[2024-01-24 14:46:35,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,239] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,239] [INFO] DQC Reference Directory: /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference
[2024-01-24 14:46:37,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,185] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,185] [INFO] Running command: gunzip -c /var/lib/cwl/stg10cca435-e9e0-4d68-a76a-d07178b2f2fb/GCF_003254335.1_ASM325433v1_genomic.fna.gz | prodigal -d GCF_003254335.1_ASM325433v1_genomic.fna/cds.fna -a GCF_003254335.1_ASM325433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:51,392] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:51,392] [INFO] Task started: HMMsearch
[2024-01-24 14:46:51,392] [INFO] Running command: hmmsearch --tblout GCF_003254335.1_ASM325433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/reference_markers.hmm GCF_003254335.1_ASM325433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:51,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:51,629] [INFO] Found 6/6 markers.
[2024-01-24 14:46:51,672] [INFO] Query marker FASTA was written to GCF_003254335.1_ASM325433v1_genomic.fna/markers.fasta
[2024-01-24 14:46:51,673] [INFO] Task started: Blastn
[2024-01-24 14:46:51,673] [INFO] Running command: blastn -query GCF_003254335.1_ASM325433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/reference_markers.fasta -out GCF_003254335.1_ASM325433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:52,759] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:52,762] [INFO] Selected 16 target genomes.
[2024-01-24 14:46:52,763] [INFO] Target genome list was writen to GCF_003254335.1_ASM325433v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:52,769] [INFO] Task started: fastANI
[2024-01-24 14:46:52,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cca435-e9e0-4d68-a76a-d07178b2f2fb/GCF_003254335.1_ASM325433v1_genomic.fna.gz --refList GCF_003254335.1_ASM325433v1_genomic.fna/target_genomes.txt --output GCF_003254335.1_ASM325433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:07,793] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:07,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:07,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:07,807] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:07,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:07,808] [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
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	100.0	1597	1601	95	conclusive
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	99.8186	1387	1601	95	conclusive
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	82.5685	808	1601	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	82.5394	884	1601	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	82.4426	891	1601	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	82.4391	882	1601	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	82.3184	815	1601	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	82.2771	840	1601	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	81.6168	733	1601	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	80.495	744	1601	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	80.4518	760	1601	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	80.326	750	1601	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.1381	692	1601	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.0536	646	1601	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.6334	659	1601	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	79.1123	568	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:07,809] [INFO] DFAST Taxonomy check result was written to GCF_003254335.1_ASM325433v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:07,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:07,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:07,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/checkm_data
[2024-01-24 14:47:07,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:07,855] [INFO] Task started: CheckM
[2024-01-24 14:47:07,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254335.1_ASM325433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254335.1_ASM325433v1_genomic.fna/checkm_input GCF_003254335.1_ASM325433v1_genomic.fna/checkm_result
[2024-01-24 14:47:55,353] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:55,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:55,369] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:55,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:55,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254335.1_ASM325433v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:55,370] [INFO] Task started: Blastn
[2024-01-24 14:47:55,371] [INFO] Running command: blastn -query GCF_003254335.1_ASM325433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge087be99-b386-4b73-8926-cde00fb28892/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254335.1_ASM325433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:57,500] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:57,503] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:57,503] [INFO] Target genome list was writen to GCF_003254335.1_ASM325433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:57,514] [INFO] Task started: fastANI
[2024-01-24 14:47:57,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cca435-e9e0-4d68-a76a-d07178b2f2fb/GCF_003254335.1_ASM325433v1_genomic.fna.gz --refList GCF_003254335.1_ASM325433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254335.1_ASM325433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:11,189] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:11,202] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:11,203] [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_003034985.1	s__Cereibacter changlensis	99.8186	1387	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	conclusive
GCF_002407205.1	s__Cereibacter_A sp002407205	82.8143	867	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720585.1	s__Cereibacter_A johrii	82.5734	807	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCA_017599285.1	s__Cereibacter_A azotoformans	82.4654	738	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	82.463	891	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_900207575.1	s__Cereibacter_A ovatus	81.6266	732	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	80.5301	750	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908165.1	s__Frigidibacter albus	80.5058	742	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_001620265.1	s__Frigidibacter mobilis	80.3153	750	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	80.1584	690	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	79.6575	620	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	79.648	659	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003243455.1	s__Rhodobacter_F sphaeroides_A	79.3996	557	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859075.1	s__Gemmobacter aquaticus	79.1445	515	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003060865.1	s__Gemmobacter_B sp003060865	79.1372	565	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:11,206] [INFO] GTDB search result was written to GCF_003254335.1_ASM325433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:11,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:11,211] [INFO] DFAST_QC result json was written to GCF_003254335.1_ASM325433v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:11,211] [INFO] DFAST_QC completed!
[2024-01-24 14:48:11,211] [INFO] Total running time: 0h1m36s