[2024-01-25 20:11:20,810] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:20,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:20,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference
[2024-01-25 20:11:21,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:21,982] [INFO] Task started: Prodigal
[2024-01-25 20:11:21,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d5ea6cc-8a83-4e35-a79a-ce4397f7ef84/GCF_900240265.1_PRJEB22823_genomic.fna.gz | prodigal -d GCF_900240265.1_PRJEB22823_genomic.fna/cds.fna -a GCF_900240265.1_PRJEB22823_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:28,805] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:28,805] [INFO] Task started: HMMsearch
[2024-01-25 20:11:28,805] [INFO] Running command: hmmsearch --tblout GCF_900240265.1_PRJEB22823_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/reference_markers.hmm GCF_900240265.1_PRJEB22823_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:28,986] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:28,987] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d5ea6cc-8a83-4e35-a79a-ce4397f7ef84/GCF_900240265.1_PRJEB22823_genomic.fna.gz]
[2024-01-25 20:11:29,011] [INFO] Query marker FASTA was written to GCF_900240265.1_PRJEB22823_genomic.fna/markers.fasta
[2024-01-25 20:11:29,012] [INFO] Task started: Blastn
[2024-01-25 20:11:29,012] [INFO] Running command: blastn -query GCF_900240265.1_PRJEB22823_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/reference_markers.fasta -out GCF_900240265.1_PRJEB22823_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:29,551] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:29,554] [INFO] Selected 22 target genomes.
[2024-01-25 20:11:29,554] [INFO] Target genome list was writen to GCF_900240265.1_PRJEB22823_genomic.fna/target_genomes.txt
[2024-01-25 20:11:29,658] [INFO] Task started: fastANI
[2024-01-25 20:11:29,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d5ea6cc-8a83-4e35-a79a-ce4397f7ef84/GCF_900240265.1_PRJEB22823_genomic.fna.gz --refList GCF_900240265.1_PRJEB22823_genomic.fna/target_genomes.txt --output GCF_900240265.1_PRJEB22823_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:11:42,117] [INFO] Task succeeded: fastANI
[2024-01-25 20:11:42,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:11:42,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:11:42,121] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:11:42,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:11:42,121] [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
Galactobacillus timonensis	strain=Marseille-P4641	GCA_900240265.1	2041840	2041840	type	True	100.0	942	944	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:11:42,122] [INFO] DFAST Taxonomy check result was written to GCF_900240265.1_PRJEB22823_genomic.fna/tc_result.tsv
[2024-01-25 20:11:42,123] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:11:42,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:11:42,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/checkm_data
[2024-01-25 20:11:42,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:11:42,153] [INFO] Task started: CheckM
[2024-01-25 20:11:42,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900240265.1_PRJEB22823_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900240265.1_PRJEB22823_genomic.fna/checkm_input GCF_900240265.1_PRJEB22823_genomic.fna/checkm_result
[2024-01-25 20:12:07,145] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:07,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:07,165] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:07,165] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:07,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900240265.1_PRJEB22823_genomic.fna/markers.fasta)
[2024-01-25 20:12:07,166] [INFO] Task started: Blastn
[2024-01-25 20:12:07,166] [INFO] Running command: blastn -query GCF_900240265.1_PRJEB22823_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e7f6f4-4388-4c31-bfb4-18c402c1fb13/dqc_reference/reference_markers_gtdb.fasta -out GCF_900240265.1_PRJEB22823_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:07,944] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:07,949] [INFO] Selected 16 target genomes.
[2024-01-25 20:12:07,949] [INFO] Target genome list was writen to GCF_900240265.1_PRJEB22823_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:07,965] [INFO] Task started: fastANI
[2024-01-25 20:12:07,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d5ea6cc-8a83-4e35-a79a-ce4397f7ef84/GCF_900240265.1_PRJEB22823_genomic.fna.gz --refList GCF_900240265.1_PRJEB22823_genomic.fna/target_genomes_gtdb.txt --output GCF_900240265.1_PRJEB22823_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:15,905] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:15,912] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:15,912] [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_900240265.1	s__Bulleidia timonensis	100.0	941	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.98	97.48	0.91	0.75	11	conclusive
GCA_900770275.1	s__Bulleidia sp900770275	89.5752	459	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696165.1	s__Bulleidia intestinalis	79.5317	180	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	-
GCA_900314905.1	s__Bulleidia sp900314905	78.4785	133	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900314345.1	s__Bulleidia sp900314345	77.7429	78	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017469885.1	s__Bulleidia sp017469885	76.9572	78	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536885.1	s__Bulleidia sp017536885	76.9309	56	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	96.20	96.20	0.80	0.80	2	-
GCA_902786245.1	s__Bulleidia sp902786245	76.6985	68	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319505.1	s__Bulleidia sp900319505	76.6343	56	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.64	99.39	0.93	0.88	3	-
GCA_017433125.1	s__Bulleidia sp017433125	76.5237	57	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_017510405.1	s__Bulleidia sp017510405	76.3455	53	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:15,914] [INFO] GTDB search result was written to GCF_900240265.1_PRJEB22823_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:15,914] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:15,916] [INFO] DFAST_QC result json was written to GCF_900240265.1_PRJEB22823_genomic.fna/dqc_result.json
[2024-01-25 20:12:15,916] [INFO] DFAST_QC completed!
[2024-01-25 20:12:15,916] [INFO] Total running time: 0h0m55s