[2023-06-26 23:16:05,889] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:16:05,891] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:16:05,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference
[2023-06-26 23:16:06,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:16:06,979] [INFO] Task started: Prodigal
[2023-06-26 23:16:06,980] [INFO] Running command: gunzip -c /var/lib/cwl/stg2737d100-2d76-4a37-bf67-6de84b760266/GCA_002290545.1_ASM229054v1_genomic.fna.gz | prodigal -d GCA_002290545.1_ASM229054v1_genomic.fna/cds.fna -a GCA_002290545.1_ASM229054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:16:24,325] [INFO] Task succeeded: Prodigal
[2023-06-26 23:16:24,325] [INFO] Task started: HMMsearch
[2023-06-26 23:16:24,325] [INFO] Running command: hmmsearch --tblout GCA_002290545.1_ASM229054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/reference_markers.hmm GCA_002290545.1_ASM229054v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:16:24,523] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:16:24,524] [INFO] Found 6/6 markers.
[2023-06-26 23:16:24,551] [INFO] Query marker FASTA was written to GCA_002290545.1_ASM229054v1_genomic.fna/markers.fasta
[2023-06-26 23:16:24,551] [INFO] Task started: Blastn
[2023-06-26 23:16:24,551] [INFO] Running command: blastn -query GCA_002290545.1_ASM229054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/reference_markers.fasta -out GCA_002290545.1_ASM229054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:16:25,098] [INFO] Task succeeded: Blastn
[2023-06-26 23:16:25,101] [INFO] Selected 19 target genomes.
[2023-06-26 23:16:25,101] [INFO] Target genome list was writen to GCA_002290545.1_ASM229054v1_genomic.fna/target_genomes.txt
[2023-06-26 23:16:25,104] [INFO] Task started: fastANI
[2023-06-26 23:16:25,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg2737d100-2d76-4a37-bf67-6de84b760266/GCA_002290545.1_ASM229054v1_genomic.fna.gz --refList GCA_002290545.1_ASM229054v1_genomic.fna/target_genomes.txt --output GCA_002290545.1_ASM229054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:16:38,784] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:38,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:16:38,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:16:38,789] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:16:38,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:16:38,789] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.8317	65	1074	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.7359	59	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:16:38,790] [INFO] DFAST Taxonomy check result was written to GCA_002290545.1_ASM229054v1_genomic.fna/tc_result.tsv
[2023-06-26 23:16:38,791] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:16:38,791] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:16:38,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/checkm_data
[2023-06-26 23:16:38,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:16:38,825] [INFO] Task started: CheckM
[2023-06-26 23:16:38,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002290545.1_ASM229054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002290545.1_ASM229054v1_genomic.fna/checkm_input GCA_002290545.1_ASM229054v1_genomic.fna/checkm_result
[2023-06-26 23:17:28,775] [INFO] Task succeeded: CheckM
[2023-06-26 23:17:28,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:17:28,822] [INFO] ===== Completeness check finished =====
[2023-06-26 23:17:28,822] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:17:28,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002290545.1_ASM229054v1_genomic.fna/markers.fasta)
[2023-06-26 23:17:28,822] [INFO] Task started: Blastn
[2023-06-26 23:17:28,822] [INFO] Running command: blastn -query GCA_002290545.1_ASM229054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bf92c2-a055-478b-a2df-552807db17a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_002290545.1_ASM229054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:17:29,780] [INFO] Task succeeded: Blastn
[2023-06-26 23:17:29,805] [INFO] Selected 20 target genomes.
[2023-06-26 23:17:29,805] [INFO] Target genome list was writen to GCA_002290545.1_ASM229054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:17:29,816] [INFO] Task started: fastANI
[2023-06-26 23:17:29,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg2737d100-2d76-4a37-bf67-6de84b760266/GCA_002290545.1_ASM229054v1_genomic.fna.gz --refList GCA_002290545.1_ASM229054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002290545.1_ASM229054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:17:43,691] [INFO] Task succeeded: fastANI
[2023-06-26 23:17:43,698] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:17:43,698] [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_002293145.1	s__UBA956 sp002293145	99.9577	1029	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA956	95.0	99.93	99.88	0.97	0.96	4	conclusive
GCA_903878115.1	s__UBA956 sp903878115	77.8408	219	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA956	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293285.1	s__UBA956 sp004293285	77.2002	146	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA956	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	76.3887	61	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_903919975.1	s__Luteolibacter sp903919975	76.3601	81	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_018969605.1	s__Luteolibacter sp018969605	75.9962	52	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402445.1	s__Luteolibacter sp018402445	75.9957	74	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	75.8781	63	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908495.1	s__Luteolibacter sp903908495	75.6383	60	1074	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:17:43,756] [INFO] GTDB search result was written to GCA_002290545.1_ASM229054v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:17:43,757] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:17:43,759] [INFO] DFAST_QC result json was written to GCA_002290545.1_ASM229054v1_genomic.fna/dqc_result.json
[2023-06-26 23:17:43,759] [INFO] DFAST_QC completed!
[2023-06-26 23:17:43,759] [INFO] Total running time: 0h1m38s