[2023-06-29 16:08:45,129] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:08:45,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:08:45,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference
[2023-06-29 16:08:46,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:08:46,369] [INFO] Task started: Prodigal
[2023-06-29 16:08:46,369] [INFO] Running command: gunzip -c /var/lib/cwl/stgce3a970b-688e-4118-a9ae-1269baac6c9a/GCA_011772795.1_ASM1177279v1_genomic.fna.gz | prodigal -d GCA_011772795.1_ASM1177279v1_genomic.fna/cds.fna -a GCA_011772795.1_ASM1177279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:08:56,956] [INFO] Task succeeded: Prodigal
[2023-06-29 16:08:56,957] [INFO] Task started: HMMsearch
[2023-06-29 16:08:56,957] [INFO] Running command: hmmsearch --tblout GCA_011772795.1_ASM1177279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/reference_markers.hmm GCA_011772795.1_ASM1177279v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:08:57,225] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:08:57,227] [INFO] Found 6/6 markers.
[2023-06-29 16:08:57,266] [INFO] Query marker FASTA was written to GCA_011772795.1_ASM1177279v1_genomic.fna/markers.fasta
[2023-06-29 16:08:57,266] [INFO] Task started: Blastn
[2023-06-29 16:08:57,267] [INFO] Running command: blastn -query GCA_011772795.1_ASM1177279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/reference_markers.fasta -out GCA_011772795.1_ASM1177279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:08:57,846] [INFO] Task succeeded: Blastn
[2023-06-29 16:08:57,851] [INFO] Selected 28 target genomes.
[2023-06-29 16:08:57,852] [INFO] Target genome list was writen to GCA_011772795.1_ASM1177279v1_genomic.fna/target_genomes.txt
[2023-06-29 16:08:57,857] [INFO] Task started: fastANI
[2023-06-29 16:08:57,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3a970b-688e-4118-a9ae-1269baac6c9a/GCA_011772795.1_ASM1177279v1_genomic.fna.gz --refList GCA_011772795.1_ASM1177279v1_genomic.fna/target_genomes.txt --output GCA_011772795.1_ASM1177279v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:09:23,715] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:23,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:09:23,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:09:23,721] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:09:23,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:09:23,721] [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 corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.8528	60	923	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.4597	62	923	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:09:23,723] [INFO] DFAST Taxonomy check result was written to GCA_011772795.1_ASM1177279v1_genomic.fna/tc_result.tsv
[2023-06-29 16:09:23,724] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:09:23,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:09:23,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/checkm_data
[2023-06-29 16:09:23,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:09:23,766] [INFO] Task started: CheckM
[2023-06-29 16:09:23,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011772795.1_ASM1177279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011772795.1_ASM1177279v1_genomic.fna/checkm_input GCA_011772795.1_ASM1177279v1_genomic.fna/checkm_result
[2023-06-29 16:09:57,162] [INFO] Task succeeded: CheckM
[2023-06-29 16:09:57,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 6.94%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 16:09:57,186] [INFO] ===== Completeness check finished =====
[2023-06-29 16:09:57,186] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:09:57,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011772795.1_ASM1177279v1_genomic.fna/markers.fasta)
[2023-06-29 16:09:57,187] [INFO] Task started: Blastn
[2023-06-29 16:09:57,187] [INFO] Running command: blastn -query GCA_011772795.1_ASM1177279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10da4d1b-453a-45c5-ab26-59df2dc03559/dqc_reference/reference_markers_gtdb.fasta -out GCA_011772795.1_ASM1177279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:57,917] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:57,922] [INFO] Selected 25 target genomes.
[2023-06-29 16:09:57,922] [INFO] Target genome list was writen to GCA_011772795.1_ASM1177279v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:09:57,940] [INFO] Task started: fastANI
[2023-06-29 16:09:57,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3a970b-688e-4118-a9ae-1269baac6c9a/GCA_011772795.1_ASM1177279v1_genomic.fna.gz --refList GCA_011772795.1_ASM1177279v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011772795.1_ASM1177279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:10:15,496] [INFO] Task succeeded: fastANI
[2023-06-29 16:10:15,507] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:10:15,507] [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_011772275.1	s__CS4-C045 sp011772275	99.8994	842	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__CS4-C045	95.0	100.00	100.00	0.98	0.98	5	conclusive
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.8059	57	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.7082	55	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153375.1	s__PALSA-1355 sp003153375	75.6641	52	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__PALSA-1355	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007751035.1	s__Lignipirellula cremea	75.4597	62	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Lignipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242585.1	s__JAFEBQ01 sp018242585	75.3432	54	923	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__JAFEBQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:10:15,509] [INFO] GTDB search result was written to GCA_011772795.1_ASM1177279v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:10:15,510] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:10:15,513] [INFO] DFAST_QC result json was written to GCA_011772795.1_ASM1177279v1_genomic.fna/dqc_result.json
[2023-06-29 16:10:15,513] [INFO] DFAST_QC completed!
[2023-06-29 16:10:15,513] [INFO] Total running time: 0h1m30s