[2023-06-28 17:01:19,936] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:01:19,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:01:19,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference
[2023-06-28 17:01:21,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:01:21,281] [INFO] Task started: Prodigal
[2023-06-28 17:01:21,281] [INFO] Running command: gunzip -c /var/lib/cwl/stgd93c2aef-dd32-454c-b420-746e830328de/GCA_020697015.1_ASM2069701v1_genomic.fna.gz | prodigal -d GCA_020697015.1_ASM2069701v1_genomic.fna/cds.fna -a GCA_020697015.1_ASM2069701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:01:28,648] [INFO] Task succeeded: Prodigal
[2023-06-28 17:01:28,649] [INFO] Task started: HMMsearch
[2023-06-28 17:01:28,649] [INFO] Running command: hmmsearch --tblout GCA_020697015.1_ASM2069701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/reference_markers.hmm GCA_020697015.1_ASM2069701v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:01:28,876] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:01:28,877] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd93c2aef-dd32-454c-b420-746e830328de/GCA_020697015.1_ASM2069701v1_genomic.fna.gz]
[2023-06-28 17:01:28,909] [INFO] Query marker FASTA was written to GCA_020697015.1_ASM2069701v1_genomic.fna/markers.fasta
[2023-06-28 17:01:28,909] [INFO] Task started: Blastn
[2023-06-28 17:01:28,909] [INFO] Running command: blastn -query GCA_020697015.1_ASM2069701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/reference_markers.fasta -out GCA_020697015.1_ASM2069701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:29,538] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:29,542] [INFO] Selected 10 target genomes.
[2023-06-28 17:01:29,543] [INFO] Target genome list was writen to GCA_020697015.1_ASM2069701v1_genomic.fna/target_genomes.txt
[2023-06-28 17:01:29,543] [INFO] Task started: fastANI
[2023-06-28 17:01:29,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgd93c2aef-dd32-454c-b420-746e830328de/GCA_020697015.1_ASM2069701v1_genomic.fna.gz --refList GCA_020697015.1_ASM2069701v1_genomic.fna/target_genomes.txt --output GCA_020697015.1_ASM2069701v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:01:38,348] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:38,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:01:38,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:01:38,358] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:01:38,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:01:38,359] [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
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.682	290	763	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.6573	291	763	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.6422	225	763	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.4044	163	763	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.2074	143	763	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.1474	69	763	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.0193	86	763	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	75.7454	149	763	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	75.6367	80	763	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	75.6249	107	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:01:38,361] [INFO] DFAST Taxonomy check result was written to GCA_020697015.1_ASM2069701v1_genomic.fna/tc_result.tsv
[2023-06-28 17:01:38,361] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:01:38,361] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:01:38,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/checkm_data
[2023-06-28 17:01:38,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:01:38,405] [INFO] Task started: CheckM
[2023-06-28 17:01:38,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020697015.1_ASM2069701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020697015.1_ASM2069701v1_genomic.fna/checkm_input GCA_020697015.1_ASM2069701v1_genomic.fna/checkm_result
[2023-06-28 17:02:05,500] [INFO] Task succeeded: CheckM
[2023-06-28 17:02:05,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 5.01%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-28 17:02:05,528] [INFO] ===== Completeness check finished =====
[2023-06-28 17:02:05,528] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:02:05,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020697015.1_ASM2069701v1_genomic.fna/markers.fasta)
[2023-06-28 17:02:05,529] [INFO] Task started: Blastn
[2023-06-28 17:02:05,529] [INFO] Running command: blastn -query GCA_020697015.1_ASM2069701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fbbf683-ec45-443b-b458-70c8d7d1a1fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_020697015.1_ASM2069701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:02:06,392] [INFO] Task succeeded: Blastn
[2023-06-28 17:02:06,395] [INFO] Selected 9 target genomes.
[2023-06-28 17:02:06,396] [INFO] Target genome list was writen to GCA_020697015.1_ASM2069701v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:02:06,407] [INFO] Task started: fastANI
[2023-06-28 17:02:06,407] [INFO] Running command: fastANI --query /var/lib/cwl/stgd93c2aef-dd32-454c-b420-746e830328de/GCA_020697015.1_ASM2069701v1_genomic.fna.gz --refList GCA_020697015.1_ASM2069701v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020697015.1_ASM2069701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:02:13,035] [INFO] Task succeeded: fastANI
[2023-06-28 17:02:13,043] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:02:13,043] [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
GCA_902826935.1	s__CADEGR01 sp902826935	78.4136	253	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCA_009908425.1	s__JAAAPF01 sp009908425	76.7632	170	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.6697	291	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_007131045.1	s__SLRI01 sp007131045	76.6687	152	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390475.1	s__SLRI01 sp011390475	76.4357	133	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378465.1	s__Elioraea tepidiphila	76.4022	183	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	76.3836	150	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.3804	153	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.3643	163	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:02:13,045] [INFO] GTDB search result was written to GCA_020697015.1_ASM2069701v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:02:13,046] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:02:13,049] [INFO] DFAST_QC result json was written to GCA_020697015.1_ASM2069701v1_genomic.fna/dqc_result.json
[2023-06-28 17:02:13,049] [INFO] DFAST_QC completed!
[2023-06-28 17:02:13,049] [INFO] Total running time: 0h0m53s