312368v1_genomic.fna.gz --refList GCF_003123685.1_ASM312368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003123685.1_ASM312368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:26,136] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:26,147] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:26,147] [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_003123685.1	s__Nocardia aurea	100.0	3028	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	conclusive
GCF_001310275.1	s__Nocardia arizonensis	82.4324	1430	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_015674855.1	s__Nocardia bovistercoris	82.4306	1641	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308695.1	s__Nocardia takedensis	82.3762	1506	3034	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	81.8242	1337	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	81.7049	1405	3034	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	81.6137	1335	3034	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	81.5593	1343	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	80.9598	1266	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_900269665.1	s__Nocardia suismassiliense	80.9406	1281	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_000250675.2	s__Nocardia brasiliensis_B	80.9151	1276	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_000308475.2	s__Nocardia brasiliensis	80.9127	1253	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_000308715.1	s__Nocardia tenerifensis	80.7771	1197	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613125.1	s__Nocardia shimofusensis	80.7126	1197	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612685.1	s__Nocardia altamirensis	80.6783	1285	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637185.1	s__Nocardia asteroides	80.511	1180	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:26,148] [INFO] GTDB search result was written to GCF_003123685.1_ASM312368v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:26,149] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:26,152] [INFO] DFAST_QC result json was written to GCF_003123685.1_ASM312368v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:26,152] [INFO] DFAST_QC completed!
[2024-01-25 20:25:26,152] [INFO] Total running time: 0h3m50s