[2024-01-24 13:46:25,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,561] [INFO] DQC Reference Directory: /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference
[2024-01-24 13:46:27,109] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,110] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,111] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1dcb578-604b-479c-b3a7-b0c90b18c374/GCF_013403245.1_ASM1340324v1_genomic.fna.gz | prodigal -d GCF_013403245.1_ASM1340324v1_genomic.fna/cds.fna -a GCF_013403245.1_ASM1340324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:35,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:35,331] [INFO] Task started: HMMsearch
[2024-01-24 13:46:35,331] [INFO] Running command: hmmsearch --tblout GCF_013403245.1_ASM1340324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/reference_markers.hmm GCF_013403245.1_ASM1340324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:35,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:35,633] [INFO] Found 6/6 markers.
[2024-01-24 13:46:35,672] [INFO] Query marker FASTA was written to GCF_013403245.1_ASM1340324v1_genomic.fna/markers.fasta
[2024-01-24 13:46:35,672] [INFO] Task started: Blastn
[2024-01-24 13:46:35,672] [INFO] Running command: blastn -query GCF_013403245.1_ASM1340324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/reference_markers.fasta -out GCF_013403245.1_ASM1340324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:36,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:36,360] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:36,360] [INFO] Target genome list was writen to GCF_013403245.1_ASM1340324v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:36,372] [INFO] Task started: fastANI
[2024-01-24 13:46:36,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1dcb578-604b-479c-b3a7-b0c90b18c374/GCF_013403245.1_ASM1340324v1_genomic.fna.gz --refList GCF_013403245.1_ASM1340324v1_genomic.fna/target_genomes.txt --output GCF_013403245.1_ASM1340324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:43,002] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:43,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:43,002] [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
Sedimentibacter hydroxybenzoicus	strain=DSM 7310	GCA_013403245.1	29345	29345	type	True	100.0	1237	1239	95	conclusive
Sedimentibacter saalensis	strain=DSM 13558	GCA_007830175.1	130788	130788	type	True	77.6566	239	1239	95	below_threshold
Sedimentibacter acidaminivorans	strain=DSM 24004	GCA_017873955.1	913099	913099	type	True	76.7648	158	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:43,004] [INFO] DFAST Taxonomy check result was written to GCF_013403245.1_ASM1340324v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:43,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:43,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:43,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/checkm_data
[2024-01-24 13:46:43,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:43,054] [INFO] Task started: CheckM
[2024-01-24 13:46:43,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403245.1_ASM1340324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403245.1_ASM1340324v1_genomic.fna/checkm_input GCF_013403245.1_ASM1340324v1_genomic.fna/checkm_result
[2024-01-24 13:47:12,561] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:12,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:12,585] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:12,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:12,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403245.1_ASM1340324v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:12,586] [INFO] Task started: Blastn
[2024-01-24 13:47:12,587] [INFO] Running command: blastn -query GCF_013403245.1_ASM1340324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24acf86-ccf8-4420-a5a5-ec3d18c120bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403245.1_ASM1340324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:13,472] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:13,476] [INFO] Selected 15 target genomes.
[2024-01-24 13:47:13,476] [INFO] Target genome list was writen to GCF_013403245.1_ASM1340324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:13,492] [INFO] Task started: fastANI
[2024-01-24 13:47:13,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1dcb578-604b-479c-b3a7-b0c90b18c374/GCF_013403245.1_ASM1340324v1_genomic.fna.gz --refList GCF_013403245.1_ASM1340324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403245.1_ASM1340324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:23,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:23,489] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:23,489] [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_013403245.1	s__Sedimentibacter hydroxybenzoicus	100.0	1237	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002331025.1	s__Sedimentibacter sp002331025	94.4545	940	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	97.64	97.63	0.83	0.82	3	-
GCA_002381185.1	s__Sedimentibacter sp002381185	78.7888	404	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	99.05	98.81	0.89	0.88	6	-
GCA_002340985.1	s__Sedimentibacter sp002340985	78.2253	270	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	98.14	96.44	0.86	0.81	4	-
GCA_018436705.1	s__Sedimentibacter sp018436705	78.1893	254	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497505.1	s__Sedimentibacter sp003497505	77.9009	190	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002409285.1	s__Sedimentibacter sp002409285	77.8997	222	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003457065.1	s__Sedimentibacter sp003457065	77.8158	211	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	98.22	98.22	0.78	0.78	2	-
GCF_007830175.1	s__Sedimentibacter saalensis	77.6106	242	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422545.1	s__Sedimentibacter sp002422545	77.4841	220	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483345.1	s__Sedimentibacter sp003483345	77.2184	127	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	97.32	97.20	0.62	0.58	3	-
GCA_012843025.1	s__Sedimentibacter sp002385835	76.8755	118	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	99.84	99.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,491] [INFO] GTDB search result was written to GCF_013403245.1_ASM1340324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:23,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:23,494] [INFO] DFAST_QC result json was written to GCF_013403245.1_ASM1340324v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:23,494] [INFO] DFAST_QC completed!
[2024-01-24 13:47:23,494] [INFO] Total running time: 0h0m58s