[2024-01-24 13:40:28,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,144] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe5d3027-0a29-4b22-aee1-ffa5bf33bfe8/GCF_008065115.1_ASM806511v1_genomic.fna.gz | prodigal -d GCF_008065115.1_ASM806511v1_genomic.fna/cds.fna -a GCF_008065115.1_ASM806511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,367] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,367] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,367] [INFO] Running command: hmmsearch --tblout GCF_008065115.1_ASM806511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/reference_markers.hmm GCF_008065115.1_ASM806511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,722] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,776] [INFO] Query marker FASTA was written to GCF_008065115.1_ASM806511v1_genomic.fna/markers.fasta
[2024-01-24 13:40:51,777] [INFO] Task started: Blastn
[2024-01-24 13:40:51,777] [INFO] Running command: blastn -query GCF_008065115.1_ASM806511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/reference_markers.fasta -out GCF_008065115.1_ASM806511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,372] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,375] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:52,376] [INFO] Target genome list was writen to GCF_008065115.1_ASM806511v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,384] [INFO] Task started: fastANI
[2024-01-24 13:40:52,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe5d3027-0a29-4b22-aee1-ffa5bf33bfe8/GCF_008065115.1_ASM806511v1_genomic.fna.gz --refList GCF_008065115.1_ASM806511v1_genomic.fna/target_genomes.txt --output GCF_008065115.1_ASM806511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,433] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:05,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,434] [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
Bythopirellula goksoeyrii	strain=Pr1d	GCA_008065115.1	1400387	1400387	type	True	100.0	2155	2157	95	conclusive
Bythopirellula polymerisocia	strain=Pla144	GCA_007860015.1	2528003	2528003	type	True	79.7577	777	2157	95	below_threshold
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	76.8296	90	2157	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.7397	87	2157	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.5832	81	2157	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.5414	56	2157	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.3095	57	2157	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.0728	63	2157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,439] [INFO] DFAST Taxonomy check result was written to GCF_008065115.1_ASM806511v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/checkm_data
[2024-01-24 13:41:05,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,522] [INFO] Task started: CheckM
[2024-01-24 13:41:05,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008065115.1_ASM806511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008065115.1_ASM806511v1_genomic.fna/checkm_input GCF_008065115.1_ASM806511v1_genomic.fna/checkm_result
[2024-01-24 13:42:04,269] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:04,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,294] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:04,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:04,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008065115.1_ASM806511v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:04,295] [INFO] Task started: Blastn
[2024-01-24 13:42:04,295] [INFO] Running command: blastn -query GCF_008065115.1_ASM806511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f17ac2f-9bce-47ff-8051-8f9882205f58/dqc_reference/reference_markers_gtdb.fasta -out GCF_008065115.1_ASM806511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:05,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:05,442] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:05,442] [INFO] Target genome list was writen to GCF_008065115.1_ASM806511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:05,471] [INFO] Task started: fastANI
[2024-01-24 13:42:05,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe5d3027-0a29-4b22-aee1-ffa5bf33bfe8/GCF_008065115.1_ASM806511v1_genomic.fna.gz --refList GCF_008065115.1_ASM806511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008065115.1_ASM806511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:20,612] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:20,628] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:20,629] [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_008065115.1	s__Bythopirellula goksoyri	100.0	2155	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007860015.1	s__Bythopirellula polymerisocia	79.7603	775	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	76.7671	86	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	76.5414	56	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.4911	67	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	76.3095	57	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152205.1	s__Bythopirellula sp013152205	76.2027	76	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152515.1	s__Bythopirellula sp013152515	76.076	57	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.8386	54	2157	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:20,631] [INFO] GTDB search result was written to GCF_008065115.1_ASM806511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:20,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:20,634] [INFO] DFAST_QC result json was written to GCF_008065115.1_ASM806511v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:20,635] [INFO] DFAST_QC completed!
[2024-01-24 13:42:20,635] [INFO] Total running time: 0h1m52s