[2024-01-25 19:09:05,457] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:05,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:05,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference
[2024-01-25 19:09:06,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:06,571] [INFO] Task started: Prodigal
[2024-01-25 19:09:06,572] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf492de5-0965-4ceb-9ce2-2f18ad28e67e/GCF_003443995.1_ASM344399v1_genomic.fna.gz | prodigal -d GCF_003443995.1_ASM344399v1_genomic.fna/cds.fna -a GCF_003443995.1_ASM344399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:19,651] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:19,651] [INFO] Task started: HMMsearch
[2024-01-25 19:09:19,651] [INFO] Running command: hmmsearch --tblout GCF_003443995.1_ASM344399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/reference_markers.hmm GCF_003443995.1_ASM344399v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:19,951] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:19,952] [INFO] Found 6/6 markers.
[2024-01-25 19:09:19,999] [INFO] Query marker FASTA was written to GCF_003443995.1_ASM344399v1_genomic.fna/markers.fasta
[2024-01-25 19:09:20,000] [INFO] Task started: Blastn
[2024-01-25 19:09:20,000] [INFO] Running command: blastn -query GCF_003443995.1_ASM344399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/reference_markers.fasta -out GCF_003443995.1_ASM344399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:20,866] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:20,869] [INFO] Selected 16 target genomes.
[2024-01-25 19:09:20,869] [INFO] Target genome list was writen to GCF_003443995.1_ASM344399v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:20,885] [INFO] Task started: fastANI
[2024-01-25 19:09:20,885] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf492de5-0965-4ceb-9ce2-2f18ad28e67e/GCF_003443995.1_ASM344399v1_genomic.fna.gz --refList GCF_003443995.1_ASM344399v1_genomic.fna/target_genomes.txt --output GCF_003443995.1_ASM344399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:34,790] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:34,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:34,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:34,801] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:34,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:34,802] [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
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	100.0	1502	1502	95	conclusive
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	85.71	967	1502	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	84.0213	941	1502	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.5818	634	1502	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.3575	618	1502	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.2882	580	1502	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.0699	607	1502	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.0528	619	1502	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.0471	621	1502	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.0369	612	1502	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.0207	597	1502	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.0172	609	1502	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.8498	546	1502	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.7413	502	1502	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	78.6624	577	1502	95	below_threshold
Cypionkella psychrotolerans	strain=PAMC 27389	GCA_001294535.1	1678131	1678131	type	True	78.3339	506	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:34,804] [INFO] DFAST Taxonomy check result was written to GCF_003443995.1_ASM344399v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:34,804] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:34,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:34,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/checkm_data
[2024-01-25 19:09:34,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:34,850] [INFO] Task started: CheckM
[2024-01-25 19:09:34,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003443995.1_ASM344399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003443995.1_ASM344399v1_genomic.fna/checkm_input GCF_003443995.1_ASM344399v1_genomic.fna/checkm_result
[2024-01-25 19:10:23,628] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:23,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:23,649] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:23,649] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:23,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003443995.1_ASM344399v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:23,651] [INFO] Task started: Blastn
[2024-01-25 19:10:23,651] [INFO] Running command: blastn -query GCF_003443995.1_ASM344399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf15f9488-7856-49ab-817c-10ba47a60a14/dqc_reference/reference_markers_gtdb.fasta -out GCF_003443995.1_ASM344399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:25,336] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:25,339] [INFO] Selected 7 target genomes.
[2024-01-25 19:10:25,339] [INFO] Target genome list was writen to GCF_003443995.1_ASM344399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:25,348] [INFO] Task started: fastANI
[2024-01-25 19:10:25,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf492de5-0965-4ceb-9ce2-2f18ad28e67e/GCF_003443995.1_ASM344399v1_genomic.fna.gz --refList GCF_003443995.1_ASM344399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003443995.1_ASM344399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:32,267] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:32,272] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:32,272] [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_003443995.1	s__ETT8 sp003443995	100.0	1502	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004745575.1	s__ETT8 sp004745575	85.7145	966	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	97.69	97.69	0.90	0.90	2	-
GCF_002900965.1	s__ETT8 sp002900965	85.1197	956	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	84.0392	939	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	83.7628	893	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936395.1	s__ETT8 sp016936395	81.9658	696	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	79.3692	617	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:32,274] [INFO] GTDB search result was written to GCF_003443995.1_ASM344399v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:32,274] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:32,277] [INFO] DFAST_QC result json was written to GCF_003443995.1_ASM344399v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:32,277] [INFO] DFAST_QC completed!
[2024-01-25 19:10:32,277] [INFO] Total running time: 0h1m27s