[2024-01-24 11:05:03,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg68b32ecb-9a08-46fa-aaa6-6798dc9d5ae2/GCF_016918045.1_ASM1691804v1_genomic.fna.gz | prodigal -d GCF_016918045.1_ASM1691804v1_genomic.fna/cds.fna -a GCF_016918045.1_ASM1691804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,504] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,504] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,504] [INFO] Running command: hmmsearch --tblout GCF_016918045.1_ASM1691804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/reference_markers.hmm GCF_016918045.1_ASM1691804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:15,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:15,788] [INFO] Found 6/6 markers.
[2024-01-24 11:05:15,817] [INFO] Query marker FASTA was written to GCF_016918045.1_ASM1691804v1_genomic.fna/markers.fasta
[2024-01-24 11:05:15,817] [INFO] Task started: Blastn
[2024-01-24 11:05:15,817] [INFO] Running command: blastn -query GCF_016918045.1_ASM1691804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/reference_markers.fasta -out GCF_016918045.1_ASM1691804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:17,008] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:17,011] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:17,011] [INFO] Target genome list was writen to GCF_016918045.1_ASM1691804v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:17,021] [INFO] Task started: fastANI
[2024-01-24 11:05:17,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg68b32ecb-9a08-46fa-aaa6-6798dc9d5ae2/GCF_016918045.1_ASM1691804v1_genomic.fna.gz --refList GCF_016918045.1_ASM1691804v1_genomic.fna/target_genomes.txt --output GCF_016918045.1_ASM1691804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:32,895] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:32,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:32,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:32,905] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:32,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:32,905] [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 daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	83.3922	834	1264	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	83.2663	861	1264	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	83.2507	864	1264	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	83.243	866	1264	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	83.187	858	1264	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	83.1638	856	1264	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	83.1544	785	1264	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	83.1154	868	1264	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	82.7938	831	1264	95	below_threshold
Nocardioides caeni	strain=DSM 23134	GCA_004912195.1	574700	574700	type	True	82.4613	796	1264	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.7242	769	1264	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.8698	689	1264	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.5629	686	1264	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.0073	613	1264	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.987	552	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:32,906] [INFO] DFAST Taxonomy check result was written to GCF_016918045.1_ASM1691804v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:32,907] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:32,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:32,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/checkm_data
[2024-01-24 11:05:32,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:32,946] [INFO] Task started: CheckM
[2024-01-24 11:05:32,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918045.1_ASM1691804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918045.1_ASM1691804v1_genomic.fna/checkm_input GCF_016918045.1_ASM1691804v1_genomic.fna/checkm_result
[2024-01-24 11:06:30,587] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:30,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,603] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:30,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:30,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918045.1_ASM1691804v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:30,604] [INFO] Task started: Blastn
[2024-01-24 11:06:30,604] [INFO] Running command: blastn -query GCF_016918045.1_ASM1691804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79822669-d043-462e-bf01-5e70b0ecde36/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918045.1_ASM1691804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:32,576] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:32,579] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:32,579] [INFO] Target genome list was writen to GCF_016918045.1_ASM1691804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:32,587] [INFO] Task started: fastANI
[2024-01-24 11:06:32,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg68b32ecb-9a08-46fa-aaa6-6798dc9d5ae2/GCF_016918045.1_ASM1691804v1_genomic.fna.gz --refList GCF_016918045.1_ASM1691804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918045.1_ASM1691804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:49,087] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:49,096] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:49,096] [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_018388425.1	s__Nocardioides sp018388425	99.9994	1262	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.59	99.18	0.98	0.96	3	conclusive
GCF_000519005.1	s__Nocardioides sp000519005	83.7733	860	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCA_019192965.1	s__Nocardioides daeguensis	83.3719	835	1264	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	83.2885	843	1264	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	83.2585	861	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	83.2482	853	1264	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	83.1925	871	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_013409625.1	s__Nocardioides kongjuensis	83.1632	857	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873635.1	s__Nocardioides sp014873635	83.1487	848	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335005.1	s__Nocardioides albidus	83.1435	786	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	83.0895	872	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_003054165.1	s__Nocardioides sp003054165	83.0823	823	1264	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	83.0217	836	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004919105.1	s__Nocardioides sp004919105	82.3065	767	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	80.5014	693	1264	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 11:06:49,099] [INFO] GTDB search result was written to GCF_016918045.1_ASM1691804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:49,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:49,102] [INFO] DFAST_QC result json was written to GCF_016918045.1_ASM1691804v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:49,102] [INFO] DFAST_QC completed!
[2024-01-24 11:06:49,102] [INFO] Total running time: 0h1m45s