[2024-01-24 13:10:19,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference
[2024-01-24 13:10:20,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,555] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg08f28612-06b8-498e-a5cd-30a6b485d64c/GCF_003583935.1_ASM358393v1_genomic.fna.gz | prodigal -d GCF_003583935.1_ASM358393v1_genomic.fna/cds.fna -a GCF_003583935.1_ASM358393v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:31,747] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:31,748] [INFO] Task started: HMMsearch
[2024-01-24 13:10:31,748] [INFO] Running command: hmmsearch --tblout GCF_003583935.1_ASM358393v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/reference_markers.hmm GCF_003583935.1_ASM358393v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:32,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:32,092] [INFO] Found 6/6 markers.
[2024-01-24 13:10:32,133] [INFO] Query marker FASTA was written to GCF_003583935.1_ASM358393v1_genomic.fna/markers.fasta
[2024-01-24 13:10:32,133] [INFO] Task started: Blastn
[2024-01-24 13:10:32,133] [INFO] Running command: blastn -query GCF_003583935.1_ASM358393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/reference_markers.fasta -out GCF_003583935.1_ASM358393v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:33,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:33,260] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:33,261] [INFO] Target genome list was writen to GCF_003583935.1_ASM358393v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:33,274] [INFO] Task started: fastANI
[2024-01-24 13:10:33,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f28612-06b8-498e-a5cd-30a6b485d64c/GCF_003583935.1_ASM358393v1_genomic.fna.gz --refList GCF_003583935.1_ASM358393v1_genomic.fna/target_genomes.txt --output GCF_003583935.1_ASM358393v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:49,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:49,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:49,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:49,383] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:49,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:49,384] [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
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	100.0	1348	1349	95	conclusive
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	85.6244	994	1349	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	82.2093	826	1349	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	82.1672	832	1349	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	82.021	815	1349	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	80.3523	561	1349	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	80.0334	597	1349	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.5437	561	1349	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.2356	601	1349	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.3785	424	1349	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.9785	377	1349	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.5945	353	1349	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	77.2378	323	1349	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	76.5598	187	1349	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	75.5851	79	1349	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	74.9818	174	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:49,385] [INFO] DFAST Taxonomy check result was written to GCF_003583935.1_ASM358393v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:49,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:49,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:49,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/checkm_data
[2024-01-24 13:10:49,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:49,428] [INFO] Task started: CheckM
[2024-01-24 13:10:49,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583935.1_ASM358393v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583935.1_ASM358393v1_genomic.fna/checkm_input GCF_003583935.1_ASM358393v1_genomic.fna/checkm_result
[2024-01-24 13:11:28,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:28,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:28,611] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:28,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:28,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583935.1_ASM358393v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:28,612] [INFO] Task started: Blastn
[2024-01-24 13:11:28,613] [INFO] Running command: blastn -query GCF_003583935.1_ASM358393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd53af00-b532-4468-97bb-cb9c699e982f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583935.1_ASM358393v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:30,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:30,448] [INFO] Selected 12 target genomes.
[2024-01-24 13:11:30,449] [INFO] Target genome list was writen to GCF_003583935.1_ASM358393v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:30,460] [INFO] Task started: fastANI
[2024-01-24 13:11:30,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f28612-06b8-498e-a5cd-30a6b485d64c/GCF_003583935.1_ASM358393v1_genomic.fna.gz --refList GCF_003583935.1_ASM358393v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583935.1_ASM358393v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:41,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:41,994] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:41,994] [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_003583935.1	s__Aureimonas flava	100.0	1348	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001463745.1	s__Aureimonas sp001463745	86.1855	989	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423245.1	s__Aureimonas sp001423245	85.8993	1007	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	85.5591	994	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_903970965.1	s__Aureimonas sp903970965	83.5045	864	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	82.14	835	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001463705.1	s__Aureimonas sp001463705	81.5665	826	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014058705.1	s__Aureimonas mangrovi	80.3395	560	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	78.3089	490	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCA_900470805.1	s__Rhizobium sp900470805	77.4386	339	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858865.1	s__Caulobacter vibrioides	76.5837	185	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.80	98.06	0.96	0.95	6	-
GCF_002310375.3	s__Caulobacter vibrioides_D	76.4441	195	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:41,996] [INFO] GTDB search result was written to GCF_003583935.1_ASM358393v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:41,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:42,000] [INFO] DFAST_QC result json was written to GCF_003583935.1_ASM358393v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:42,000] [INFO] DFAST_QC completed!
[2024-01-24 13:11:42,001] [INFO] Total running time: 0h1m23s