[2024-01-24 14:05:15,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:15,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:15,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference
[2024-01-24 14:05:16,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:16,457] [INFO] Task started: Prodigal
[2024-01-24 14:05:16,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cfbccbb-8ef1-4e13-b824-4233b3288fb6/GCF_005234135.1_ASM523413v1_genomic.fna.gz | prodigal -d GCF_005234135.1_ASM523413v1_genomic.fna/cds.fna -a GCF_005234135.1_ASM523413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:30,692] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:30,692] [INFO] Task started: HMMsearch
[2024-01-24 14:05:30,693] [INFO] Running command: hmmsearch --tblout GCF_005234135.1_ASM523413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/reference_markers.hmm GCF_005234135.1_ASM523413v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:30,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:30,982] [INFO] Found 6/6 markers.
[2024-01-24 14:05:31,029] [INFO] Query marker FASTA was written to GCF_005234135.1_ASM523413v1_genomic.fna/markers.fasta
[2024-01-24 14:05:31,030] [INFO] Task started: Blastn
[2024-01-24 14:05:31,030] [INFO] Running command: blastn -query GCF_005234135.1_ASM523413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/reference_markers.fasta -out GCF_005234135.1_ASM523413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:31,785] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:31,790] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:31,791] [INFO] Target genome list was writen to GCF_005234135.1_ASM523413v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:31,800] [INFO] Task started: fastANI
[2024-01-24 14:05:31,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfbccbb-8ef1-4e13-b824-4233b3288fb6/GCF_005234135.1_ASM523413v1_genomic.fna.gz --refList GCF_005234135.1_ASM523413v1_genomic.fna/target_genomes.txt --output GCF_005234135.1_ASM523413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:42,536] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:42,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:42,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:42,553] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:42,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:42,554] [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
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	100.0	1410	1414	95	conclusive
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	87.8132	944	1414	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	79.4082	523	1414	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	79.3954	527	1414	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	78.6228	501	1414	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	78.621	502	1414	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.6746	365	1414	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.1729	242	1414	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.0528	306	1414	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.9116	259	1414	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	76.9054	193	1414	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.8996	239	1414	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.29	202	1414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:42,555] [INFO] DFAST Taxonomy check result was written to GCF_005234135.1_ASM523413v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:42,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:42,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:42,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/checkm_data
[2024-01-24 14:05:42,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:42,599] [INFO] Task started: CheckM
[2024-01-24 14:05:42,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005234135.1_ASM523413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005234135.1_ASM523413v1_genomic.fna/checkm_input GCF_005234135.1_ASM523413v1_genomic.fna/checkm_result
[2024-01-24 14:06:27,261] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:27,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,283] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:27,283] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:27,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005234135.1_ASM523413v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:27,284] [INFO] Task started: Blastn
[2024-01-24 14:06:27,284] [INFO] Running command: blastn -query GCF_005234135.1_ASM523413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd682c7b2-d21b-4722-82da-07f6977a64b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_005234135.1_ASM523413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:28,606] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:28,613] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:28,613] [INFO] Target genome list was writen to GCF_005234135.1_ASM523413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:28,623] [INFO] Task started: fastANI
[2024-01-24 14:06:28,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfbccbb-8ef1-4e13-b824-4233b3288fb6/GCF_005234135.1_ASM523413v1_genomic.fna.gz --refList GCF_005234135.1_ASM523413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005234135.1_ASM523413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:37,057] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:37,066] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:37,066] [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_005234135.1	s__Pseudorhodobacter turbinis	100.0	1411	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001202025.1	s__Pseudorhodobacter aquimaris	87.801	945	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	80.0084	584	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420745.1	s__Pseudorhodobacter ferrugineus	79.4418	519	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001202035.1	s__Pseudorhodobacter wandonensis	79.4039	528	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110135.1	s__Pseudorhodobacter antarcticus	78.621	502	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009380135.2	s__Fertoeibacter niger	77.4455	340	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	77.2389	322	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693875.1	s__SSD5 sp013693875	76.5884	205	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:37,068] [INFO] GTDB search result was written to GCF_005234135.1_ASM523413v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:37,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:37,073] [INFO] DFAST_QC result json was written to GCF_005234135.1_ASM523413v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:37,073] [INFO] DFAST_QC completed!
[2024-01-24 14:06:37,074] [INFO] Total running time: 0h1m22s