[2024-01-24 10:57:23,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:23,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:23,308] [INFO] DQC Reference Directory: /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference
[2024-01-24 10:57:24,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:24,554] [INFO] Task started: Prodigal
[2024-01-24 10:57:24,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg31e84445-6e22-4ee7-915b-7ad866d00d10/GCF_002156925.1_ASM215692v1_genomic.fna.gz | prodigal -d GCF_002156925.1_ASM215692v1_genomic.fna/cds.fna -a GCF_002156925.1_ASM215692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:32,625] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:32,626] [INFO] Task started: HMMsearch
[2024-01-24 10:57:32,626] [INFO] Running command: hmmsearch --tblout GCF_002156925.1_ASM215692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/reference_markers.hmm GCF_002156925.1_ASM215692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,959] [INFO] Found 6/6 markers.
[2024-01-24 10:57:33,003] [INFO] Query marker FASTA was written to GCF_002156925.1_ASM215692v1_genomic.fna/markers.fasta
[2024-01-24 10:57:33,004] [INFO] Task started: Blastn
[2024-01-24 10:57:33,004] [INFO] Running command: blastn -query GCF_002156925.1_ASM215692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/reference_markers.fasta -out GCF_002156925.1_ASM215692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,606] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,609] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:33,610] [INFO] Target genome list was writen to GCF_002156925.1_ASM215692v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,637] [INFO] Task started: fastANI
[2024-01-24 10:57:33,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg31e84445-6e22-4ee7-915b-7ad866d00d10/GCF_002156925.1_ASM215692v1_genomic.fna.gz --refList GCF_002156925.1_ASM215692v1_genomic.fna/target_genomes.txt --output GCF_002156925.1_ASM215692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:42,912] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:42,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:42,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:42,920] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:42,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:42,921] [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
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	100.0	1557	1562	95	conclusive
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	99.9757	1543	1562	95	conclusive
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	84.0861	1007	1562	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	81.2918	750	1562	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	81.2349	763	1562	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.0491	124	1562	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	76.7607	76	1562	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	76.5491	96	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:42,922] [INFO] DFAST Taxonomy check result was written to GCF_002156925.1_ASM215692v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:42,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:42,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:42,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/checkm_data
[2024-01-24 10:57:42,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:42,970] [INFO] Task started: CheckM
[2024-01-24 10:57:42,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156925.1_ASM215692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156925.1_ASM215692v1_genomic.fna/checkm_input GCF_002156925.1_ASM215692v1_genomic.fna/checkm_result
[2024-01-24 10:58:12,670] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:12,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,689] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:12,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:12,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156925.1_ASM215692v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:12,690] [INFO] Task started: Blastn
[2024-01-24 10:58:12,690] [INFO] Running command: blastn -query GCF_002156925.1_ASM215692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge642d041-3451-413b-8c8c-1f91689dbb8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156925.1_ASM215692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:13,535] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:13,539] [INFO] Selected 7 target genomes.
[2024-01-24 10:58:13,539] [INFO] Target genome list was writen to GCF_002156925.1_ASM215692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:13,544] [INFO] Task started: fastANI
[2024-01-24 10:58:13,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg31e84445-6e22-4ee7-915b-7ad866d00d10/GCF_002156925.1_ASM215692v1_genomic.fna.gz --refList GCF_002156925.1_ASM215692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156925.1_ASM215692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:22,118] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:22,125] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:22,125] [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_002128425.1	s__Gottfriedia acidiceler	99.9757	1543	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.12	96.26	0.94	0.89	3	conclusive
GCF_004138285.1	s__Gottfriedia acidiceleris_A	92.8776	1321	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564465.1	s__Gottfriedia sp002564465	92.0005	1306	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.47	95.21	0.86	0.86	4	-
GCF_002559405.1	s__Gottfriedia sp002559405	91.9068	1094	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420605.1	s__Gottfriedia sp001420605	91.8133	1319	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712755.1	s__Gottfriedia luciferensis_B	91.668	1319	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
GCF_002574545.1	s__Gottfriedia sp002574545	90.3403	1208	1562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:22,127] [INFO] GTDB search result was written to GCF_002156925.1_ASM215692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:22,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:22,130] [INFO] DFAST_QC result json was written to GCF_002156925.1_ASM215692v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:22,130] [INFO] DFAST_QC completed!
[2024-01-24 10:58:22,130] [INFO] Total running time: 0h0m59s