[2023-06-28 10:27:03,811] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:27:03,826] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:27:03,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference
[2023-06-28 10:27:05,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:27:05,710] [INFO] Task started: Prodigal
[2023-06-28 10:27:05,710] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd2f37a6-246e-4374-8d05-3abdfbf53385/GCA_020849895.1_ASM2084989v1_genomic.fna.gz | prodigal -d GCA_020849895.1_ASM2084989v1_genomic.fna/cds.fna -a GCA_020849895.1_ASM2084989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:27:22,224] [INFO] Task succeeded: Prodigal
[2023-06-28 10:27:22,225] [INFO] Task started: HMMsearch
[2023-06-28 10:27:22,225] [INFO] Running command: hmmsearch --tblout GCA_020849895.1_ASM2084989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/reference_markers.hmm GCA_020849895.1_ASM2084989v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:27:22,443] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:27:22,445] [INFO] Found 6/6 markers.
[2023-06-28 10:27:22,477] [INFO] Query marker FASTA was written to GCA_020849895.1_ASM2084989v1_genomic.fna/markers.fasta
[2023-06-28 10:27:22,477] [INFO] Task started: Blastn
[2023-06-28 10:27:22,477] [INFO] Running command: blastn -query GCA_020849895.1_ASM2084989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/reference_markers.fasta -out GCA_020849895.1_ASM2084989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:27:23,178] [INFO] Task succeeded: Blastn
[2023-06-28 10:27:23,183] [INFO] Selected 30 target genomes.
[2023-06-28 10:27:23,184] [INFO] Target genome list was writen to GCA_020849895.1_ASM2084989v1_genomic.fna/target_genomes.txt
[2023-06-28 10:27:23,186] [INFO] Task started: fastANI
[2023-06-28 10:27:23,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd2f37a6-246e-4374-8d05-3abdfbf53385/GCA_020849895.1_ASM2084989v1_genomic.fna.gz --refList GCA_020849895.1_ASM2084989v1_genomic.fna/target_genomes.txt --output GCA_020849895.1_ASM2084989v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:27:44,470] [INFO] Task succeeded: fastANI
[2023-06-28 10:27:44,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:27:44,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:27:44,476] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:27:44,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:27:44,477] [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
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	74.8044	53	917	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	74.6844	52	917	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.6776	85	917	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:27:44,479] [INFO] DFAST Taxonomy check result was written to GCA_020849895.1_ASM2084989v1_genomic.fna/tc_result.tsv
[2023-06-28 10:27:44,479] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:27:44,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:27:44,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/checkm_data
[2023-06-28 10:27:44,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:27:44,514] [INFO] Task started: CheckM
[2023-06-28 10:27:44,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020849895.1_ASM2084989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020849895.1_ASM2084989v1_genomic.fna/checkm_input GCA_020849895.1_ASM2084989v1_genomic.fna/checkm_result
[2023-06-28 10:28:31,392] [INFO] Task succeeded: CheckM
[2023-06-28 10:28:31,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:28:31,416] [INFO] ===== Completeness check finished =====
[2023-06-28 10:28:31,416] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:28:31,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020849895.1_ASM2084989v1_genomic.fna/markers.fasta)
[2023-06-28 10:28:31,417] [INFO] Task started: Blastn
[2023-06-28 10:28:31,417] [INFO] Running command: blastn -query GCA_020849895.1_ASM2084989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e4a04df-5ea3-4053-a1ef-4489bbbb4527/dqc_reference/reference_markers_gtdb.fasta -out GCA_020849895.1_ASM2084989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:28:32,388] [INFO] Task succeeded: Blastn
[2023-06-28 10:28:32,393] [INFO] Selected 26 target genomes.
[2023-06-28 10:28:32,393] [INFO] Target genome list was writen to GCA_020849895.1_ASM2084989v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:28:32,401] [INFO] Task started: fastANI
[2023-06-28 10:28:32,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd2f37a6-246e-4374-8d05-3abdfbf53385/GCA_020849895.1_ASM2084989v1_genomic.fna.gz --refList GCA_020849895.1_ASM2084989v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020849895.1_ASM2084989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:28:47,617] [INFO] Task succeeded: fastANI
[2023-06-28 10:28:47,626] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:28:47,626] [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_013360985.1	s__JABWAM01 sp013360985	78.8251	340	917	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__JABWAM01;f__JABWAM01;g__JABWAM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199935.1	s__JACQFS01 sp016199935	75.5482	83	917	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACQFS01;g__JACQFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871715.1	s__VHCO01 sp016871715	75.2589	53	917	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__VHCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873715.1	s__VGWF01 sp016873715	75.1255	60	917	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__PWTM01;f__CAACVY01;g__VGWF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:28:47,628] [INFO] GTDB search result was written to GCA_020849895.1_ASM2084989v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:28:47,629] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:28:47,633] [INFO] DFAST_QC result json was written to GCA_020849895.1_ASM2084989v1_genomic.fna/dqc_result.json
[2023-06-28 10:28:47,633] [INFO] DFAST_QC completed!
[2023-06-28 10:28:47,633] [INFO] Total running time: 0h1m44s