[2024-01-24 13:12:55,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference
[2024-01-24 13:12:57,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,155] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca47010-16ce-43ed-8cd6-1dade9ded552/GCF_019448115.1_ASM1944811v1_genomic.fna.gz | prodigal -d GCF_019448115.1_ASM1944811v1_genomic.fna/cds.fna -a GCF_019448115.1_ASM1944811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:01,117] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:01,118] [INFO] Task started: HMMsearch
[2024-01-24 13:13:01,118] [INFO] Running command: hmmsearch --tblout GCF_019448115.1_ASM1944811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/reference_markers.hmm GCF_019448115.1_ASM1944811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:01,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:01,387] [INFO] Found 6/6 markers.
[2024-01-24 13:13:01,411] [INFO] Query marker FASTA was written to GCF_019448115.1_ASM1944811v1_genomic.fna/markers.fasta
[2024-01-24 13:13:01,412] [INFO] Task started: Blastn
[2024-01-24 13:13:01,412] [INFO] Running command: blastn -query GCF_019448115.1_ASM1944811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/reference_markers.fasta -out GCF_019448115.1_ASM1944811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:02,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:02,013] [INFO] Selected 30 target genomes.
[2024-01-24 13:13:02,014] [INFO] Target genome list was writen to GCF_019448115.1_ASM1944811v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:02,068] [INFO] Task started: fastANI
[2024-01-24 13:13:02,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca47010-16ce-43ed-8cd6-1dade9ded552/GCF_019448115.1_ASM1944811v1_genomic.fna.gz --refList GCF_019448115.1_ASM1944811v1_genomic.fna/target_genomes.txt --output GCF_019448115.1_ASM1944811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:18,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:18,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:18,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:18,485] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:18,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:18,485] [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
Succinivibrio dextrinosolvens	strain=DSM 3072	GCA_900167015.1	83771	83771	type	True	78.6341	199	674	95	below_threshold
Anaerobiospirillum succiniciproducens	strain=DSM 6400	GCA_000482845.1	13335	13335	type	True	77.3907	54	674	95	below_threshold
Anaerobiospirillum thomasii	strain=NCTC12467	GCA_900445255.1	179995	179995	type	True	76.8309	54	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:18,487] [INFO] DFAST Taxonomy check result was written to GCF_019448115.1_ASM1944811v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:18,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:18,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:18,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/checkm_data
[2024-01-24 13:13:18,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:18,518] [INFO] Task started: CheckM
[2024-01-24 13:13:18,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019448115.1_ASM1944811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019448115.1_ASM1944811v1_genomic.fna/checkm_input GCF_019448115.1_ASM1944811v1_genomic.fna/checkm_result
[2024-01-24 13:13:38,718] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:38,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,742] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:38,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:38,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019448115.1_ASM1944811v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:38,743] [INFO] Task started: Blastn
[2024-01-24 13:13:38,743] [INFO] Running command: blastn -query GCF_019448115.1_ASM1944811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a94aab-d4ca-4ff7-bdee-dabf13ef6dd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019448115.1_ASM1944811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:39,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:39,599] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:39,599] [INFO] Target genome list was writen to GCF_019448115.1_ASM1944811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:39,648] [INFO] Task started: fastANI
[2024-01-24 13:13:39,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca47010-16ce-43ed-8cd6-1dade9ded552/GCF_019448115.1_ASM1944811v1_genomic.fna.gz --refList GCF_019448115.1_ASM1944811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019448115.1_ASM1944811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:46,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:46,319] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:46,320] [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
GCA_004556245.1	s__Succinivibrio hippei_B	98.288	464	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902785325.1	s__Succinivibrio sp003456415	80.1223	190	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.60	98.18	0.90	0.86	5	-
GCA_900315395.1	s__Succinivibrio sp900315395	79.4067	200	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.82	99.64	0.93	0.87	3	-
GCA_012519775.1	s__Succinivibrio sp012519775	79.1707	182	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449335.1	s__Succinivibrio sp002449335	79.1424	212	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.89	95.86	0.90	0.86	3	-
GCA_900316175.1	s__Succinivibrio sp900316175	79.118	175	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.29	98.66	0.86	0.80	9	-
GCA_000431835.1	s__Succinivibrio sp000431835	79.0508	220	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.12	95.78	0.87	0.82	11	-
GCF_900167015.1	s__Succinivibrio dextrinosolvens	78.6341	199	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	96.59	96.11	0.85	0.83	6	-
GCA_900316375.1	s__Succinivibrio sp900316375	78.6086	152	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.95	99.95	0.97	0.97	2	-
GCF_011065405.1	s__Succinivibrio dextrinosolvens_A	78.4572	185	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.30	97.32	0.93	0.84	6	-
GCA_905186145.1	s__Succinivibrio sp905186145	77.4093	89	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548485.1	s__Succinivibrio sp900548485	76.8567	57	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.05	99.05	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:46,321] [INFO] GTDB search result was written to GCF_019448115.1_ASM1944811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:46,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:46,324] [INFO] DFAST_QC result json was written to GCF_019448115.1_ASM1944811v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:46,325] [INFO] DFAST_QC completed!
[2024-01-24 13:13:46,325] [INFO] Total running time: 0h0m51s