[2024-01-24 13:36:45,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference
[2024-01-24 13:36:46,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,938] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a1790fb-d67f-4636-8cbf-fda9c6f23097/GCF_007859955.1_ASM785995v1_genomic.fna.gz | prodigal -d GCF_007859955.1_ASM785995v1_genomic.fna/cds.fna -a GCF_007859955.1_ASM785995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:01,591] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:01,591] [INFO] Task started: HMMsearch
[2024-01-24 13:37:01,591] [INFO] Running command: hmmsearch --tblout GCF_007859955.1_ASM785995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/reference_markers.hmm GCF_007859955.1_ASM785995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,995] [INFO] Found 6/6 markers.
[2024-01-24 13:37:02,039] [INFO] Query marker FASTA was written to GCF_007859955.1_ASM785995v1_genomic.fna/markers.fasta
[2024-01-24 13:37:02,039] [INFO] Task started: Blastn
[2024-01-24 13:37:02,039] [INFO] Running command: blastn -query GCF_007859955.1_ASM785995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/reference_markers.fasta -out GCF_007859955.1_ASM785995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:02,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:02,678] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:02,678] [INFO] Target genome list was writen to GCF_007859955.1_ASM785995v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:02,684] [INFO] Task started: fastANI
[2024-01-24 13:37:02,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1790fb-d67f-4636-8cbf-fda9c6f23097/GCF_007859955.1_ASM785995v1_genomic.fna.gz --refList GCF_007859955.1_ASM785995v1_genomic.fna/target_genomes.txt --output GCF_007859955.1_ASM785995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:12,365] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:12,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:12,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:12,374] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:12,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:12,374] [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
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	100.0	1744	1744	95	conclusive
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	81.2162	1023	1744	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	78.837	380	1744	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	78.6625	563	1744	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	78.1543	532	1744	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	78.0348	495	1744	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	77.8119	445	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:12,376] [INFO] DFAST Taxonomy check result was written to GCF_007859955.1_ASM785995v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:12,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:12,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:12,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/checkm_data
[2024-01-24 13:37:12,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:12,441] [INFO] Task started: CheckM
[2024-01-24 13:37:12,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859955.1_ASM785995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859955.1_ASM785995v1_genomic.fna/checkm_input GCF_007859955.1_ASM785995v1_genomic.fna/checkm_result
[2024-01-24 13:37:56,872] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:56,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:56,895] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:56,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:56,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859955.1_ASM785995v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:56,896] [INFO] Task started: Blastn
[2024-01-24 13:37:56,896] [INFO] Running command: blastn -query GCF_007859955.1_ASM785995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4b655f-5e74-4502-9a6b-926b22f8e6ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859955.1_ASM785995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:57,835] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:57,839] [INFO] Selected 8 target genomes.
[2024-01-24 13:37:57,839] [INFO] Target genome list was writen to GCF_007859955.1_ASM785995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:57,858] [INFO] Task started: fastANI
[2024-01-24 13:37:57,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1790fb-d67f-4636-8cbf-fda9c6f23097/GCF_007859955.1_ASM785995v1_genomic.fna.gz --refList GCF_007859955.1_ASM785995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859955.1_ASM785995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:06,379] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,392] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:06,392] [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_007859955.1	s__Botrimarina colliarenosi	100.0	1744	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007753265.1	s__Botrimarina mediterranea	81.2031	1026	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_007745835.1	s__Botrimarina sp007745835	80.241	779	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859815.1	s__Botrimarina hoheduenensis	78.7985	384	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	78.6861	560	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	78.1566	532	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286045.1	s__JABDGM01 sp013286045	76.0223	51	1744	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__JABDGM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,394] [INFO] GTDB search result was written to GCF_007859955.1_ASM785995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:06,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:06,397] [INFO] DFAST_QC result json was written to GCF_007859955.1_ASM785995v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:06,398] [INFO] DFAST_QC completed!
[2024-01-24 13:38:06,398] [INFO] Total running time: 0h1m21s