[2023-06-29 21:38:50,556] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:38:50,559] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:38:50,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference
[2023-06-29 21:38:51,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:38:51,876] [INFO] Task started: Prodigal
[2023-06-29 21:38:51,876] [INFO] Running command: gunzip -c /var/lib/cwl/stga07d81a5-2168-405f-9118-629f7d69f3f2/GCA_007134565.1_ASM713456v1_genomic.fna.gz | prodigal -d GCA_007134565.1_ASM713456v1_genomic.fna/cds.fna -a GCA_007134565.1_ASM713456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:38:56,803] [INFO] Task succeeded: Prodigal
[2023-06-29 21:38:56,804] [INFO] Task started: HMMsearch
[2023-06-29 21:38:56,804] [INFO] Running command: hmmsearch --tblout GCA_007134565.1_ASM713456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/reference_markers.hmm GCA_007134565.1_ASM713456v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:38:57,061] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:38:57,063] [INFO] Found 6/6 markers.
[2023-06-29 21:38:57,093] [INFO] Query marker FASTA was written to GCA_007134565.1_ASM713456v1_genomic.fna/markers.fasta
[2023-06-29 21:38:57,094] [INFO] Task started: Blastn
[2023-06-29 21:38:57,094] [INFO] Running command: blastn -query GCA_007134565.1_ASM713456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/reference_markers.fasta -out GCA_007134565.1_ASM713456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:38:57,734] [INFO] Task succeeded: Blastn
[2023-06-29 21:38:57,738] [INFO] Selected 24 target genomes.
[2023-06-29 21:38:57,739] [INFO] Target genome list was writen to GCA_007134565.1_ASM713456v1_genomic.fna/target_genomes.txt
[2023-06-29 21:38:57,744] [INFO] Task started: fastANI
[2023-06-29 21:38:57,744] [INFO] Running command: fastANI --query /var/lib/cwl/stga07d81a5-2168-405f-9118-629f7d69f3f2/GCA_007134565.1_ASM713456v1_genomic.fna.gz --refList GCA_007134565.1_ASM713456v1_genomic.fna/target_genomes.txt --output GCA_007134565.1_ASM713456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:39:13,785] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:13,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:39:13,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:39:13,792] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:39:13,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:39:13,792] [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
Desulfosalsimonas propionicica	strain=DSM 17721	GCA_013761005.1	332175	332175	type	True	76.7294	62	473	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:39:13,795] [INFO] DFAST Taxonomy check result was written to GCA_007134565.1_ASM713456v1_genomic.fna/tc_result.tsv
[2023-06-29 21:39:13,795] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:39:13,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:39:13,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/checkm_data
[2023-06-29 21:39:13,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:39:13,819] [INFO] Task started: CheckM
[2023-06-29 21:39:13,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007134565.1_ASM713456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007134565.1_ASM713456v1_genomic.fna/checkm_input GCA_007134565.1_ASM713456v1_genomic.fna/checkm_result
[2023-06-29 21:39:35,317] [INFO] Task succeeded: CheckM
[2023-06-29 21:39:35,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:39:35,339] [INFO] ===== Completeness check finished =====
[2023-06-29 21:39:35,340] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:39:35,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007134565.1_ASM713456v1_genomic.fna/markers.fasta)
[2023-06-29 21:39:35,341] [INFO] Task started: Blastn
[2023-06-29 21:39:35,341] [INFO] Running command: blastn -query GCA_007134565.1_ASM713456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf403f114-4be0-4c89-878c-839a538491e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_007134565.1_ASM713456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:36,270] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:36,275] [INFO] Selected 14 target genomes.
[2023-06-29 21:39:36,275] [INFO] Target genome list was writen to GCA_007134565.1_ASM713456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:39:36,350] [INFO] Task started: fastANI
[2023-06-29 21:39:36,351] [INFO] Running command: fastANI --query /var/lib/cwl/stga07d81a5-2168-405f-9118-629f7d69f3f2/GCA_007134565.1_ASM713456v1_genomic.fna.gz --refList GCA_007134565.1_ASM713456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007134565.1_ASM713456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:39:44,169] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:44,180] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:39:44,181] [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_007127175.1	s__B1SED10-16 sp007127175	98.485	362	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	98.75	98.64	0.76	0.72	3	conclusive
GCA_007136525.1	s__B1SED10-16 sp007136525	89.9415	265	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389515.1	s__B1SED10-16 sp011389515	79.4835	231	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389935.1	s__B1SED10-16 sp011389935	79.4191	244	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551985.1	s__B1SED10-16 sp003551985	78.886	108	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003597945.1	s__SURF-33 sp003597945	78.4643	50	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134875.1	s__B1SED10-16 sp007134875	77.5384	111	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335195.1	s__Desulfosalsimonas sp018335195	76.9759	54	473	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	99.35	99.35	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:39:44,183] [INFO] GTDB search result was written to GCA_007134565.1_ASM713456v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:39:44,184] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:39:44,187] [INFO] DFAST_QC result json was written to GCA_007134565.1_ASM713456v1_genomic.fna/dqc_result.json
[2023-06-29 21:39:44,187] [INFO] DFAST_QC completed!
[2023-06-29 21:39:44,187] [INFO] Total running time: 0h0m54s