[2024-01-24 13:28:11,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference
[2024-01-24 13:28:13,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,011] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg0797d11b-0d36-4362-8b35-7b1dbef2cae0/GCF_007859935.1_ASM785993v1_genomic.fna.gz | prodigal -d GCF_007859935.1_ASM785993v1_genomic.fna/cds.fna -a GCF_007859935.1_ASM785993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:30,906] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:30,907] [INFO] Task started: HMMsearch
[2024-01-24 13:28:30,907] [INFO] Running command: hmmsearch --tblout GCF_007859935.1_ASM785993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/reference_markers.hmm GCF_007859935.1_ASM785993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:31,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:31,212] [INFO] Found 6/6 markers.
[2024-01-24 13:28:31,261] [INFO] Query marker FASTA was written to GCF_007859935.1_ASM785993v1_genomic.fna/markers.fasta
[2024-01-24 13:28:31,261] [INFO] Task started: Blastn
[2024-01-24 13:28:31,261] [INFO] Running command: blastn -query GCF_007859935.1_ASM785993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/reference_markers.fasta -out GCF_007859935.1_ASM785993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:31,916] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:31,919] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:31,920] [INFO] Target genome list was writen to GCF_007859935.1_ASM785993v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:31,955] [INFO] Task started: fastANI
[2024-01-24 13:28:31,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg0797d11b-0d36-4362-8b35-7b1dbef2cae0/GCF_007859935.1_ASM785993v1_genomic.fna.gz --refList GCF_007859935.1_ASM785993v1_genomic.fna/target_genomes.txt --output GCF_007859935.1_ASM785993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,195] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:43,196] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:43,196] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	100.0	2073	2074	95	conclusive
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	83.3468	1361	2074	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	78.6375	595	2074	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	78.1463	540	2074	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	77.8992	598	2074	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	77.8672	509	2074	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.7616	261	2074	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	76.5853	247	2074	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.7179	108	2074	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,197] [INFO] DFAST Taxonomy check result was written to GCF_007859935.1_ASM785993v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/checkm_data
[2024-01-24 13:28:43,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:43,258] [INFO] Task started: CheckM
[2024-01-24 13:28:43,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859935.1_ASM785993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859935.1_ASM785993v1_genomic.fna/checkm_input GCF_007859935.1_ASM785993v1_genomic.fna/checkm_result
[2024-01-24 13:29:33,464] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:33,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:33,489] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:33,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:33,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859935.1_ASM785993v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:33,490] [INFO] Task started: Blastn
[2024-01-24 13:29:33,490] [INFO] Running command: blastn -query GCF_007859935.1_ASM785993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc68498-bffe-4499-a8b0-7b2b527fc47d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859935.1_ASM785993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:34,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:34,452] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:34,452] [INFO] Target genome list was writen to GCF_007859935.1_ASM785993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:34,537] [INFO] Task started: fastANI
[2024-01-24 13:29:34,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg0797d11b-0d36-4362-8b35-7b1dbef2cae0/GCF_007859935.1_ASM785993v1_genomic.fna.gz --refList GCF_007859935.1_ASM785993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859935.1_ASM785993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:50,308] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:50,323] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:50,324] [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_007859935.1	s__Posidoniimonas polymericola	100.0	2073	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859765.1	s__Posidoniimonas corsicana	83.3419	1361	2074	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	78.6448	594	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	78.519	545	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	78.1436	538	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	77.9142	594	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	77.8472	512	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_002702655.1	s__GCA-2702655 sp002702655	77.2535	434	2074	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_003576855.1	s__Lacipirellula sp003576855	76.7953	271	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748035.1	s__Aeoliella mucimassa	76.5853	247	2074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:50,325] [INFO] GTDB search result was written to GCF_007859935.1_ASM785993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:50,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:50,331] [INFO] DFAST_QC result json was written to GCF_007859935.1_ASM785993v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:50,332] [INFO] DFAST_QC completed!
[2024-01-24 13:29:50,332] [INFO] Total running time: 0h1m39s