[2024-01-24 13:28:18,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:18,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:18,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference
[2024-01-24 13:28:20,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,234] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,234] [INFO] Running command: gunzip -c /var/lib/cwl/stg7edccdde-bfde-41a7-9bd8-e4af397cc0a0/GCF_000165715.2_ASM16571v3_genomic.fna.gz | prodigal -d GCF_000165715.2_ASM16571v3_genomic.fna/cds.fna -a GCF_000165715.2_ASM16571v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,454] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,454] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,454] [INFO] Running command: hmmsearch --tblout GCF_000165715.2_ASM16571v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/reference_markers.hmm GCF_000165715.2_ASM16571v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,847] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,899] [INFO] Query marker FASTA was written to GCF_000165715.2_ASM16571v3_genomic.fna/markers.fasta
[2024-01-24 13:28:41,899] [INFO] Task started: Blastn
[2024-01-24 13:28:41,899] [INFO] Running command: blastn -query GCF_000165715.2_ASM16571v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/reference_markers.fasta -out GCF_000165715.2_ASM16571v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,547] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,551] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:42,551] [INFO] Target genome list was writen to GCF_000165715.2_ASM16571v3_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,565] [INFO] Task started: fastANI
[2024-01-24 13:28:42,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg7edccdde-bfde-41a7-9bd8-e4af397cc0a0/GCF_000165715.2_ASM16571v3_genomic.fna.gz --refList GCF_000165715.2_ASM16571v3_genomic.fna/target_genomes.txt --output GCF_000165715.2_ASM16571v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:57,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:57,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:57,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:57,091] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:57,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:57,092] [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
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	100.0	2001	2002	95	conclusive
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	77.3009	305	2002	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.5307	122	2002	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	76.4758	100	2002	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	76.2209	79	2002	95	below_threshold
Rubinisphaera italica	strain=Pan54	GCA_007859715.1	2527969	2527969	type	True	76.1674	152	2002	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.9494	69	2002	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.8434	68	2002	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.748	92	2002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,094] [INFO] DFAST Taxonomy check result was written to GCF_000165715.2_ASM16571v3_genomic.fna/tc_result.tsv
[2024-01-24 13:28:57,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:57,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:57,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/checkm_data
[2024-01-24 13:28:57,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:57,158] [INFO] Task started: CheckM
[2024-01-24 13:28:57,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000165715.2_ASM16571v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000165715.2_ASM16571v3_genomic.fna/checkm_input GCF_000165715.2_ASM16571v3_genomic.fna/checkm_result
[2024-01-24 13:29:53,701] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:53,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:53,725] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:53,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:53,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000165715.2_ASM16571v3_genomic.fna/markers.fasta)
[2024-01-24 13:29:53,727] [INFO] Task started: Blastn
[2024-01-24 13:29:53,727] [INFO] Running command: blastn -query GCF_000165715.2_ASM16571v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg366fee91-83e7-4003-a12f-c720e51b0abc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000165715.2_ASM16571v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:54,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:54,558] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:54,559] [INFO] Target genome list was writen to GCF_000165715.2_ASM16571v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:54,585] [INFO] Task started: fastANI
[2024-01-24 13:29:54,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg7edccdde-bfde-41a7-9bd8-e4af397cc0a0/GCF_000165715.2_ASM16571v3_genomic.fna.gz --refList GCF_000165715.2_ASM16571v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000165715.2_ASM16571v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:10,134] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:10,142] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:10,142] [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_000165715.2	s__Rubinisphaera brasiliensis	100.0	2002	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017795105.1	s__Rubinisphaera sp017795105	77.5379	312	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584345.1	s__Rubinisphaera sp014584345	76.6453	207	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	76.4999	125	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359185.1	s__Rubinisphaera sp002359185	76.2345	157	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	99.90	99.90	0.94	0.94	2	-
GCF_007859715.1	s__Rubinisphaera italica	76.1916	150	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007744515.1	s__Calycomorphotria sp007744515	76.0686	50	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125225.1	s__DSVQ01 sp016125225	75.4084	74	2002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__DSVQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:10,144] [INFO] GTDB search result was written to GCF_000165715.2_ASM16571v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:10,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:10,149] [INFO] DFAST_QC result json was written to GCF_000165715.2_ASM16571v3_genomic.fna/dqc_result.json
[2024-01-24 13:30:10,149] [INFO] DFAST_QC completed!
[2024-01-24 13:30:10,149] [INFO] Total running time: 0h1m51s