[2024-01-24 14:55:36,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:36,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:36,731] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference
[2024-01-24 14:55:38,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:38,072] [INFO] Task started: Prodigal
[2024-01-24 14:55:38,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a14807f-68ef-4720-a33e-67b7f6c45554/GCF_014199205.1_ASM1419920v1_genomic.fna.gz | prodigal -d GCF_014199205.1_ASM1419920v1_genomic.fna/cds.fna -a GCF_014199205.1_ASM1419920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:51,366] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:51,366] [INFO] Task started: HMMsearch
[2024-01-24 14:55:51,366] [INFO] Running command: hmmsearch --tblout GCF_014199205.1_ASM1419920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/reference_markers.hmm GCF_014199205.1_ASM1419920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:51,689] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:51,691] [INFO] Found 6/6 markers.
[2024-01-24 14:55:51,748] [INFO] Query marker FASTA was written to GCF_014199205.1_ASM1419920v1_genomic.fna/markers.fasta
[2024-01-24 14:55:51,753] [INFO] Task started: Blastn
[2024-01-24 14:55:51,753] [INFO] Running command: blastn -query GCF_014199205.1_ASM1419920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/reference_markers.fasta -out GCF_014199205.1_ASM1419920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:52,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:52,671] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:52,672] [INFO] Target genome list was writen to GCF_014199205.1_ASM1419920v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:52,684] [INFO] Task started: fastANI
[2024-01-24 14:55:52,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a14807f-68ef-4720-a33e-67b7f6c45554/GCF_014199205.1_ASM1419920v1_genomic.fna.gz --refList GCF_014199205.1_ASM1419920v1_genomic.fna/target_genomes.txt --output GCF_014199205.1_ASM1419920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:09,294] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:09,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:09,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:09,307] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:09,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:09,307] [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
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	100.0	1584	1585	95	conclusive
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	84.9314	1060	1585	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	83.4632	1023	1585	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	82.9016	937	1585	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.9144	718	1585	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	79.9006	680	1585	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	79.8396	699	1585	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.9605	620	1585	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.9074	612	1585	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.8518	627	1585	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.4941	511	1585	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.4791	584	1585	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.1138	450	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:09,309] [INFO] DFAST Taxonomy check result was written to GCF_014199205.1_ASM1419920v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:09,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:09,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:09,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/checkm_data
[2024-01-24 14:56:09,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:09,364] [INFO] Task started: CheckM
[2024-01-24 14:56:09,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199205.1_ASM1419920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199205.1_ASM1419920v1_genomic.fna/checkm_input GCF_014199205.1_ASM1419920v1_genomic.fna/checkm_result
[2024-01-24 14:56:52,438] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:52,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:52,463] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:52,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:52,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199205.1_ASM1419920v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:52,465] [INFO] Task started: Blastn
[2024-01-24 14:56:52,465] [INFO] Running command: blastn -query GCF_014199205.1_ASM1419920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdb7f831-b52f-4a86-911f-16f7a6d36158/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199205.1_ASM1419920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:54,227] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:54,230] [INFO] Selected 8 target genomes.
[2024-01-24 14:56:54,230] [INFO] Target genome list was writen to GCF_014199205.1_ASM1419920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:54,236] [INFO] Task started: fastANI
[2024-01-24 14:56:54,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a14807f-68ef-4720-a33e-67b7f6c45554/GCF_014199205.1_ASM1419920v1_genomic.fna.gz --refList GCF_014199205.1_ASM1419920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199205.1_ASM1419920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:05,803] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:05,815] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:05,816] [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_014199205.1	s__Roseomonas pecuniae	100.0	1584	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900141905.1	s__Roseomonas rosea	84.9134	1062	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438825.1	s__Roseomonas nepalensis	84.0168	1065	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813365.1	s__Roseomonas sp017813365	83.925	1011	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813395.1	s__Roseomonas sp017813395	83.7128	1016	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	83.5082	1016	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	83.4228	997	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848505.1	s__Roseomonas deserti_A	82.8786	940	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:05,817] [INFO] GTDB search result was written to GCF_014199205.1_ASM1419920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:05,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:05,822] [INFO] DFAST_QC result json was written to GCF_014199205.1_ASM1419920v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:05,823] [INFO] DFAST_QC completed!
[2024-01-24 14:57:05,823] [INFO] Total running time: 0h1m29s