[2023-06-29 20:09:02,887] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:09:02,889] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:09:02,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference
[2023-06-29 20:09:04,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:09:04,180] [INFO] Task started: Prodigal
[2023-06-29 20:09:04,180] [INFO] Running command: gunzip -c /var/lib/cwl/stge56d919b-7ec8-44af-9ad4-fe65e6652299/GCA_023382995.1_ASM2338299v1_genomic.fna.gz | prodigal -d GCA_023382995.1_ASM2338299v1_genomic.fna/cds.fna -a GCA_023382995.1_ASM2338299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:09:19,135] [INFO] Task succeeded: Prodigal
[2023-06-29 20:09:19,135] [INFO] Task started: HMMsearch
[2023-06-29 20:09:19,136] [INFO] Running command: hmmsearch --tblout GCA_023382995.1_ASM2338299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/reference_markers.hmm GCA_023382995.1_ASM2338299v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:09:19,421] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:09:19,422] [INFO] Found 6/6 markers.
[2023-06-29 20:09:19,472] [INFO] Query marker FASTA was written to GCA_023382995.1_ASM2338299v1_genomic.fna/markers.fasta
[2023-06-29 20:09:19,473] [INFO] Task started: Blastn
[2023-06-29 20:09:19,473] [INFO] Running command: blastn -query GCA_023382995.1_ASM2338299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/reference_markers.fasta -out GCA_023382995.1_ASM2338299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:09:20,059] [INFO] Task succeeded: Blastn
[2023-06-29 20:09:20,063] [INFO] Selected 19 target genomes.
[2023-06-29 20:09:20,064] [INFO] Target genome list was writen to GCA_023382995.1_ASM2338299v1_genomic.fna/target_genomes.txt
[2023-06-29 20:09:20,066] [INFO] Task started: fastANI
[2023-06-29 20:09:20,066] [INFO] Running command: fastANI --query /var/lib/cwl/stge56d919b-7ec8-44af-9ad4-fe65e6652299/GCA_023382995.1_ASM2338299v1_genomic.fna.gz --refList GCA_023382995.1_ASM2338299v1_genomic.fna/target_genomes.txt --output GCA_023382995.1_ASM2338299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:09:36,386] [INFO] Task succeeded: fastANI
[2023-06-29 20:09:36,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:09:36,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:09:36,400] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:09:36,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:09:36,400] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.2509	70	1256	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.7434	105	1256	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.6525	82	1256	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.6292	74	1256	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.6151	89	1256	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.3718	54	1256	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.0877	87	1256	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:09:36,402] [INFO] DFAST Taxonomy check result was written to GCA_023382995.1_ASM2338299v1_genomic.fna/tc_result.tsv
[2023-06-29 20:09:36,403] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:09:36,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:09:36,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/checkm_data
[2023-06-29 20:09:36,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:09:36,466] [INFO] Task started: CheckM
[2023-06-29 20:09:36,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023382995.1_ASM2338299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023382995.1_ASM2338299v1_genomic.fna/checkm_input GCA_023382995.1_ASM2338299v1_genomic.fna/checkm_result
[2023-06-29 20:10:20,568] [INFO] Task succeeded: CheckM
[2023-06-29 20:10:20,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:10:20,594] [INFO] ===== Completeness check finished =====
[2023-06-29 20:10:20,594] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:10:20,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023382995.1_ASM2338299v1_genomic.fna/markers.fasta)
[2023-06-29 20:10:20,595] [INFO] Task started: Blastn
[2023-06-29 20:10:20,595] [INFO] Running command: blastn -query GCA_023382995.1_ASM2338299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e7b95d6-c18d-4dd1-8fb8-541f1648f18f/dqc_reference/reference_markers_gtdb.fasta -out GCA_023382995.1_ASM2338299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:10:21,377] [INFO] Task succeeded: Blastn
[2023-06-29 20:10:21,383] [INFO] Selected 27 target genomes.
[2023-06-29 20:10:21,383] [INFO] Target genome list was writen to GCA_023382995.1_ASM2338299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:10:21,391] [INFO] Task started: fastANI
[2023-06-29 20:10:21,391] [INFO] Running command: fastANI --query /var/lib/cwl/stge56d919b-7ec8-44af-9ad4-fe65e6652299/GCA_023382995.1_ASM2338299v1_genomic.fna.gz --refList GCA_023382995.1_ASM2338299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023382995.1_ASM2338299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:10:42,575] [INFO] Task succeeded: fastANI
[2023-06-29 20:10:42,594] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:10:42,595] [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_011367845.1	s__DSXL01 sp011367845	76.8143	170	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__DSXL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360685.1	s__JABWBD01 sp013360685	76.6118	166	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744395.1	s__JAAYCB01 sp012744395	76.5847	164	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119795.1	s__SKOZ01 sp007119795	76.3301	77	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SKOZ01	95.0	99.25	99.25	0.71	0.71	2	-
GCA_016936015.1	s__JAFGPV01 sp016936015	76.2455	116	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGPV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	76.1662	166	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018897395.1	s__JAHIKV01 sp018897395	76.135	97	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	99.63	99.63	0.95	0.95	2	-
GCA_016931075.1	s__JAFGFF01 sp016931075	76.1301	103	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928165.1	s__JAHIKV01 sp016928165	75.9614	82	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	75.9524	130	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576845.1	s__PLA5 sp003576845	75.7122	92	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.6646	70	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122045.1	s__PWXP01 sp007122045	75.6337	94	1256	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__PWXP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:10:42,597] [INFO] GTDB search result was written to GCA_023382995.1_ASM2338299v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:10:42,597] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:10:42,601] [INFO] DFAST_QC result json was written to GCA_023382995.1_ASM2338299v1_genomic.fna/dqc_result.json
[2023-06-29 20:10:42,601] [INFO] DFAST_QC completed!
[2023-06-29 20:10:42,601] [INFO] Total running time: 0h1m40s