[2023-06-05 23:13:01,007] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:13:01,011] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:13:01,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference
[2023-06-05 23:13:02,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:13:02,582] [INFO] Task started: Prodigal
[2023-06-05 23:13:02,582] [INFO] Running command: gunzip -c /var/lib/cwl/stgd72e1021-7f8b-4b45-a625-2d270679854d/GCA_004558765.1_ASM455876v1_genomic.fna.gz | prodigal -d GCA_004558765.1_ASM455876v1_genomic.fna/cds.fna -a GCA_004558765.1_ASM455876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:13:08,646] [INFO] Task succeeded: Prodigal
[2023-06-05 23:13:08,647] [INFO] Task started: HMMsearch
[2023-06-05 23:13:08,647] [INFO] Running command: hmmsearch --tblout GCA_004558765.1_ASM455876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/reference_markers.hmm GCA_004558765.1_ASM455876v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:13:08,900] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:13:08,901] [INFO] Found 6/6 markers.
[2023-06-05 23:13:08,922] [INFO] Query marker FASTA was written to GCA_004558765.1_ASM455876v1_genomic.fna/markers.fasta
[2023-06-05 23:13:08,922] [INFO] Task started: Blastn
[2023-06-05 23:13:08,922] [INFO] Running command: blastn -query GCA_004558765.1_ASM455876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/reference_markers.fasta -out GCA_004558765.1_ASM455876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:13:09,506] [INFO] Task succeeded: Blastn
[2023-06-05 23:13:09,509] [INFO] Selected 30 target genomes.
[2023-06-05 23:13:09,510] [INFO] Target genome list was writen to GCA_004558765.1_ASM455876v1_genomic.fna/target_genomes.txt
[2023-06-05 23:13:09,513] [INFO] Task started: fastANI
[2023-06-05 23:13:09,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72e1021-7f8b-4b45-a625-2d270679854d/GCA_004558765.1_ASM455876v1_genomic.fna.gz --refList GCA_004558765.1_ASM455876v1_genomic.fna/target_genomes.txt --output GCA_004558765.1_ASM455876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:13:26,649] [INFO] Task succeeded: fastANI
[2023-06-05 23:13:26,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:13:26,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:13:26,651] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:13:26,651] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:13:26,651] [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
--------------------------------------------------------------------------------
[2023-06-05 23:13:26,652] [INFO] DFAST Taxonomy check result was written to GCA_004558765.1_ASM455876v1_genomic.fna/tc_result.tsv
[2023-06-05 23:13:26,653] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:13:26,653] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:13:26,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/checkm_data
[2023-06-05 23:13:26,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:13:26,681] [INFO] Task started: CheckM
[2023-06-05 23:13:26,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004558765.1_ASM455876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004558765.1_ASM455876v1_genomic.fna/checkm_input GCA_004558765.1_ASM455876v1_genomic.fna/checkm_result
[2023-06-05 23:13:48,592] [INFO] Task succeeded: CheckM
[2023-06-05 23:13:48,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:13:48,609] [INFO] ===== Completeness check finished =====
[2023-06-05 23:13:48,609] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:13:48,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004558765.1_ASM455876v1_genomic.fna/markers.fasta)
[2023-06-05 23:13:48,610] [INFO] Task started: Blastn
[2023-06-05 23:13:48,610] [INFO] Running command: blastn -query GCA_004558765.1_ASM455876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87c4eac-9c5c-444e-bf8d-b7e5a659a5ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_004558765.1_ASM455876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:13:49,533] [INFO] Task succeeded: Blastn
[2023-06-05 23:13:49,536] [INFO] Selected 9 target genomes.
[2023-06-05 23:13:49,536] [INFO] Target genome list was writen to GCA_004558765.1_ASM455876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:13:49,541] [INFO] Task started: fastANI
[2023-06-05 23:13:49,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72e1021-7f8b-4b45-a625-2d270679854d/GCA_004558765.1_ASM455876v1_genomic.fna.gz --refList GCA_004558765.1_ASM455876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004558765.1_ASM455876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:13:54,313] [INFO] Task succeeded: fastANI
[2023-06-05 23:13:54,320] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:13:54,320] [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_004556155.1	s__SFMI01 sp004556155	98.8261	703	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	98.69	98.33	0.93	0.91	8	conclusive
GCA_902787835.1	s__SFMI01 sp902787835	80.1733	250	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764185.1	s__SFMI01 sp902764185	79.6785	258	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781945.1	s__SFMI01 sp902781945	79.6319	304	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761825.1	s__SFMI01 sp902761825	79.4794	267	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017532155.1	s__SFMI01 sp017532155	79.2938	208	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	97.62	97.62	0.79	0.79	2	-
GCA_017469605.1	s__SFMI01 sp017469605	79.293	207	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464225.1	s__SFMI01 sp017464225	78.954	231	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549335.1	s__SFMI01 sp017549335	78.895	215	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFMI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:13:54,322] [INFO] GTDB search result was written to GCA_004558765.1_ASM455876v1_genomic.fna/result_gtdb.tsv
[2023-06-05 23:13:54,322] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:13:54,349] [INFO] DFAST_QC result json was written to GCA_004558765.1_ASM455876v1_genomic.fna/dqc_result.json
[2023-06-05 23:13:54,349] [INFO] DFAST_QC completed!
[2023-06-05 23:13:54,349] [INFO] Total running time: 0h0m53s