[2024-01-25 20:03:35,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference
[2024-01-25 20:03:36,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,652] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg85b03598-7c97-4932-b02c-65e3e4247add/GCF_900186975.1_50569_F01_genomic.fna.gz | prodigal -d GCF_900186975.1_50569_F01_genomic.fna/cds.fna -a GCF_900186975.1_50569_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:43,569] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:43,570] [INFO] Task started: HMMsearch
[2024-01-25 20:03:43,570] [INFO] Running command: hmmsearch --tblout GCF_900186975.1_50569_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/reference_markers.hmm GCF_900186975.1_50569_F01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:43,758] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:43,759] [INFO] Found 6/6 markers.
[2024-01-25 20:03:43,781] [INFO] Query marker FASTA was written to GCF_900186975.1_50569_F01_genomic.fna/markers.fasta
[2024-01-25 20:03:43,781] [INFO] Task started: Blastn
[2024-01-25 20:03:43,781] [INFO] Running command: blastn -query GCF_900186975.1_50569_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/reference_markers.fasta -out GCF_900186975.1_50569_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:44,690] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:44,693] [INFO] Selected 17 target genomes.
[2024-01-25 20:03:44,693] [INFO] Target genome list was writen to GCF_900186975.1_50569_F01_genomic.fna/target_genomes.txt
[2024-01-25 20:03:44,707] [INFO] Task started: fastANI
[2024-01-25 20:03:44,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b03598-7c97-4932-b02c-65e3e4247add/GCF_900186975.1_50569_F01_genomic.fna.gz --refList GCF_900186975.1_50569_F01_genomic.fna/target_genomes.txt --output GCF_900186975.1_50569_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:54,289] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:54,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:54,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:54,301] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:03:54,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:54,301] [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
Cutibacterium granulosum	strain=NCTC11865	GCA_900186975.1	33011	33011	type	True	100.0	724	725	95	conclusive
Cutibacterium granulosum	strain=DSM 20700	GCA_001700755.2	33011	33011	type	True	99.9726	689	725	95	conclusive
Cutibacterium granulosum	strain=DSM 20700	GCA_000463665.1	33011	33011	type	True	98.4741	529	725	95	conclusive
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	80.7398	325	725	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	79.3631	310	725	95	below_threshold
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	79.2505	255	725	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	79.0977	307	725	95	below_threshold
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	79.0185	277	725	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	79.0011	205	725	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	77.5472	133	725	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.0912	139	725	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	76.8658	80	725	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	76.8148	127	725	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.3544	105	725	95	below_threshold
Jatrophihabitans telluris	strain=N237	GCA_023516435.1	2038343	2038343	type	True	76.2866	59	725	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	76.2452	102	725	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	76.1825	57	725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:54,306] [INFO] DFAST Taxonomy check result was written to GCF_900186975.1_50569_F01_genomic.fna/tc_result.tsv
[2024-01-25 20:03:54,306] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:54,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:54,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/checkm_data
[2024-01-25 20:03:54,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:54,336] [INFO] Task started: CheckM
[2024-01-25 20:03:54,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900186975.1_50569_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900186975.1_50569_F01_genomic.fna/checkm_input GCF_900186975.1_50569_F01_genomic.fna/checkm_result
[2024-01-25 20:04:57,819] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:57,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:57,835] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:57,835] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:57,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900186975.1_50569_F01_genomic.fna/markers.fasta)
[2024-01-25 20:04:57,836] [INFO] Task started: Blastn
[2024-01-25 20:04:57,836] [INFO] Running command: blastn -query GCF_900186975.1_50569_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg232c85b2-54c6-4104-9f78-ef08f3346732/dqc_reference/reference_markers_gtdb.fasta -out GCF_900186975.1_50569_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:59,182] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:59,185] [INFO] Selected 13 target genomes.
[2024-01-25 20:04:59,185] [INFO] Target genome list was writen to GCF_900186975.1_50569_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:59,207] [INFO] Task started: fastANI
[2024-01-25 20:04:59,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b03598-7c97-4932-b02c-65e3e4247add/GCF_900186975.1_50569_F01_genomic.fna.gz --refList GCF_900186975.1_50569_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900186975.1_50569_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:07,098] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:07,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:07,107] [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_900186975.1	s__Cutibacterium granulosum	100.0	724	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	98.45	97.35	0.97	0.94	5	conclusive
GCF_000227295.1	s__Cutibacterium avidum	80.7398	325	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_900605005.1	s__Cutibacterium timonense	80.5715	373	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	79.3328	311	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_000423445.1	s__Acidipropionibacterium thoenii	79.2321	256	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325455.1	s__Acidipropionibacterium virtanenii	79.0957	308	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425285.1	s__Acidipropionibacterium jensenii	79.002	278	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	-
GCF_003030305.1	s__Cutibacterium acnes	78.9513	205	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	-
GCF_014164775.1	s__Arachnia sp014164775	76.9063	114	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.46	97.46	0.87	0.87	2	-
GCA_012837465.1	s__Arachnia sp012837465	76.894	116	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	76.88	84	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	76.8148	127	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_001424755.1	s__Marmoricola sp001424755	76.6474	97	725	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:07,109] [INFO] GTDB search result was written to GCF_900186975.1_50569_F01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:07,110] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:07,113] [INFO] DFAST_QC result json was written to GCF_900186975.1_50569_F01_genomic.fna/dqc_result.json
[2024-01-25 20:05:07,113] [INFO] DFAST_QC completed!
[2024-01-25 20:05:07,113] [INFO] Total running time: 0h1m32s