[2023-06-28 15:27:03,010] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:27:03,012] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:27:03,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference
[2023-06-28 15:27:04,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:27:04,253] [INFO] Task started: Prodigal
[2023-06-28 15:27:04,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad10c23-40d6-4af2-b2dd-1c0cbdda9549/GCA_944363995.1_BRZ_FP_bin56_genomic.fna.gz | prodigal -d GCA_944363995.1_BRZ_FP_bin56_genomic.fna/cds.fna -a GCA_944363995.1_BRZ_FP_bin56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:27:06,199] [INFO] Task succeeded: Prodigal
[2023-06-28 15:27:06,200] [INFO] Task started: HMMsearch
[2023-06-28 15:27:06,200] [INFO] Running command: hmmsearch --tblout GCA_944363995.1_BRZ_FP_bin56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/reference_markers.hmm GCA_944363995.1_BRZ_FP_bin56_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:27:06,437] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:27:06,439] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbad10c23-40d6-4af2-b2dd-1c0cbdda9549/GCA_944363995.1_BRZ_FP_bin56_genomic.fna.gz]
[2023-06-28 15:27:06,482] [INFO] Query marker FASTA was written to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/markers.fasta
[2023-06-28 15:27:06,483] [INFO] Task started: Blastn
[2023-06-28 15:27:06,483] [INFO] Running command: blastn -query GCA_944363995.1_BRZ_FP_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/reference_markers.fasta -out GCA_944363995.1_BRZ_FP_bin56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:27:07,071] [INFO] Task succeeded: Blastn
[2023-06-28 15:27:07,076] [INFO] Selected 23 target genomes.
[2023-06-28 15:27:07,076] [INFO] Target genome list was writen to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/target_genomes.txt
[2023-06-28 15:27:07,081] [INFO] Task started: fastANI
[2023-06-28 15:27:07,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad10c23-40d6-4af2-b2dd-1c0cbdda9549/GCA_944363995.1_BRZ_FP_bin56_genomic.fna.gz --refList GCA_944363995.1_BRZ_FP_bin56_genomic.fna/target_genomes.txt --output GCA_944363995.1_BRZ_FP_bin56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:27:17,983] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:17,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:27:17,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:27:17,990] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:27:17,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:27:17,990] [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
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	74.6345	54	376	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:27:17,994] [INFO] DFAST Taxonomy check result was written to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/tc_result.tsv
[2023-06-28 15:27:17,995] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:27:17,996] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:27:17,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/checkm_data
[2023-06-28 15:27:17,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:27:18,018] [INFO] Task started: CheckM
[2023-06-28 15:27:18,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944363995.1_BRZ_FP_bin56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944363995.1_BRZ_FP_bin56_genomic.fna/checkm_input GCA_944363995.1_BRZ_FP_bin56_genomic.fna/checkm_result
[2023-06-28 15:27:32,397] [INFO] Task succeeded: CheckM
[2023-06-28 15:27:32,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:27:32,420] [INFO] ===== Completeness check finished =====
[2023-06-28 15:27:32,421] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:27:32,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944363995.1_BRZ_FP_bin56_genomic.fna/markers.fasta)
[2023-06-28 15:27:32,422] [INFO] Task started: Blastn
[2023-06-28 15:27:32,422] [INFO] Running command: blastn -query GCA_944363995.1_BRZ_FP_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb5f6f40-d0b0-4532-9c13-96e35898c65f/dqc_reference/reference_markers_gtdb.fasta -out GCA_944363995.1_BRZ_FP_bin56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:27:33,288] [INFO] Task succeeded: Blastn
[2023-06-28 15:27:33,295] [INFO] Selected 20 target genomes.
[2023-06-28 15:27:33,295] [INFO] Target genome list was writen to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:27:33,343] [INFO] Task started: fastANI
[2023-06-28 15:27:33,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad10c23-40d6-4af2-b2dd-1c0cbdda9549/GCA_944363995.1_BRZ_FP_bin56_genomic.fna.gz --refList GCA_944363995.1_BRZ_FP_bin56_genomic.fna/target_genomes_gtdb.txt --output GCA_944363995.1_BRZ_FP_bin56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:27:38,634] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:38,658] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:27:38,659] [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_018716405.1	s__Faecisoma merdavium	82.5371	185	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_017887425.1	s__Faecisoma sp017887425	80.9827	220	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753645.1	s__Faecisoma sp900753645	78.8028	92	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432255.1	s__Faecisoma sp000432255	77.5719	105	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_016288305.1	s__Faecisoma sp016288305	77.4328	95	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059285.1	s__SIG208 sp015059285	76.9336	89	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	76.7262	73	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_015059545.1	s__UBA5026 sp015059545	76.6976	76	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536505.1	s__UMGS1613 sp017536505	76.5091	61	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	76.5049	59	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.4756	79	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773675.1	s__RUG11890 sp902773675	75.9855	80	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11890	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795975.1	s__UBA5578 sp902795975	75.5939	62	376	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:27:38,662] [INFO] GTDB search result was written to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/result_gtdb.tsv
[2023-06-28 15:27:38,663] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:27:38,666] [INFO] DFAST_QC result json was written to GCA_944363995.1_BRZ_FP_bin56_genomic.fna/dqc_result.json
[2023-06-28 15:27:38,666] [INFO] DFAST_QC completed!
[2023-06-28 15:27:38,666] [INFO] Total running time: 0h0m36s