[2024-01-24 14:30:59,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference
[2024-01-24 14:31:00,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,855] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,855] [INFO] Running command: gunzip -c /var/lib/cwl/stga6cea4d6-9a15-485d-aa74-527d31fc165a/GCF_003148565.1_ASM314856v1_genomic.fna.gz | prodigal -d GCF_003148565.1_ASM314856v1_genomic.fna/cds.fna -a GCF_003148565.1_ASM314856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:17,770] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:17,771] [INFO] Task started: HMMsearch
[2024-01-24 14:31:17,771] [INFO] Running command: hmmsearch --tblout GCF_003148565.1_ASM314856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/reference_markers.hmm GCF_003148565.1_ASM314856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:18,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:18,097] [INFO] Found 6/6 markers.
[2024-01-24 14:31:18,141] [INFO] Query marker FASTA was written to GCF_003148565.1_ASM314856v1_genomic.fna/markers.fasta
[2024-01-24 14:31:18,141] [INFO] Task started: Blastn
[2024-01-24 14:31:18,141] [INFO] Running command: blastn -query GCF_003148565.1_ASM314856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/reference_markers.fasta -out GCF_003148565.1_ASM314856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,807] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,811] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:18,811] [INFO] Target genome list was writen to GCF_003148565.1_ASM314856v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,818] [INFO] Task started: fastANI
[2024-01-24 14:31:18,818] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cea4d6-9a15-485d-aa74-527d31fc165a/GCF_003148565.1_ASM314856v1_genomic.fna.gz --refList GCF_003148565.1_ASM314856v1_genomic.fna/target_genomes.txt --output GCF_003148565.1_ASM314856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:35,898] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:35,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:35,914] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:35,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:35,914] [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
Tumebacillus permanentifrigoris	strain=DSM 18773	GCA_003148565.1	378543	378543	type	True	100.0	1530	1534	95	conclusive
Tumebacillus amylolyticus	strain=ITR2	GCA_016722965.1	2801339	2801339	type	True	81.4076	908	1534	95	below_threshold
Tumebacillus flagellatus	strain=GST4	GCA_000714935.1	1157490	1157490	type	True	80.8335	866	1534	95	below_threshold
Tumebacillus avium	strain=AR23208	GCA_002162355.1	1903704	1903704	type	True	78.0792	396	1534	95	below_threshold
Tumebacillus algifaecis	strain=THMBR28	GCA_002243515.1	1214604	1214604	type	True	77.8194	276	1534	95	below_threshold
Effusibacillus pohliae	strain=DSM 22757	GCA_000376225.1	232270	232270	type	True	75.7265	54	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,916] [INFO] DFAST Taxonomy check result was written to GCF_003148565.1_ASM314856v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:35,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:35,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:35,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/checkm_data
[2024-01-24 14:31:35,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:35,978] [INFO] Task started: CheckM
[2024-01-24 14:31:35,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148565.1_ASM314856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148565.1_ASM314856v1_genomic.fna/checkm_input GCF_003148565.1_ASM314856v1_genomic.fna/checkm_result
[2024-01-24 14:32:25,331] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:25,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:25,356] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:25,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:25,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148565.1_ASM314856v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:25,357] [INFO] Task started: Blastn
[2024-01-24 14:32:25,357] [INFO] Running command: blastn -query GCF_003148565.1_ASM314856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg090ca144-a86a-4e01-b275-e93d00c8b3a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148565.1_ASM314856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:26,242] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:26,246] [INFO] Selected 26 target genomes.
[2024-01-24 14:32:26,247] [INFO] Target genome list was writen to GCF_003148565.1_ASM314856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:26,324] [INFO] Task started: fastANI
[2024-01-24 14:32:26,324] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cea4d6-9a15-485d-aa74-527d31fc165a/GCF_003148565.1_ASM314856v1_genomic.fna.gz --refList GCF_003148565.1_ASM314856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148565.1_ASM314856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:47,354] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:47,363] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:47,363] [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_003148565.1	s__Tumebacillus permanentifrigoris	100.0	1530	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016722965.1	s__Tumebacillus sp016722965	81.4052	907	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714935.1	s__Tumebacillus flagellatus	80.8337	866	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162355.1	s__Tumebacillus_A avium	78.0783	393	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243515.1	s__Tumebacillus_A algifaecis	77.8215	275	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454065.1	s__Brevibacillus thermoruber	76.1897	59	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_000376225.1	s__Effusibacillus pohliae	75.7055	55	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Effusibacillaceae;g__Effusibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:47,365] [INFO] GTDB search result was written to GCF_003148565.1_ASM314856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:47,366] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:47,369] [INFO] DFAST_QC result json was written to GCF_003148565.1_ASM314856v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:47,369] [INFO] DFAST_QC completed!
[2024-01-24 14:32:47,369] [INFO] Total running time: 0h1m48s