[2023-06-29 15:27:14,976] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:27:14,978] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:27:14,978] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference
[2023-06-29 15:27:16,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:27:16,325] [INFO] Task started: Prodigal
[2023-06-29 15:27:16,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d6d997d-e27a-49fb-85ab-e717b2df05ea/GCA_021820065.1_ASM2182006v1_genomic.fna.gz | prodigal -d GCA_021820065.1_ASM2182006v1_genomic.fna/cds.fna -a GCA_021820065.1_ASM2182006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:27:23,046] [INFO] Task succeeded: Prodigal
[2023-06-29 15:27:23,046] [INFO] Task started: HMMsearch
[2023-06-29 15:27:23,046] [INFO] Running command: hmmsearch --tblout GCA_021820065.1_ASM2182006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/reference_markers.hmm GCA_021820065.1_ASM2182006v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:27:23,298] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:27:23,300] [INFO] Found 6/6 markers.
[2023-06-29 15:27:23,347] [INFO] Query marker FASTA was written to GCA_021820065.1_ASM2182006v1_genomic.fna/markers.fasta
[2023-06-29 15:27:23,348] [INFO] Task started: Blastn
[2023-06-29 15:27:23,348] [INFO] Running command: blastn -query GCA_021820065.1_ASM2182006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/reference_markers.fasta -out GCA_021820065.1_ASM2182006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:27:23,960] [INFO] Task succeeded: Blastn
[2023-06-29 15:27:23,965] [INFO] Selected 18 target genomes.
[2023-06-29 15:27:23,965] [INFO] Target genome list was writen to GCA_021820065.1_ASM2182006v1_genomic.fna/target_genomes.txt
[2023-06-29 15:27:23,967] [INFO] Task started: fastANI
[2023-06-29 15:27:23,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6d997d-e27a-49fb-85ab-e717b2df05ea/GCA_021820065.1_ASM2182006v1_genomic.fna.gz --refList GCA_021820065.1_ASM2182006v1_genomic.fna/target_genomes.txt --output GCA_021820065.1_ASM2182006v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:27:34,901] [INFO] Task succeeded: fastANI
[2023-06-29 15:27:34,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:27:34,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:27:34,905] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:27:34,905] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:27:34,906] [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
--------------------------------------------------------------------------------
[2023-06-29 15:27:34,908] [INFO] DFAST Taxonomy check result was written to GCA_021820065.1_ASM2182006v1_genomic.fna/tc_result.tsv
[2023-06-29 15:27:34,909] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:27:34,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:27:34,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/checkm_data
[2023-06-29 15:27:34,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:27:34,948] [INFO] Task started: CheckM
[2023-06-29 15:27:34,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021820065.1_ASM2182006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021820065.1_ASM2182006v1_genomic.fna/checkm_input GCA_021820065.1_ASM2182006v1_genomic.fna/checkm_result
[2023-06-29 15:28:01,841] [INFO] Task succeeded: CheckM
[2023-06-29 15:28:01,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:28:01,866] [INFO] ===== Completeness check finished =====
[2023-06-29 15:28:01,866] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:28:01,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021820065.1_ASM2182006v1_genomic.fna/markers.fasta)
[2023-06-29 15:28:01,867] [INFO] Task started: Blastn
[2023-06-29 15:28:01,867] [INFO] Running command: blastn -query GCA_021820065.1_ASM2182006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d8a145-0982-4b7d-9320-0fbf33850b95/dqc_reference/reference_markers_gtdb.fasta -out GCA_021820065.1_ASM2182006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:28:02,670] [INFO] Task succeeded: Blastn
[2023-06-29 15:28:02,675] [INFO] Selected 18 target genomes.
[2023-06-29 15:28:02,675] [INFO] Target genome list was writen to GCA_021820065.1_ASM2182006v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:28:02,679] [INFO] Task started: fastANI
[2023-06-29 15:28:02,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6d997d-e27a-49fb-85ab-e717b2df05ea/GCA_021820065.1_ASM2182006v1_genomic.fna.gz --refList GCA_021820065.1_ASM2182006v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021820065.1_ASM2182006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:28:12,130] [INFO] Task succeeded: fastANI
[2023-06-29 15:28:12,143] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:28:12,143] [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_012026935.1	s__Fen-1258 sp012026935	77.1532	181	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234355.1	s__Fen-1258 sp016234355	76.9662	128	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280825.1	s__Fen-1258 sp007280825	76.8551	122	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177735.1	s__DSXH01 sp016177735	76.5283	164	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__DSXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773205.1	s__XYB12-FULL-38-5 sp009773205	76.3054	94	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__XYB12-FULL-38-5	95.0	99.94	99.94	0.94	0.94	2	-
GCA_003155655.1	s__Fen-1258 sp003155655	76.1355	119	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	99.91	99.91	0.97	0.97	2	-
GCA_018333725.1	s__DSXH01 sp018333725	76.0363	66	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__DSXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873835.1	s__DSXH01 sp016873835	75.9814	75	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__DSXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839795.1	s__Fen-1258 sp002839795	75.8812	92	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599415.1	s__SURF-24 sp003599415	75.6145	54	1004	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__SURF-24;g__SURF-24	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:28:12,145] [INFO] GTDB search result was written to GCA_021820065.1_ASM2182006v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:28:12,146] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:28:12,148] [INFO] DFAST_QC result json was written to GCA_021820065.1_ASM2182006v1_genomic.fna/dqc_result.json
[2023-06-29 15:28:12,149] [INFO] DFAST_QC completed!
[2023-06-29 15:28:12,149] [INFO] Total running time: 0h0m57s