[2024-01-24 11:51:20,007] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:20,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:20,010] [INFO] DQC Reference Directory: /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference
[2024-01-24 11:51:21,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:21,266] [INFO] Task started: Prodigal
[2024-01-24 11:51:21,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c2a4707-42e9-4d75-9bef-04713981e178/GCF_004137255.1_ASM413725v1_genomic.fna.gz | prodigal -d GCF_004137255.1_ASM413725v1_genomic.fna/cds.fna -a GCF_004137255.1_ASM413725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:33,680] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:33,680] [INFO] Task started: HMMsearch
[2024-01-24 11:51:33,680] [INFO] Running command: hmmsearch --tblout GCF_004137255.1_ASM413725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/reference_markers.hmm GCF_004137255.1_ASM413725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:34,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:34,008] [INFO] Found 6/6 markers.
[2024-01-24 11:51:34,052] [INFO] Query marker FASTA was written to GCF_004137255.1_ASM413725v1_genomic.fna/markers.fasta
[2024-01-24 11:51:34,052] [INFO] Task started: Blastn
[2024-01-24 11:51:34,052] [INFO] Running command: blastn -query GCF_004137255.1_ASM413725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/reference_markers.fasta -out GCF_004137255.1_ASM413725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,379] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,383] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:35,383] [INFO] Target genome list was writen to GCF_004137255.1_ASM413725v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,389] [INFO] Task started: fastANI
[2024-01-24 11:51:35,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c2a4707-42e9-4d75-9bef-04713981e178/GCF_004137255.1_ASM413725v1_genomic.fna.gz --refList GCF_004137255.1_ASM413725v1_genomic.fna/target_genomes.txt --output GCF_004137255.1_ASM413725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:48,319] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:48,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:48,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:48,333] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:48,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:48,333] [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
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	91.1623	1324	1487	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.9308	1073	1487	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.7813	1026	1487	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.7715	1053	1487	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.7598	1064	1487	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.75	1049	1487	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	85.7276	1010	1487	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.5387	999	1487	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	85.4345	1025	1487	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	85.3484	946	1487	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.3198	970	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,335] [INFO] DFAST Taxonomy check result was written to GCF_004137255.1_ASM413725v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:48,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:48,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:48,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/checkm_data
[2024-01-24 11:51:48,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:48,381] [INFO] Task started: CheckM
[2024-01-24 11:51:48,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137255.1_ASM413725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137255.1_ASM413725v1_genomic.fna/checkm_input GCF_004137255.1_ASM413725v1_genomic.fna/checkm_result
[2024-01-24 11:52:56,248] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:56,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:56,272] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:56,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:56,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137255.1_ASM413725v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:56,273] [INFO] Task started: Blastn
[2024-01-24 11:52:56,274] [INFO] Running command: blastn -query GCF_004137255.1_ASM413725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga97e6858-98f8-4810-b7b3-364b30d8b01f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137255.1_ASM413725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,347] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,351] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:58,352] [INFO] Target genome list was writen to GCF_004137255.1_ASM413725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,363] [INFO] Task started: fastANI
[2024-01-24 11:52:58,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c2a4707-42e9-4d75-9bef-04713981e178/GCF_004137255.1_ASM413725v1_genomic.fna.gz --refList GCF_004137255.1_ASM413725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137255.1_ASM413725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:14,269] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:14,284] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:14,284] [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_004137255.1	s__Nocardioides oleivorans	100.0	1487	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900105585.1	s__Nocardioides exalbidus	91.1372	1326	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	85.9698	1069	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410035.1	s__Nocardioides cavernae_A	85.8789	1094	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137245.1	s__Nocardioides glacieisoli	85.7746	1026	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	85.7722	1006	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003633575.1	s__Nocardioides sp003633575	85.6799	1084	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	85.6669	1100	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	85.6257	1056	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	85.5963	969	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	85.564	1044	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785795.1	s__Nocardioides eburneiflavus	85.4572	1023	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155335.1	s__Nocardioides sp013155335	85.4143	1022	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	85.3464	946	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:14,286] [INFO] GTDB search result was written to GCF_004137255.1_ASM413725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:14,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:14,293] [INFO] DFAST_QC result json was written to GCF_004137255.1_ASM413725v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:14,293] [INFO] DFAST_QC completed!
[2024-01-24 11:53:14,293] [INFO] Total running time: 0h1m54s