[2024-01-24 11:20:19,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference
[2024-01-24 11:20:20,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,457] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg0feb932a-2bc1-45d8-9aef-e4a7ccba3499/GCF_017813395.1_ASM1781339v1_genomic.fna.gz | prodigal -d GCF_017813395.1_ASM1781339v1_genomic.fna/cds.fna -a GCF_017813395.1_ASM1781339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:35,626] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:35,627] [INFO] Task started: HMMsearch
[2024-01-24 11:20:35,627] [INFO] Running command: hmmsearch --tblout GCF_017813395.1_ASM1781339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/reference_markers.hmm GCF_017813395.1_ASM1781339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:35,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:35,961] [INFO] Found 6/6 markers.
[2024-01-24 11:20:36,011] [INFO] Query marker FASTA was written to GCF_017813395.1_ASM1781339v1_genomic.fna/markers.fasta
[2024-01-24 11:20:36,011] [INFO] Task started: Blastn
[2024-01-24 11:20:36,012] [INFO] Running command: blastn -query GCF_017813395.1_ASM1781339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/reference_markers.fasta -out GCF_017813395.1_ASM1781339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:36,920] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:36,924] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:36,925] [INFO] Target genome list was writen to GCF_017813395.1_ASM1781339v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:36,931] [INFO] Task started: fastANI
[2024-01-24 11:20:36,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg0feb932a-2bc1-45d8-9aef-e4a7ccba3499/GCF_017813395.1_ASM1781339v1_genomic.fna.gz --refList GCF_017813395.1_ASM1781339v1_genomic.fna/target_genomes.txt --output GCF_017813395.1_ASM1781339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:52,486] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:52,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:52,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:52,500] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:52,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:52,500] [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 rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	85.6902	1172	1698	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	83.705	1017	1698	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	82.906	1028	1698	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	82.0363	998	1698	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	79.569	646	1698	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	79.4895	657	1698	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	79.4515	662	1698	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	79.1782	655	1698	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.9752	622	1698	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.6767	669	1698	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.6174	611	1698	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.37	587	1698	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.2699	525	1698	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.1882	472	1698	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.1417	415	1698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,502] [INFO] DFAST Taxonomy check result was written to GCF_017813395.1_ASM1781339v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:52,502] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:52,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:52,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/checkm_data
[2024-01-24 11:20:52,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:52,557] [INFO] Task started: CheckM
[2024-01-24 11:20:52,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813395.1_ASM1781339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813395.1_ASM1781339v1_genomic.fna/checkm_input GCF_017813395.1_ASM1781339v1_genomic.fna/checkm_result
[2024-01-24 11:21:46,151] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:46,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:46,172] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:46,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:46,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813395.1_ASM1781339v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:46,173] [INFO] Task started: Blastn
[2024-01-24 11:21:46,173] [INFO] Running command: blastn -query GCF_017813395.1_ASM1781339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14be1fc5-cb57-42d0-9036-90fe5b9ff2d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813395.1_ASM1781339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:47,854] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:47,858] [INFO] Selected 8 target genomes.
[2024-01-24 11:21:47,859] [INFO] Target genome list was writen to GCF_017813395.1_ASM1781339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:47,865] [INFO] Task started: fastANI
[2024-01-24 11:21:47,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg0feb932a-2bc1-45d8-9aef-e4a7ccba3499/GCF_017813395.1_ASM1781339v1_genomic.fna.gz --refList GCF_017813395.1_ASM1781339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813395.1_ASM1781339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:59,022] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:59,034] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:59,034] [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_017813395.1	s__Roseomonas sp017813395	100.0	1689	1698	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	85.6911	1171	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199205.1	s__Roseomonas pecuniae	83.6632	1022	1698	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	82.9079	1027	1698	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	82.5614	1053	1698	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	82.053	996	1698	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	81.9609	1002	1698	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	81.877	976	1698	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 11:21:59,036] [INFO] GTDB search result was written to GCF_017813395.1_ASM1781339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:59,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:59,039] [INFO] DFAST_QC result json was written to GCF_017813395.1_ASM1781339v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:59,040] [INFO] DFAST_QC completed!
[2024-01-24 11:21:59,040] [INFO] Total running time: 0h1m40s