[2024-01-24 12:13:43,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:43,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:43,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference
[2024-01-24 12:13:45,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:45,009] [INFO] Task started: Prodigal
[2024-01-24 12:13:45,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4f9e49c-4f50-4b1d-9428-6d9433c7b7b1/GCF_007750855.1_ASM775085v1_genomic.fna.gz | prodigal -d GCF_007750855.1_ASM775085v1_genomic.fna/cds.fna -a GCF_007750855.1_ASM775085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:04,909] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:04,909] [INFO] Task started: HMMsearch
[2024-01-24 12:14:04,909] [INFO] Running command: hmmsearch --tblout GCF_007750855.1_ASM775085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/reference_markers.hmm GCF_007750855.1_ASM775085v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:05,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:05,378] [INFO] Found 6/6 markers.
[2024-01-24 12:14:05,439] [INFO] Query marker FASTA was written to GCF_007750855.1_ASM775085v1_genomic.fna/markers.fasta
[2024-01-24 12:14:05,440] [INFO] Task started: Blastn
[2024-01-24 12:14:05,440] [INFO] Running command: blastn -query GCF_007750855.1_ASM775085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/reference_markers.fasta -out GCF_007750855.1_ASM775085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:06,138] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:06,317] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:06,318] [INFO] Target genome list was writen to GCF_007750855.1_ASM775085v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:06,324] [INFO] Task started: fastANI
[2024-01-24 12:14:06,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f9e49c-4f50-4b1d-9428-6d9433c7b7b1/GCF_007750855.1_ASM775085v1_genomic.fna.gz --refList GCF_007750855.1_ASM775085v1_genomic.fna/target_genomes.txt --output GCF_007750855.1_ASM775085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:20,995] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:20,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:20,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:21,005] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:21,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:21,005] [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
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	100.0	2206	2206	95	conclusive
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	78.1775	620	2206	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	77.9633	511	2206	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	77.9632	597	2206	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	77.8178	425	2206	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	77.7198	458	2206	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.717	257	2206	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.6414	266	2206	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	76.3365	192	2206	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.4861	136	2206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:21,007] [INFO] DFAST Taxonomy check result was written to GCF_007750855.1_ASM775085v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:21,007] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:21,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:21,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/checkm_data
[2024-01-24 12:14:21,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:21,075] [INFO] Task started: CheckM
[2024-01-24 12:14:21,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007750855.1_ASM775085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007750855.1_ASM775085v1_genomic.fna/checkm_input GCF_007750855.1_ASM775085v1_genomic.fna/checkm_result
[2024-01-24 12:15:17,593] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:17,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,618] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:17,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:17,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007750855.1_ASM775085v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:17,619] [INFO] Task started: Blastn
[2024-01-24 12:15:17,619] [INFO] Running command: blastn -query GCF_007750855.1_ASM775085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3139f31a-a06e-43db-a5a4-fdbe503c9921/dqc_reference/reference_markers_gtdb.fasta -out GCF_007750855.1_ASM775085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:18,483] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:18,486] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:18,486] [INFO] Target genome list was writen to GCF_007750855.1_ASM775085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:18,518] [INFO] Task started: fastANI
[2024-01-24 12:15:18,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f9e49c-4f50-4b1d-9428-6d9433c7b7b1/GCF_007750855.1_ASM775085v1_genomic.fna.gz --refList GCF_007750855.1_ASM775085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007750855.1_ASM775085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:34,621] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:34,637] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:34,638] [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_007750855.1	s__Pirellulimonas nuda	100.0	2206	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859765.1	s__Posidoniimonas corsicana	78.1947	616	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	77.9739	595	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	77.9735	510	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	77.8457	421	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCF_007859955.1	s__Botrimarina colliarenosi	77.7344	456	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	77.6914	480	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	77.144	365	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.9101	192	2206	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	76.7495	253	2206	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	76.6564	264	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464525.1	s__Ga0077529 sp001464525	76.5711	177	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Ga0077529	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	76.0345	194	2206	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199325.1	s__JACQGW01 sp016199325	74.6523	52	2206	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__JACQGW01;f__JACQGW01;g__JACQGW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,639] [INFO] GTDB search result was written to GCF_007750855.1_ASM775085v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:34,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:34,643] [INFO] DFAST_QC result json was written to GCF_007750855.1_ASM775085v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:34,644] [INFO] DFAST_QC completed!
[2024-01-24 12:15:34,644] [INFO] Total running time: 0h1m51s