[2023-06-08 15:04:31,983] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:04:31,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:04:31,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference
[2023-06-08 15:04:33,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:04:33,311] [INFO] Task started: Prodigal
[2023-06-08 15:04:33,311] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3693de4-5b8b-4acb-a939-161b049b0e5e/GCA_947463525.1_RE-9nov16-114_genomic.fna.gz | prodigal -d GCA_947463525.1_RE-9nov16-114_genomic.fna/cds.fna -a GCA_947463525.1_RE-9nov16-114_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:04:35,673] [INFO] Task succeeded: Prodigal
[2023-06-08 15:04:35,674] [INFO] Task started: HMMsearch
[2023-06-08 15:04:35,674] [INFO] Running command: hmmsearch --tblout GCA_947463525.1_RE-9nov16-114_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/reference_markers.hmm GCA_947463525.1_RE-9nov16-114_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:04:35,896] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:04:35,897] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3693de4-5b8b-4acb-a939-161b049b0e5e/GCA_947463525.1_RE-9nov16-114_genomic.fna.gz]
[2023-06-08 15:04:35,918] [INFO] Query marker FASTA was written to GCA_947463525.1_RE-9nov16-114_genomic.fna/markers.fasta
[2023-06-08 15:04:35,919] [INFO] Task started: Blastn
[2023-06-08 15:04:35,919] [INFO] Running command: blastn -query GCA_947463525.1_RE-9nov16-114_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/reference_markers.fasta -out GCA_947463525.1_RE-9nov16-114_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:04:36,562] [INFO] Task succeeded: Blastn
[2023-06-08 15:04:36,566] [INFO] Selected 15 target genomes.
[2023-06-08 15:04:36,567] [INFO] Target genome list was writen to GCA_947463525.1_RE-9nov16-114_genomic.fna/target_genomes.txt
[2023-06-08 15:04:36,569] [INFO] Task started: fastANI
[2023-06-08 15:04:36,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3693de4-5b8b-4acb-a939-161b049b0e5e/GCA_947463525.1_RE-9nov16-114_genomic.fna.gz --refList GCA_947463525.1_RE-9nov16-114_genomic.fna/target_genomes.txt --output GCA_947463525.1_RE-9nov16-114_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:04:47,123] [INFO] Task succeeded: fastANI
[2023-06-08 15:04:47,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:04:47,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:04:47,125] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:04:47,125] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 15:04:47,125] [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
--------------------------------------------------------------------------------
[2023-06-08 15:04:47,127] [INFO] DFAST Taxonomy check result was written to GCA_947463525.1_RE-9nov16-114_genomic.fna/tc_result.tsv
[2023-06-08 15:04:47,127] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:04:47,127] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:04:47,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/checkm_data
[2023-06-08 15:04:47,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:04:47,143] [INFO] Task started: CheckM
[2023-06-08 15:04:47,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947463525.1_RE-9nov16-114_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947463525.1_RE-9nov16-114_genomic.fna/checkm_input GCA_947463525.1_RE-9nov16-114_genomic.fna/checkm_result
[2023-06-08 15:05:01,490] [INFO] Task succeeded: CheckM
[2023-06-08 15:05:01,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 15:05:01,519] [INFO] ===== Completeness check finished =====
[2023-06-08 15:05:01,520] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:05:01,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947463525.1_RE-9nov16-114_genomic.fna/markers.fasta)
[2023-06-08 15:05:01,520] [INFO] Task started: Blastn
[2023-06-08 15:05:01,520] [INFO] Running command: blastn -query GCA_947463525.1_RE-9nov16-114_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67f13cd-319b-4ce5-8646-5de8aaf71e66/dqc_reference/reference_markers_gtdb.fasta -out GCA_947463525.1_RE-9nov16-114_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:05:02,336] [INFO] Task succeeded: Blastn
[2023-06-08 15:05:02,339] [INFO] Selected 10 target genomes.
[2023-06-08 15:05:02,340] [INFO] Target genome list was writen to GCA_947463525.1_RE-9nov16-114_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:05:02,342] [INFO] Task started: fastANI
[2023-06-08 15:05:02,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3693de4-5b8b-4acb-a939-161b049b0e5e/GCA_947463525.1_RE-9nov16-114_genomic.fna.gz --refList GCA_947463525.1_RE-9nov16-114_genomic.fna/target_genomes_gtdb.txt --output GCA_947463525.1_RE-9nov16-114_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:05:04,169] [INFO] Task succeeded: fastANI
[2023-06-08 15:05:04,178] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:05:04,178] [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_003670745.1	s__Limnocylindrus sp003670745	99.4705	222	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009692905.1	s__Limnocylindrus sp009692905	79.0943	78	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670455.1	s__Limnocylindrus sp003670455	79.0163	97	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463555.1	s__Limnocylindrus sp016463555	79.0064	96	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.54	98.47	0.78	0.78	3	-
GCA_903847005.1	s__Limnocylindrus sp903847005	78.9559	86	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670475.1	s__Limnocylindrus sp003670475	78.9503	106	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.28	98.28	0.88	0.88	2	-
GCA_903820655.1	s__Limnocylindrus sp903820655	78.4686	83	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938075.1	s__Limnocylindrus sp903938075	78.4362	95	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009925905.1	s__Limnocylindrus frankliniae	78.2121	94	262	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 15:05:04,180] [INFO] GTDB search result was written to GCA_947463525.1_RE-9nov16-114_genomic.fna/result_gtdb.tsv
[2023-06-08 15:05:04,181] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:05:04,184] [INFO] DFAST_QC result json was written to GCA_947463525.1_RE-9nov16-114_genomic.fna/dqc_result.json
[2023-06-08 15:05:04,184] [INFO] DFAST_QC completed!
[2023-06-08 15:05:04,184] [INFO] Total running time: 0h0m32s