[2023-06-29 00:37:23,255] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:23,261] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:23,262] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference
[2023-06-29 00:37:24,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:24,896] [INFO] Task started: Prodigal
[2023-06-29 00:37:24,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgf10658a1-01b5-4f8b-b9d0-b3b2cc9e79d9/GCA_017936205.1_ASM1793620v1_genomic.fna.gz | prodigal -d GCA_017936205.1_ASM1793620v1_genomic.fna/cds.fna -a GCA_017936205.1_ASM1793620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:30,404] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:30,404] [INFO] Task started: HMMsearch
[2023-06-29 00:37:30,404] [INFO] Running command: hmmsearch --tblout GCA_017936205.1_ASM1793620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/reference_markers.hmm GCA_017936205.1_ASM1793620v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:30,661] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:30,663] [INFO] Found 6/6 markers.
[2023-06-29 00:37:30,690] [INFO] Query marker FASTA was written to GCA_017936205.1_ASM1793620v1_genomic.fna/markers.fasta
[2023-06-29 00:37:30,691] [INFO] Task started: Blastn
[2023-06-29 00:37:30,691] [INFO] Running command: blastn -query GCA_017936205.1_ASM1793620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/reference_markers.fasta -out GCA_017936205.1_ASM1793620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:31,382] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:31,388] [INFO] Selected 21 target genomes.
[2023-06-29 00:37:31,389] [INFO] Target genome list was writen to GCA_017936205.1_ASM1793620v1_genomic.fna/target_genomes.txt
[2023-06-29 00:37:31,389] [INFO] Task started: fastANI
[2023-06-29 00:37:31,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgf10658a1-01b5-4f8b-b9d0-b3b2cc9e79d9/GCA_017936205.1_ASM1793620v1_genomic.fna.gz --refList GCA_017936205.1_ASM1793620v1_genomic.fna/target_genomes.txt --output GCA_017936205.1_ASM1793620v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:44,465] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:44,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:44,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:44,469] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:44,469] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:37:44,469] [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 00:37:44,471] [INFO] DFAST Taxonomy check result was written to GCA_017936205.1_ASM1793620v1_genomic.fna/tc_result.tsv
[2023-06-29 00:37:44,472] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:44,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:44,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/checkm_data
[2023-06-29 00:37:44,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:44,505] [INFO] Task started: CheckM
[2023-06-29 00:37:44,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017936205.1_ASM1793620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017936205.1_ASM1793620v1_genomic.fna/checkm_input GCA_017936205.1_ASM1793620v1_genomic.fna/checkm_result
[2023-06-29 00:38:09,516] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:09,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.08%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:09,545] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:09,545] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:09,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017936205.1_ASM1793620v1_genomic.fna/markers.fasta)
[2023-06-29 00:38:09,546] [INFO] Task started: Blastn
[2023-06-29 00:38:09,546] [INFO] Running command: blastn -query GCA_017936205.1_ASM1793620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f25df6-ba53-4247-9f3e-a568f12f10c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017936205.1_ASM1793620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:10,601] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:10,606] [INFO] Selected 21 target genomes.
[2023-06-29 00:38:10,606] [INFO] Target genome list was writen to GCA_017936205.1_ASM1793620v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:10,619] [INFO] Task started: fastANI
[2023-06-29 00:38:10,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgf10658a1-01b5-4f8b-b9d0-b3b2cc9e79d9/GCA_017936205.1_ASM1793620v1_genomic.fna.gz --refList GCA_017936205.1_ASM1793620v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017936205.1_ASM1793620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:17,671] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:17,685] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:17,686] [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_017936205.1	s__Faecousia sp017936205	100.0	609	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017391305.1	s__Faecousia sp017391305	80.1397	224	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481325.1	s__Faecousia sp017481325	78.6067	72	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399355.1	s__Faecousia sp017399355	78.137	89	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067565.1	s__Faecousia sp015067565	77.604	82	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769995.1	s__Faecousia sp900769995	77.2637	54	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544705.1	s__Faecousia sp900544705	76.8714	56	623	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.60	98.49	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:17,687] [INFO] GTDB search result was written to GCA_017936205.1_ASM1793620v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:17,688] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:17,691] [INFO] DFAST_QC result json was written to GCA_017936205.1_ASM1793620v1_genomic.fna/dqc_result.json
[2023-06-29 00:38:17,691] [INFO] DFAST_QC completed!
[2023-06-29 00:38:17,691] [INFO] Total running time: 0h0m54s