[2023-06-13 14:45:31,981] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:31,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:31,983] [INFO] DQC Reference Directory: /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference
[2023-06-13 14:45:33,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:33,168] [INFO] Task started: Prodigal
[2023-06-13 14:45:33,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg985c5e80-370f-4ff6-9fb7-b0eae55e7b3e/GCA_022771445.1_ASM2277144v1_genomic.fna.gz | prodigal -d GCA_022771445.1_ASM2277144v1_genomic.fna/cds.fna -a GCA_022771445.1_ASM2277144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:37,472] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:37,473] [INFO] Task started: HMMsearch
[2023-06-13 14:45:37,473] [INFO] Running command: hmmsearch --tblout GCA_022771445.1_ASM2277144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/reference_markers.hmm GCA_022771445.1_ASM2277144v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:37,653] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:37,654] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg985c5e80-370f-4ff6-9fb7-b0eae55e7b3e/GCA_022771445.1_ASM2277144v1_genomic.fna.gz]
[2023-06-13 14:45:37,674] [INFO] Query marker FASTA was written to GCA_022771445.1_ASM2277144v1_genomic.fna/markers.fasta
[2023-06-13 14:45:37,674] [INFO] Task started: Blastn
[2023-06-13 14:45:37,674] [INFO] Running command: blastn -query GCA_022771445.1_ASM2277144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/reference_markers.fasta -out GCA_022771445.1_ASM2277144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:38,215] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:38,218] [INFO] Selected 22 target genomes.
[2023-06-13 14:45:38,219] [INFO] Target genome list was writen to GCA_022771445.1_ASM2277144v1_genomic.fna/target_genomes.txt
[2023-06-13 14:45:38,223] [INFO] Task started: fastANI
[2023-06-13 14:45:38,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg985c5e80-370f-4ff6-9fb7-b0eae55e7b3e/GCA_022771445.1_ASM2277144v1_genomic.fna.gz --refList GCA_022771445.1_ASM2277144v1_genomic.fna/target_genomes.txt --output GCA_022771445.1_ASM2277144v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:50,376] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:50,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:50,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:50,380] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 14:45:50,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:45:50,380] [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	97.3031	512	591	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 14:45:50,382] [INFO] DFAST Taxonomy check result was written to GCA_022771445.1_ASM2277144v1_genomic.fna/tc_result.tsv
[2023-06-13 14:45:50,382] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:50,382] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:50,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/checkm_data
[2023-06-13 14:45:50,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:50,405] [INFO] Task started: CheckM
[2023-06-13 14:45:50,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022771445.1_ASM2277144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022771445.1_ASM2277144v1_genomic.fna/checkm_input GCA_022771445.1_ASM2277144v1_genomic.fna/checkm_result
[2023-06-13 14:46:08,968] [INFO] Task succeeded: CheckM
[2023-06-13 14:46:08,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:46:08,983] [INFO] ===== Completeness check finished =====
[2023-06-13 14:46:08,984] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:46:08,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022771445.1_ASM2277144v1_genomic.fna/markers.fasta)
[2023-06-13 14:46:08,984] [INFO] Task started: Blastn
[2023-06-13 14:46:08,984] [INFO] Running command: blastn -query GCA_022771445.1_ASM2277144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab418f14-97ca-4328-96d4-6bd284fd812d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022771445.1_ASM2277144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:09,780] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:09,783] [INFO] Selected 17 target genomes.
[2023-06-13 14:46:09,783] [INFO] Target genome list was writen to GCA_022771445.1_ASM2277144v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:46:09,787] [INFO] Task started: fastANI
[2023-06-13 14:46:09,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg985c5e80-370f-4ff6-9fb7-b0eae55e7b3e/GCA_022771445.1_ASM2277144v1_genomic.fna.gz --refList GCA_022771445.1_ASM2277144v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022771445.1_ASM2277144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:46:17,170] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:17,177] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:46:17,177] [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	97.3031	512	591	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	89.4355	405	591	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	79.3607	108	591	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	78.4768	106	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCA_017469885.1	s__Bulleidia sp017469885	77.4063	58	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314345.1	s__Bulleidia sp900314345	77.1442	69	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902786245.1	s__Bulleidia sp902786245	77.0597	52	591	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	76.6447	51	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	96.20	96.20	0.80	0.80	2	-
GCA_900319505.1	s__Bulleidia sp900319505	76.6216	52	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.64	99.39	0.93	0.88	3	-
GCA_017512725.1	s__Bulleidia sp017512725	76.6	64	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:46:17,179] [INFO] GTDB search result was written to GCA_022771445.1_ASM2277144v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:46:17,179] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:46:17,182] [INFO] DFAST_QC result json was written to GCA_022771445.1_ASM2277144v1_genomic.fna/dqc_result.json
[2023-06-13 14:46:17,182] [INFO] DFAST_QC completed!
[2023-06-13 14:46:17,182] [INFO] Total running time: 0h0m45s