[2023-06-28 23:57:22,757] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:57:22,762] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:57:22,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference
[2023-06-28 23:57:24,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:57:24,122] [INFO] Task started: Prodigal
[2023-06-28 23:57:24,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c5d2458-ecc9-4bca-a8b8-f122d098c730/GCA_017621695.1_ASM1762169v1_genomic.fna.gz | prodigal -d GCA_017621695.1_ASM1762169v1_genomic.fna/cds.fna -a GCA_017621695.1_ASM1762169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:57:31,542] [INFO] Task succeeded: Prodigal
[2023-06-28 23:57:31,542] [INFO] Task started: HMMsearch
[2023-06-28 23:57:31,542] [INFO] Running command: hmmsearch --tblout GCA_017621695.1_ASM1762169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/reference_markers.hmm GCA_017621695.1_ASM1762169v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:57:31,786] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:57:31,787] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c5d2458-ecc9-4bca-a8b8-f122d098c730/GCA_017621695.1_ASM1762169v1_genomic.fna.gz]
[2023-06-28 23:57:31,813] [INFO] Query marker FASTA was written to GCA_017621695.1_ASM1762169v1_genomic.fna/markers.fasta
[2023-06-28 23:57:31,813] [INFO] Task started: Blastn
[2023-06-28 23:57:31,814] [INFO] Running command: blastn -query GCA_017621695.1_ASM1762169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/reference_markers.fasta -out GCA_017621695.1_ASM1762169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:32,497] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:32,502] [INFO] Selected 25 target genomes.
[2023-06-28 23:57:32,503] [INFO] Target genome list was writen to GCA_017621695.1_ASM1762169v1_genomic.fna/target_genomes.txt
[2023-06-28 23:57:32,506] [INFO] Task started: fastANI
[2023-06-28 23:57:32,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c5d2458-ecc9-4bca-a8b8-f122d098c730/GCA_017621695.1_ASM1762169v1_genomic.fna.gz --refList GCA_017621695.1_ASM1762169v1_genomic.fna/target_genomes.txt --output GCA_017621695.1_ASM1762169v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:57:46,891] [INFO] Task succeeded: fastANI
[2023-06-28 23:57:46,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:57:46,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:57:46,894] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:57:46,894] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:57:46,894] [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
--------------------------------------------------------------------------------
[2023-06-28 23:57:46,896] [INFO] DFAST Taxonomy check result was written to GCA_017621695.1_ASM1762169v1_genomic.fna/tc_result.tsv
[2023-06-28 23:57:46,897] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:57:46,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:57:46,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/checkm_data
[2023-06-28 23:57:46,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:57:46,931] [INFO] Task started: CheckM
[2023-06-28 23:57:46,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621695.1_ASM1762169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621695.1_ASM1762169v1_genomic.fna/checkm_input GCA_017621695.1_ASM1762169v1_genomic.fna/checkm_result
[2023-06-28 23:58:14,734] [INFO] Task succeeded: CheckM
[2023-06-28 23:58:14,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:58:14,763] [INFO] ===== Completeness check finished =====
[2023-06-28 23:58:14,764] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:58:14,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621695.1_ASM1762169v1_genomic.fna/markers.fasta)
[2023-06-28 23:58:14,764] [INFO] Task started: Blastn
[2023-06-28 23:58:14,765] [INFO] Running command: blastn -query GCA_017621695.1_ASM1762169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2ef4fe-722d-4d60-98ec-510f52fc5a2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621695.1_ASM1762169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:58:15,749] [INFO] Task succeeded: Blastn
[2023-06-28 23:58:15,754] [INFO] Selected 10 target genomes.
[2023-06-28 23:58:15,755] [INFO] Target genome list was writen to GCA_017621695.1_ASM1762169v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:58:15,770] [INFO] Task started: fastANI
[2023-06-28 23:58:15,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c5d2458-ecc9-4bca-a8b8-f122d098c730/GCA_017621695.1_ASM1762169v1_genomic.fna.gz --refList GCA_017621695.1_ASM1762169v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621695.1_ASM1762169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:58:21,889] [INFO] Task succeeded: fastANI
[2023-06-28 23:58:21,902] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:58:21,902] [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_017621695.1	s__CAG-448 sp017621695	100.0	796	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	98.14	98.14	0.85	0.85	2	conclusive
GCA_015063685.1	s__CAG-448 sp015063685	83.1987	472	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017456905.1	s__CAG-448 sp017456905	82.4108	432	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938885.1	s__CAG-448 sp017938885	81.7344	313	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017420845.1	s__CAG-448 sp017420845	81.5333	213	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064015.1	s__CAG-448 sp015064015	81.5183	312	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626655.1	s__CAG-448 sp017626655	81.38	236	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064695.1	s__CAG-448 sp015064695	80.2335	207	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017532045.1	s__CAG-448 sp017532045	79.8849	175	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:58:21,904] [INFO] GTDB search result was written to GCA_017621695.1_ASM1762169v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:58:21,905] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:58:21,908] [INFO] DFAST_QC result json was written to GCA_017621695.1_ASM1762169v1_genomic.fna/dqc_result.json
[2023-06-28 23:58:21,908] [INFO] DFAST_QC completed!
[2023-06-28 23:58:21,908] [INFO] Total running time: 0h0m59s