[2024-01-24 13:01:22,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:22,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:22,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference
[2024-01-24 13:01:23,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:23,432] [INFO] Task started: Prodigal
[2024-01-24 13:01:23,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ae8aa14-4dbd-4498-bea3-fdae66186456/GCF_006335005.1_ASM633500v1_genomic.fna.gz | prodigal -d GCF_006335005.1_ASM633500v1_genomic.fna/cds.fna -a GCF_006335005.1_ASM633500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:35,755] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:35,755] [INFO] Task started: HMMsearch
[2024-01-24 13:01:35,756] [INFO] Running command: hmmsearch --tblout GCF_006335005.1_ASM633500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/reference_markers.hmm GCF_006335005.1_ASM633500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:36,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:36,049] [INFO] Found 6/6 markers.
[2024-01-24 13:01:36,100] [INFO] Query marker FASTA was written to GCF_006335005.1_ASM633500v1_genomic.fna/markers.fasta
[2024-01-24 13:01:36,101] [INFO] Task started: Blastn
[2024-01-24 13:01:36,102] [INFO] Running command: blastn -query GCF_006335005.1_ASM633500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/reference_markers.fasta -out GCF_006335005.1_ASM633500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:37,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:37,394] [INFO] Selected 11 target genomes.
[2024-01-24 13:01:37,394] [INFO] Target genome list was writen to GCF_006335005.1_ASM633500v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:37,399] [INFO] Task started: fastANI
[2024-01-24 13:01:37,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae8aa14-4dbd-4498-bea3-fdae66186456/GCF_006335005.1_ASM633500v1_genomic.fna.gz --refList GCF_006335005.1_ASM633500v1_genomic.fna/target_genomes.txt --output GCF_006335005.1_ASM633500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:50,967] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:50,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:50,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:50,982] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:50,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:50,982] [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 albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	100.0	1478	1482	95	conclusive
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	87.5289	1195	1482	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	87.0384	1017	1482	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	86.5897	1105	1482	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	86.169	1070	1482	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	86.0048	1071	1482	95	below_threshold
Nocardioides caeni	strain=DSM 23134	GCA_004912195.1	574700	574700	type	True	83.4184	871	1482	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.5316	760	1482	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.2641	768	1482	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.1138	632	1482	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.0529	657	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:50,984] [INFO] DFAST Taxonomy check result was written to GCF_006335005.1_ASM633500v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:50,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:50,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:50,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/checkm_data
[2024-01-24 13:01:50,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:51,028] [INFO] Task started: CheckM
[2024-01-24 13:01:51,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006335005.1_ASM633500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006335005.1_ASM633500v1_genomic.fna/checkm_input GCF_006335005.1_ASM633500v1_genomic.fna/checkm_result
[2024-01-24 13:02:45,453] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:45,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:45,475] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:45,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:45,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006335005.1_ASM633500v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:45,476] [INFO] Task started: Blastn
[2024-01-24 13:02:45,476] [INFO] Running command: blastn -query GCF_006335005.1_ASM633500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebe0e1fa-fa5f-4be1-a9cf-25ededf67321/dqc_reference/reference_markers_gtdb.fasta -out GCF_006335005.1_ASM633500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:47,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:47,599] [INFO] Selected 13 target genomes.
[2024-01-24 13:02:47,600] [INFO] Target genome list was writen to GCF_006335005.1_ASM633500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:47,610] [INFO] Task started: fastANI
[2024-01-24 13:02:47,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae8aa14-4dbd-4498-bea3-fdae66186456/GCF_006335005.1_ASM633500v1_genomic.fna.gz --refList GCF_006335005.1_ASM633500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006335005.1_ASM633500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:04,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:04,350] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:04,351] [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_006335005.1	s__Nocardioides albidus	100.0	1478	1482	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_013409625.1	s__Nocardioides kongjuensis	87.5076	1197	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	87.3558	1113	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	87.3184	1139	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	87.0293	1018	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	86.6049	1103	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	86.2293	1064	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408525.1	s__Nocardioides aromaticivorans	84.6715	1029	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_003054165.1	s__Nocardioides sp003054165	84.5829	1012	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428825.1	s__Nocardioides sp001428825	84.5347	985	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004912195.1	s__Nocardioides caeni	83.5012	863	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428565.1	s__Nocardioides sp001428565	83.2846	933	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008123405.1	s__Nocardioides sp008123405	80.9277	751	1482	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 13:03:04,353] [INFO] GTDB search result was written to GCF_006335005.1_ASM633500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:04,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:04,357] [INFO] DFAST_QC result json was written to GCF_006335005.1_ASM633500v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:04,358] [INFO] DFAST_QC completed!
[2024-01-24 13:03:04,358] [INFO] Total running time: 0h1m42s