[2024-01-25 20:18:05,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:05,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:05,592] [INFO] DQC Reference Directory: /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference
[2024-01-25 20:18:06,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:06,724] [INFO] Task started: Prodigal
[2024-01-25 20:18:06,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg19016240-d275-4708-b99c-8e59e54f7b96/GCF_014904065.1_ASM1490406v1_genomic.fna.gz | prodigal -d GCF_014904065.1_ASM1490406v1_genomic.fna/cds.fna -a GCF_014904065.1_ASM1490406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:13,728] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:13,728] [INFO] Task started: HMMsearch
[2024-01-25 20:18:13,728] [INFO] Running command: hmmsearch --tblout GCF_014904065.1_ASM1490406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/reference_markers.hmm GCF_014904065.1_ASM1490406v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:13,927] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:13,928] [INFO] Found 6/6 markers.
[2024-01-25 20:18:13,953] [INFO] Query marker FASTA was written to GCF_014904065.1_ASM1490406v1_genomic.fna/markers.fasta
[2024-01-25 20:18:13,953] [INFO] Task started: Blastn
[2024-01-25 20:18:13,953] [INFO] Running command: blastn -query GCF_014904065.1_ASM1490406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/reference_markers.fasta -out GCF_014904065.1_ASM1490406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:15,114] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:15,117] [INFO] Selected 18 target genomes.
[2024-01-25 20:18:15,117] [INFO] Target genome list was writen to GCF_014904065.1_ASM1490406v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:15,135] [INFO] Task started: fastANI
[2024-01-25 20:18:15,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg19016240-d275-4708-b99c-8e59e54f7b96/GCF_014904065.1_ASM1490406v1_genomic.fna.gz --refList GCF_014904065.1_ASM1490406v1_genomic.fna/target_genomes.txt --output GCF_014904065.1_ASM1490406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:26,452] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:26,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:26,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:26,463] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:26,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:26,464] [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
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	84.31	633	865	95	below_threshold
Gulosibacter molinativorax	strain=DSM 13485	GCA_000425685.1	256821	256821	type	True	79.5901	380	865	95	below_threshold
Gulosibacter molinativorax	strain=ON4	GCA_003010915.2	256821	256821	type	True	79.5701	388	865	95	below_threshold
Gulosibacter macacae	strain=YIM 102482-1	GCA_003865375.1	2488791	2488791	type	True	79.465	350	865	95	below_threshold
Gulosibacter bifidus	strain=NBRC 103089	GCA_001570925.1	272239	272239	type	True	78.4358	246	865	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	78.3552	348	865	95	below_threshold
Gulosibacter chungangensis	strain=KCTC 13959	GCA_008831155.1	979746	979746	type	True	78.3416	246	865	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_008831135.1	587635	587635	type	True	78.3152	345	865	95	below_threshold
Gulosibacter hominis	strain=401352-2018	GCA_904842695.1	2770504	2770504	type	True	78.0977	204	865	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.7387	257	865	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	77.6982	316	865	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	77.6194	286	865	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	77.5455	285	865	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	77.2548	223	865	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.1284	238	865	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.4445	221	865	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.302	228	865	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.2813	184	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:26,465] [INFO] DFAST Taxonomy check result was written to GCF_014904065.1_ASM1490406v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:26,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:26,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:26,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/checkm_data
[2024-01-25 20:18:26,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:26,495] [INFO] Task started: CheckM
[2024-01-25 20:18:26,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014904065.1_ASM1490406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014904065.1_ASM1490406v1_genomic.fna/checkm_input GCF_014904065.1_ASM1490406v1_genomic.fna/checkm_result
[2024-01-25 20:18:50,017] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:50,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:50,045] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:50,045] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:50,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014904065.1_ASM1490406v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:50,045] [INFO] Task started: Blastn
[2024-01-25 20:18:50,046] [INFO] Running command: blastn -query GCF_014904065.1_ASM1490406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd260a57b-790a-4f73-bd27-82f1fe43cdbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014904065.1_ASM1490406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:52,027] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:52,030] [INFO] Selected 12 target genomes.
[2024-01-25 20:18:52,031] [INFO] Target genome list was writen to GCF_014904065.1_ASM1490406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:52,040] [INFO] Task started: fastANI
[2024-01-25 20:18:52,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg19016240-d275-4708-b99c-8e59e54f7b96/GCF_014904065.1_ASM1490406v1_genomic.fna.gz --refList GCF_014904065.1_ASM1490406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014904065.1_ASM1490406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:59,419] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:59,427] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:59,427] [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_900626105.1	s__Gulosibacter sp900626105	98.804	799	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	conclusive
GCF_000381765.1	s__Gulosibacter faecalis	84.2771	637	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719255.1	s__Gulosibacter sp012719255	80.1539	378	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163695.1	s__Gulosibacter sp900163695	79.9181	436	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425685.1	s__Gulosibacter molinativorax	79.6112	378	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	99.97	99.97	0.98	0.98	2	-
GCF_003865375.1	s__Gulosibacter macacae	79.465	350	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910822395.1	s__Pseudoclavibacter sp910822395	79.0644	345	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570925.1	s__Gulosibacter bifidus	78.4515	245	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410545.1	s__Pseudoclavibacter chungangensis	78.3555	348	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016907355.1	s__Agromyces aurantiacus	77.7069	315	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	77.5997	288	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003581425.1	s__Amnibacterium setariae	77.2574	223	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:59,428] [INFO] GTDB search result was written to GCF_014904065.1_ASM1490406v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:59,429] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:59,432] [INFO] DFAST_QC result json was written to GCF_014904065.1_ASM1490406v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:59,432] [INFO] DFAST_QC completed!
[2024-01-25 20:18:59,432] [INFO] Total running time: 0h0m54s