[2024-01-24 12:44:11,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference
[2024-01-24 12:44:12,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,467] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b46d8bc-d5ad-46df-a753-23e330f9fff4/GCF_014652415.1_ASM1465241v1_genomic.fna.gz | prodigal -d GCF_014652415.1_ASM1465241v1_genomic.fna/cds.fna -a GCF_014652415.1_ASM1465241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:24,292] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:24,292] [INFO] Task started: HMMsearch
[2024-01-24 12:44:24,293] [INFO] Running command: hmmsearch --tblout GCF_014652415.1_ASM1465241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/reference_markers.hmm GCF_014652415.1_ASM1465241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:24,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:24,660] [INFO] Found 6/6 markers.
[2024-01-24 12:44:24,696] [INFO] Query marker FASTA was written to GCF_014652415.1_ASM1465241v1_genomic.fna/markers.fasta
[2024-01-24 12:44:24,697] [INFO] Task started: Blastn
[2024-01-24 12:44:24,697] [INFO] Running command: blastn -query GCF_014652415.1_ASM1465241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/reference_markers.fasta -out GCF_014652415.1_ASM1465241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:25,428] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:25,431] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:25,432] [INFO] Target genome list was writen to GCF_014652415.1_ASM1465241v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:25,438] [INFO] Task started: fastANI
[2024-01-24 12:44:25,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b46d8bc-d5ad-46df-a753-23e330f9fff4/GCF_014652415.1_ASM1465241v1_genomic.fna.gz --refList GCF_014652415.1_ASM1465241v1_genomic.fna/target_genomes.txt --output GCF_014652415.1_ASM1465241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:34,814] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:34,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:34,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:34,827] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:34,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:34,828] [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
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	100.0	1412	1413	95	conclusive
Undibacterium baiyunense	strain=BYS107W	GCA_018139645.1	2828731	2828731	type	True	94.3326	1275	1413	95	below_threshold
Undibacterium fentianense	strain=FT137W	GCA_018139545.1	2828728	2828728	type	True	83.3349	542	1413	95	below_threshold
Undibacterium amnicola	strain=KCTC 52442	GCA_014284275.1	1834038	1834038	type	True	81.4408	918	1413	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	80.9807	698	1413	95	below_threshold
Undibacterium flavidum	strain=LX15W	GCA_014284175.1	2762297	2762297	type	True	80.4463	633	1413	95	below_threshold
Undibacterium nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	80.093	379	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:34,830] [INFO] DFAST Taxonomy check result was written to GCF_014652415.1_ASM1465241v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:34,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:34,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:34,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/checkm_data
[2024-01-24 12:44:34,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:34,873] [INFO] Task started: CheckM
[2024-01-24 12:44:34,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652415.1_ASM1465241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652415.1_ASM1465241v1_genomic.fna/checkm_input GCF_014652415.1_ASM1465241v1_genomic.fna/checkm_result
[2024-01-24 12:45:14,989] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:14,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:15,015] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:15,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:15,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652415.1_ASM1465241v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:15,016] [INFO] Task started: Blastn
[2024-01-24 12:45:15,016] [INFO] Running command: blastn -query GCF_014652415.1_ASM1465241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg821bb990-ce52-4e8b-aab9-99a5561faae5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652415.1_ASM1465241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:16,128] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:16,132] [INFO] Selected 8 target genomes.
[2024-01-24 12:45:16,132] [INFO] Target genome list was writen to GCF_014652415.1_ASM1465241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:16,141] [INFO] Task started: fastANI
[2024-01-24 12:45:16,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b46d8bc-d5ad-46df-a753-23e330f9fff4/GCF_014652415.1_ASM1465241v1_genomic.fna.gz --refList GCF_014652415.1_ASM1465241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652415.1_ASM1465241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:24,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:24,168] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:24,169] [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_014652415.1	s__Undibacterium macrobrachii	100.0	1412	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139645.1	s__Undibacterium sp018139645	94.3326	1275	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139545.1	s__Undibacterium sp018139545	83.3469	541	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284275.1	s__Undibacterium amnicola	81.433	920	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482715.1	s__Undibacterium sp002482715	80.997	708	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284305.1	s__Undibacterium seohonense	80.9802	698	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284175.1	s__Undibacterium sp014284175	80.4272	635	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284115.1	s__Undibacterium sp014284115	80.0259	387	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:24,170] [INFO] GTDB search result was written to GCF_014652415.1_ASM1465241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:24,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:24,174] [INFO] DFAST_QC result json was written to GCF_014652415.1_ASM1465241v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:24,174] [INFO] DFAST_QC completed!
[2024-01-24 12:45:24,174] [INFO] Total running time: 0h1m13s