[2023-06-29 04:17:15,854] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:17:15,856] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:17:15,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference
[2023-06-29 04:17:17,036] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:17:17,037] [INFO] Task started: Prodigal
[2023-06-29 04:17:17,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg79ff695d-6f3a-490b-83ee-78333eba2aa0/GCA_020847515.1_ASM2084751v1_genomic.fna.gz | prodigal -d GCA_020847515.1_ASM2084751v1_genomic.fna/cds.fna -a GCA_020847515.1_ASM2084751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:17:27,132] [INFO] Task succeeded: Prodigal
[2023-06-29 04:17:27,133] [INFO] Task started: HMMsearch
[2023-06-29 04:17:27,133] [INFO] Running command: hmmsearch --tblout GCA_020847515.1_ASM2084751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/reference_markers.hmm GCA_020847515.1_ASM2084751v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:17:27,321] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:17:27,322] [INFO] Found 6/6 markers.
[2023-06-29 04:17:27,353] [INFO] Query marker FASTA was written to GCA_020847515.1_ASM2084751v1_genomic.fna/markers.fasta
[2023-06-29 04:17:27,353] [INFO] Task started: Blastn
[2023-06-29 04:17:27,353] [INFO] Running command: blastn -query GCA_020847515.1_ASM2084751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/reference_markers.fasta -out GCA_020847515.1_ASM2084751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:17:27,997] [INFO] Task succeeded: Blastn
[2023-06-29 04:17:28,000] [INFO] Selected 11 target genomes.
[2023-06-29 04:17:28,000] [INFO] Target genome list was writen to GCA_020847515.1_ASM2084751v1_genomic.fna/target_genomes.txt
[2023-06-29 04:17:28,002] [INFO] Task started: fastANI
[2023-06-29 04:17:28,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ff695d-6f3a-490b-83ee-78333eba2aa0/GCA_020847515.1_ASM2084751v1_genomic.fna.gz --refList GCA_020847515.1_ASM2084751v1_genomic.fna/target_genomes.txt --output GCA_020847515.1_ASM2084751v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:17:38,262] [INFO] Task succeeded: fastANI
[2023-06-29 04:17:38,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:17:38,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:17:38,269] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:17:38,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:17:38,269] [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
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	77.1	315	1243	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	77.0965	312	1243	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.45	174	1243	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.4162	165	1243	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.4084	186	1243	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.1344	140	1243	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:17:38,271] [INFO] DFAST Taxonomy check result was written to GCA_020847515.1_ASM2084751v1_genomic.fna/tc_result.tsv
[2023-06-29 04:17:38,272] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:17:38,272] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:17:38,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/checkm_data
[2023-06-29 04:17:38,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:17:38,312] [INFO] Task started: CheckM
[2023-06-29 04:17:38,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020847515.1_ASM2084751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020847515.1_ASM2084751v1_genomic.fna/checkm_input GCA_020847515.1_ASM2084751v1_genomic.fna/checkm_result
[2023-06-29 04:18:10,288] [INFO] Task succeeded: CheckM
[2023-06-29 04:18:10,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:18:10,310] [INFO] ===== Completeness check finished =====
[2023-06-29 04:18:10,310] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:18:10,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020847515.1_ASM2084751v1_genomic.fna/markers.fasta)
[2023-06-29 04:18:10,311] [INFO] Task started: Blastn
[2023-06-29 04:18:10,311] [INFO] Running command: blastn -query GCA_020847515.1_ASM2084751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e56bf1-41a0-4d15-87c8-c5c715f89d4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020847515.1_ASM2084751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:18:11,282] [INFO] Task succeeded: Blastn
[2023-06-29 04:18:11,286] [INFO] Selected 14 target genomes.
[2023-06-29 04:18:11,286] [INFO] Target genome list was writen to GCA_020847515.1_ASM2084751v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:18:11,294] [INFO] Task started: fastANI
[2023-06-29 04:18:11,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ff695d-6f3a-490b-83ee-78333eba2aa0/GCA_020847515.1_ASM2084751v1_genomic.fna.gz --refList GCA_020847515.1_ASM2084751v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020847515.1_ASM2084751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:18:23,249] [INFO] Task succeeded: fastANI
[2023-06-29 04:18:23,257] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:18:23,258] [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_003576855.1	s__Lacipirellula sp003576855	79.1273	505	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746075.1	s__Lacipirellula limnantheis	77.0889	313	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	-
GCF_009177095.1	s__Lacipirellula parvula	77.0766	318	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	77.0004	242	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.978	239	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	76.462	173	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793185.1	s__JAEUIK01 sp016793185	75.8182	69	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JAEUIK01;g__JAEUIK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.7518	98	1243	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:18:23,260] [INFO] GTDB search result was written to GCA_020847515.1_ASM2084751v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:18:23,261] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:18:23,264] [INFO] DFAST_QC result json was written to GCA_020847515.1_ASM2084751v1_genomic.fna/dqc_result.json
[2023-06-29 04:18:23,264] [INFO] DFAST_QC completed!
[2023-06-29 04:18:23,264] [INFO] Total running time: 0h1m7s