[2024-01-24 13:51:12,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference
[2024-01-24 13:51:13,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,766] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg2abdf71d-8ba7-4db1-91d9-4a2036663f01/GCF_009604405.1_ASM960440v1_genomic.fna.gz | prodigal -d GCF_009604405.1_ASM960440v1_genomic.fna/cds.fna -a GCF_009604405.1_ASM960440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:51,248] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:51,249] [INFO] Task started: HMMsearch
[2024-01-24 13:51:51,249] [INFO] Running command: hmmsearch --tblout GCF_009604405.1_ASM960440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/reference_markers.hmm GCF_009604405.1_ASM960440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:51,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:51,632] [INFO] Found 6/6 markers.
[2024-01-24 13:51:51,705] [INFO] Query marker FASTA was written to GCF_009604405.1_ASM960440v1_genomic.fna/markers.fasta
[2024-01-24 13:51:51,706] [INFO] Task started: Blastn
[2024-01-24 13:51:51,706] [INFO] Running command: blastn -query GCF_009604405.1_ASM960440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/reference_markers.fasta -out GCF_009604405.1_ASM960440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:52,871] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:52,875] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:52,876] [INFO] Target genome list was writen to GCF_009604405.1_ASM960440v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:52,887] [INFO] Task started: fastANI
[2024-01-24 13:51:52,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg2abdf71d-8ba7-4db1-91d9-4a2036663f01/GCF_009604405.1_ASM960440v1_genomic.fna.gz --refList GCF_009604405.1_ASM960440v1_genomic.fna/target_genomes.txt --output GCF_009604405.1_ASM960440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:15,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:15,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:15,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:15,037] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:15,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:15,037] [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 macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	100.0	2818	2819	95	conclusive
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	88.1037	2218	2819	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	88.0748	2117	2819	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	87.6335	2014	2819	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	87.1186	1938	2819	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	81.4684	1389	2819	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	81.4419	1365	2819	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	79.6962	1042	2819	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	79.512	931	2819	95	below_threshold
Rhodococcus ruber	strain=DSM 43338	GCA_001646835.1	1830	1830	type	True	77.9149	548	2819	95	below_threshold
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	77.9095	575	2819	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	77.5277	479	2819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:15,039] [INFO] DFAST Taxonomy check result was written to GCF_009604405.1_ASM960440v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:15,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:15,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:15,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/checkm_data
[2024-01-24 13:52:15,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:15,120] [INFO] Task started: CheckM
[2024-01-24 13:52:15,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009604405.1_ASM960440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009604405.1_ASM960440v1_genomic.fna/checkm_input GCF_009604405.1_ASM960440v1_genomic.fna/checkm_result
[2024-01-24 13:54:04,866] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:04,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:04,896] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:04,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:04,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009604405.1_ASM960440v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:04,897] [INFO] Task started: Blastn
[2024-01-24 13:54:04,897] [INFO] Running command: blastn -query GCF_009604405.1_ASM960440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fd7909-9b9a-4f86-911e-0d7754de3941/dqc_reference/reference_markers_gtdb.fasta -out GCF_009604405.1_ASM960440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:06,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:06,720] [INFO] Selected 13 target genomes.
[2024-01-24 13:54:06,720] [INFO] Target genome list was writen to GCF_009604405.1_ASM960440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:06,730] [INFO] Task started: fastANI
[2024-01-24 13:54:06,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg2abdf71d-8ba7-4db1-91d9-4a2036663f01/GCF_009604405.1_ASM960440v1_genomic.fna.gz --refList GCF_009604405.1_ASM960440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009604405.1_ASM960440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:31,962] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:31,973] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:54:31,973] [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_009604405.1	s__Nocardia sp009604405	100.0	2818	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000308615.1	s__Nocardia jiangxiensis	88.0586	2120	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	87.6028	2019	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613305.1	s__Nocardia vaccinii	87.1209	1938	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860155.1	s__Nocardia sp018860155	82.6685	1514	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308875.1	s__Nocardia transvalensis	81.4371	1366	2819	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	81.0766	1340	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523235.1	s__Nocardia nova_A	80.9384	1319	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354405.1	s__Nocardia sp015354405	80.6072	1206	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708175.1	s__Nocardia sp009708175	79.8638	1060	2819	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	79.7089	1053	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001612745.1	s__Nocardia amamiensis	79.5108	930	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894945.1	s__Rhodococcus ruber	77.9056	574	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:54:31,975] [INFO] GTDB search result was written to GCF_009604405.1_ASM960440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:31,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:31,981] [INFO] DFAST_QC result json was written to GCF_009604405.1_ASM960440v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:31,981] [INFO] DFAST_QC completed!
[2024-01-24 13:54:31,981] [INFO] Total running time: 0h3m20s