[2024-01-24 13:46:25,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference
[2024-01-24 13:46:26,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,964] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,964] [INFO] Running command: gunzip -c /var/lib/cwl/stga2ece99d-01bb-4202-94a4-75e08ad4880d/GCF_000482845.1_ASM48284v1_genomic.fna.gz | prodigal -d GCF_000482845.1_ASM48284v1_genomic.fna/cds.fna -a GCF_000482845.1_ASM48284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:34,505] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:34,505] [INFO] Task started: HMMsearch
[2024-01-24 13:46:34,505] [INFO] Running command: hmmsearch --tblout GCF_000482845.1_ASM48284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/reference_markers.hmm GCF_000482845.1_ASM48284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:34,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:34,779] [INFO] Found 6/6 markers.
[2024-01-24 13:46:34,812] [INFO] Query marker FASTA was written to GCF_000482845.1_ASM48284v1_genomic.fna/markers.fasta
[2024-01-24 13:46:34,813] [INFO] Task started: Blastn
[2024-01-24 13:46:34,813] [INFO] Running command: blastn -query GCF_000482845.1_ASM48284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/reference_markers.fasta -out GCF_000482845.1_ASM48284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:35,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:35,464] [INFO] Selected 26 target genomes.
[2024-01-24 13:46:35,465] [INFO] Target genome list was writen to GCF_000482845.1_ASM48284v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:35,490] [INFO] Task started: fastANI
[2024-01-24 13:46:35,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ece99d-01bb-4202-94a4-75e08ad4880d/GCF_000482845.1_ASM48284v1_genomic.fna.gz --refList GCF_000482845.1_ASM48284v1_genomic.fna/target_genomes.txt --output GCF_000482845.1_ASM48284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:53,490] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:53,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:53,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:53,495] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:53,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:53,496] [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
Anaerobiospirillum succiniciproducens	strain=DSM 6400	GCA_000482845.1	13335	13335	type	True	100.0	1180	1191	95	conclusive
Anaerobiospirillum thomasii	strain=NCTC12467	GCA_900445255.1	179995	179995	type	True	77.6183	82	1191	95	below_threshold
Succinivibrio dextrinosolvens	strain=DSM 3072	GCA_900167015.1	83771	83771	type	True	77.3728	71	1191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:53,497] [INFO] DFAST Taxonomy check result was written to GCF_000482845.1_ASM48284v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:53,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:53,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:53,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/checkm_data
[2024-01-24 13:46:53,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:53,537] [INFO] Task started: CheckM
[2024-01-24 13:46:53,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482845.1_ASM48284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482845.1_ASM48284v1_genomic.fna/checkm_input GCF_000482845.1_ASM48284v1_genomic.fna/checkm_result
[2024-01-24 13:47:21,089] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:21,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:21,111] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:21,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:21,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482845.1_ASM48284v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:21,112] [INFO] Task started: Blastn
[2024-01-24 13:47:21,112] [INFO] Running command: blastn -query GCF_000482845.1_ASM48284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803a675f-7ea0-4e05-8439-5868626d7ba2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482845.1_ASM48284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:21,871] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:21,915] [INFO] Selected 17 target genomes.
[2024-01-24 13:47:21,915] [INFO] Target genome list was writen to GCF_000482845.1_ASM48284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:21,931] [INFO] Task started: fastANI
[2024-01-24 13:47:21,932] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ece99d-01bb-4202-94a4-75e08ad4880d/GCF_000482845.1_ASM48284v1_genomic.fna.gz --refList GCF_000482845.1_ASM48284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482845.1_ASM48284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:30,805] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:30,814] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:30,814] [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_000482845.1	s__Anaerobiospirillum succiniciproducens	100.0	1180	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900543125.1	s__Anaerobiospirillum sp900543125	79.0147	247	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	99.86	99.86	0.90	0.90	2	-
GCA_019113025.1	s__Anaerobiospirillum stercoravium	78.0549	117	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114785.1	s__Anaerobiospirillum pullistercoris	78.046	180	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018884035.1	s__Anaerobiospirillum pullicola	77.7463	123	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552905.1	s__Succinivibrio sp900552905	77.69	50	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.96	98.95	0.94	0.94	3	-
GCA_905186145.1	s__Succinivibrio sp905186145	77.2821	72	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315395.1	s__Succinivibrio sp900315395	77.0678	72	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.82	99.64	0.93	0.87	3	-
GCA_002449335.1	s__Succinivibrio sp002449335	76.3697	75	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.89	95.86	0.90	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,816] [INFO] GTDB search result was written to GCF_000482845.1_ASM48284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:30,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:30,820] [INFO] DFAST_QC result json was written to GCF_000482845.1_ASM48284v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:30,820] [INFO] DFAST_QC completed!
[2024-01-24 13:47:30,820] [INFO] Total running time: 0h1m5s