[2024-01-24 12:21:59,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,289] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference
[2024-01-24 12:22:00,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,718] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgc58efebe-aad0-4315-900c-d19a2e8d87b2/GCF_003014495.1_ASM301449v1_genomic.fna.gz | prodigal -d GCF_003014495.1_ASM301449v1_genomic.fna/cds.fna -a GCF_003014495.1_ASM301449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:25,754] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:25,755] [INFO] Task started: HMMsearch
[2024-01-24 12:22:25,755] [INFO] Running command: hmmsearch --tblout GCF_003014495.1_ASM301449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/reference_markers.hmm GCF_003014495.1_ASM301449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:26,072] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:26,074] [INFO] Found 6/6 markers.
[2024-01-24 12:22:26,117] [INFO] Query marker FASTA was written to GCF_003014495.1_ASM301449v1_genomic.fna/markers.fasta
[2024-01-24 12:22:26,118] [INFO] Task started: Blastn
[2024-01-24 12:22:26,118] [INFO] Running command: blastn -query GCF_003014495.1_ASM301449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/reference_markers.fasta -out GCF_003014495.1_ASM301449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:26,766] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:26,773] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:26,774] [INFO] Target genome list was writen to GCF_003014495.1_ASM301449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:26,780] [INFO] Task started: fastANI
[2024-01-24 12:22:26,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgc58efebe-aad0-4315-900c-d19a2e8d87b2/GCF_003014495.1_ASM301449v1_genomic.fna.gz --refList GCF_003014495.1_ASM301449v1_genomic.fna/target_genomes.txt --output GCF_003014495.1_ASM301449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:35,033] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:35,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:35,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:35,040] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:35,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:35,040] [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
Prolixibacter denitrificans	strain=DSM 27267	GCA_003014495.1	1541063	1541063	type	True	100.0	1555	1557	95	conclusive
Prolixibacter denitrificans	strain=MIC1-1	GCA_009617855.1	1541063	1541063	type	True	99.9991	1556	1557	95	conclusive
Prolixibacter bellariivorans	strain=JCM 13498	GCA_000614865.1	314319	314319	type	True	85.3167	1244	1557	95	below_threshold
Prolixibacter bellariivorans	strain=JCM 13498	GCA_009617915.1	314319	314319	type	True	85.3068	1251	1557	95	below_threshold
Prolixibacter bellariivorans	strain=ATCC BAA-1284	GCA_000621705.1	314319	314319	type	True	85.2951	1248	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:35,042] [INFO] DFAST Taxonomy check result was written to GCF_003014495.1_ASM301449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:35,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:35,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:35,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/checkm_data
[2024-01-24 12:22:35,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:35,091] [INFO] Task started: CheckM
[2024-01-24 12:22:35,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014495.1_ASM301449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014495.1_ASM301449v1_genomic.fna/checkm_input GCF_003014495.1_ASM301449v1_genomic.fna/checkm_result
[2024-01-24 12:23:43,719] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:43,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:43,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:43,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:43,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014495.1_ASM301449v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:43,742] [INFO] Task started: Blastn
[2024-01-24 12:23:43,742] [INFO] Running command: blastn -query GCF_003014495.1_ASM301449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f49a02-f018-4521-89d6-c1abbcebd838/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014495.1_ASM301449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:44,526] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:44,531] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:44,531] [INFO] Target genome list was writen to GCF_003014495.1_ASM301449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:44,556] [INFO] Task started: fastANI
[2024-01-24 12:23:44,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgc58efebe-aad0-4315-900c-d19a2e8d87b2/GCF_003014495.1_ASM301449v1_genomic.fna.gz --refList GCF_003014495.1_ASM301449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014495.1_ASM301449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:53,329] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:53,338] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:53,339] [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_003014495.1	s__Prolixibacter denitrificans	100.0	1555	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009617875.1	s__Prolixibacter sp009617875	93.3737	1366	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621705.1	s__Prolixibacter bellariivorans	85.2911	1248	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	99.99	99.97	1.00	1.00	3	-
GCF_009617895.1	s__Prolixibacter sp009617895	84.0201	962	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:53,340] [INFO] GTDB search result was written to GCF_003014495.1_ASM301449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:53,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:53,343] [INFO] DFAST_QC result json was written to GCF_003014495.1_ASM301449v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:53,344] [INFO] DFAST_QC completed!
[2024-01-24 12:23:53,344] [INFO] Total running time: 0h1m54s