[2024-01-24 14:30:30,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference
[2024-01-24 14:30:31,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,643] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg63a4a1ec-e0e8-49e0-8a06-4189adbfdf07/GCF_000423565.1_ASM42356v1_genomic.fna.gz | prodigal -d GCF_000423565.1_ASM42356v1_genomic.fna/cds.fna -a GCF_000423565.1_ASM42356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:10,514] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:10,514] [INFO] Task started: HMMsearch
[2024-01-24 14:31:10,514] [INFO] Running command: hmmsearch --tblout GCF_000423565.1_ASM42356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/reference_markers.hmm GCF_000423565.1_ASM42356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:10,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:10,856] [INFO] Found 6/6 markers.
[2024-01-24 14:31:10,919] [INFO] Query marker FASTA was written to GCF_000423565.1_ASM42356v1_genomic.fna/markers.fasta
[2024-01-24 14:31:10,919] [INFO] Task started: Blastn
[2024-01-24 14:31:10,919] [INFO] Running command: blastn -query GCF_000423565.1_ASM42356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/reference_markers.fasta -out GCF_000423565.1_ASM42356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:11,539] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:11,542] [INFO] Selected 21 target genomes.
[2024-01-24 14:31:11,543] [INFO] Target genome list was writen to GCF_000423565.1_ASM42356v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:11,568] [INFO] Task started: fastANI
[2024-01-24 14:31:11,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a4a1ec-e0e8-49e0-8a06-4189adbfdf07/GCF_000423565.1_ASM42356v1_genomic.fna.gz --refList GCF_000423565.1_ASM42356v1_genomic.fna/target_genomes.txt --output GCF_000423565.1_ASM42356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:32,672] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:32,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:32,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:32,680] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:32,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:32,681] [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
Runella zeae	strain=DSM 19591	GCA_000423565.1	94255	94255	type	True	100.0	2483	2493	95	conclusive
Runella limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	79.5291	612	2493	95	below_threshold
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	78.9748	654	2493	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	77.8296	474	2493	95	below_threshold
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	77.6168	617	2493	95	below_threshold
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	77.4078	642	2493	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	75.7236	50	2493	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	75.2889	52	2493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:32,682] [INFO] DFAST Taxonomy check result was written to GCF_000423565.1_ASM42356v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:32,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:32,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:32,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/checkm_data
[2024-01-24 14:31:32,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:32,753] [INFO] Task started: CheckM
[2024-01-24 14:31:32,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423565.1_ASM42356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423565.1_ASM42356v1_genomic.fna/checkm_input GCF_000423565.1_ASM42356v1_genomic.fna/checkm_result
[2024-01-24 14:33:08,897] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:08,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:08,922] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:08,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:08,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423565.1_ASM42356v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:08,923] [INFO] Task started: Blastn
[2024-01-24 14:33:08,923] [INFO] Running command: blastn -query GCF_000423565.1_ASM42356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55d476d-46f6-4188-961c-a1f12db29e96/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423565.1_ASM42356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:09,676] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:09,679] [INFO] Selected 17 target genomes.
[2024-01-24 14:33:09,679] [INFO] Target genome list was writen to GCF_000423565.1_ASM42356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:09,701] [INFO] Task started: fastANI
[2024-01-24 14:33:09,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a4a1ec-e0e8-49e0-8a06-4189adbfdf07/GCF_000423565.1_ASM42356v1_genomic.fna.gz --refList GCF_000423565.1_ASM42356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423565.1_ASM42356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:27,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:27,876] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:27,876] [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
GCF_000423565.1	s__Runella zeae	100.0	2483	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	99.21	99.21	0.93	0.93	2	conclusive
GCF_000482465.1	s__Runella limosa	79.5157	614	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195535.1	s__Runella defluvii	78.9921	653	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	95.53	95.36	0.92	0.90	3	-
GCF_003711225.1	s__Runella sp003711225	78.4575	593	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218895.1	s__Runella slithyformis	77.8296	474	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905605.1	s__Runella sp009905605	77.499	657	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339505.1	s__Runella sp003339505	77.4033	643	2493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:27,878] [INFO] GTDB search result was written to GCF_000423565.1_ASM42356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:27,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:27,881] [INFO] DFAST_QC result json was written to GCF_000423565.1_ASM42356v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:27,881] [INFO] DFAST_QC completed!
[2024-01-24 14:33:27,881] [INFO] Total running time: 0h2m58s