[2024-01-24 13:58:25,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference
[2024-01-24 13:58:26,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,918] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d521eda-9682-4199-8fa6-521f027ce25c/GCF_005876985.1_ASM587698v1_genomic.fna.gz | prodigal -d GCF_005876985.1_ASM587698v1_genomic.fna/cds.fna -a GCF_005876985.1_ASM587698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:42,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:42,104] [INFO] Task started: HMMsearch
[2024-01-24 13:58:42,104] [INFO] Running command: hmmsearch --tblout GCF_005876985.1_ASM587698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/reference_markers.hmm GCF_005876985.1_ASM587698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:42,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:42,390] [INFO] Found 6/6 markers.
[2024-01-24 13:58:42,426] [INFO] Query marker FASTA was written to GCF_005876985.1_ASM587698v1_genomic.fna/markers.fasta
[2024-01-24 13:58:42,426] [INFO] Task started: Blastn
[2024-01-24 13:58:42,426] [INFO] Running command: blastn -query GCF_005876985.1_ASM587698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/reference_markers.fasta -out GCF_005876985.1_ASM587698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,339] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:43,340] [INFO] Target genome list was writen to GCF_005876985.1_ASM587698v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:43,388] [INFO] Task started: fastANI
[2024-01-24 13:58:43,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d521eda-9682-4199-8fa6-521f027ce25c/GCF_005876985.1_ASM587698v1_genomic.fna.gz --refList GCF_005876985.1_ASM587698v1_genomic.fna/target_genomes.txt --output GCF_005876985.1_ASM587698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:00,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:00,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:00,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:00,733] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:00,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:00,734] [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
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	100.0	1221	1221	95	conclusive
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	80.8036	673	1221	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	80.6915	694	1221	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	80.1936	606	1221	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	80.0419	454	1221	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	79.3134	472	1221	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.1352	432	1221	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	78.8027	444	1221	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	78.7884	373	1221	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	78.7149	431	1221	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	78.6652	369	1221	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	78.6231	374	1221	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	78.5986	366	1221	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.5905	427	1221	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	78.4815	399	1221	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	78.4791	273	1221	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.2607	345	1221	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	78.2262	270	1221	95	below_threshold
Brachymonas chironomi	strain=DSM 19884	GCA_000374625.1	491919	491919	type	True	78.1504	228	1221	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.0968	327	1221	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	78.0513	303	1221	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.0215	336	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:00,740] [INFO] DFAST Taxonomy check result was written to GCF_005876985.1_ASM587698v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:00,740] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:00,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:00,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/checkm_data
[2024-01-24 13:59:00,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:00,781] [INFO] Task started: CheckM
[2024-01-24 13:59:00,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005876985.1_ASM587698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005876985.1_ASM587698v1_genomic.fna/checkm_input GCF_005876985.1_ASM587698v1_genomic.fna/checkm_result
[2024-01-24 13:59:42,658] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:42,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:42,681] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:42,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:42,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005876985.1_ASM587698v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:42,682] [INFO] Task started: Blastn
[2024-01-24 13:59:42,682] [INFO] Running command: blastn -query GCF_005876985.1_ASM587698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d6f0df-77a5-4d54-994d-c90dc4fb5f2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005876985.1_ASM587698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:44,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:44,106] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:44,106] [INFO] Target genome list was writen to GCF_005876985.1_ASM587698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:44,115] [INFO] Task started: fastANI
[2024-01-24 13:59:44,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d521eda-9682-4199-8fa6-521f027ce25c/GCF_005876985.1_ASM587698v1_genomic.fna.gz --refList GCF_005876985.1_ASM587698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005876985.1_ASM587698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:52,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:52,572] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:52,572] [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_005876985.1	s__Rhodoferax bucti	100.0	1221	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002163715.1	s__Rhodoferax sp002163715	86.1912	927	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	97.64	97.64	0.97	0.97	2	-
GCA_009925925.1	s__Rhodoferax sp009925925	85.6328	757	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390825.1	s__Rhodoferax sp002390825	84.1436	723	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297935.1	s__Rhodoferax sp013297935	83.8406	832	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795455.1	s__Rhodoferax sp001795455	82.9993	828	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_002943465.1	s__Rhodoferax sp002943465	82.5893	847	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251855.1	s__Rhodoferax sp002251855	82.3945	810	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955715.1	s__Rhodoferax saidenbachensis	80.8198	669	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:52,574] [INFO] GTDB search result was written to GCF_005876985.1_ASM587698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:52,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:52,578] [INFO] DFAST_QC result json was written to GCF_005876985.1_ASM587698v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:52,579] [INFO] DFAST_QC completed!
[2024-01-24 13:59:52,579] [INFO] Total running time: 0h1m27s