[2024-01-24 10:48:09,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,956] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f0e12b7-e5d6-4e97-be6d-e636fcda77d0/GCF_023078355.1_ASM2307835v1_genomic.fna.gz | prodigal -d GCF_023078355.1_ASM2307835v1_genomic.fna/cds.fna -a GCF_023078355.1_ASM2307835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:48,695] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:48,696] [INFO] Task started: HMMsearch
[2024-01-24 10:48:48,696] [INFO] Running command: hmmsearch --tblout GCF_023078355.1_ASM2307835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/reference_markers.hmm GCF_023078355.1_ASM2307835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:49,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:49,015] [INFO] Found 6/6 markers.
[2024-01-24 10:48:49,058] [INFO] Query marker FASTA was written to GCF_023078355.1_ASM2307835v1_genomic.fna/markers.fasta
[2024-01-24 10:48:49,058] [INFO] Task started: Blastn
[2024-01-24 10:48:49,058] [INFO] Running command: blastn -query GCF_023078355.1_ASM2307835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/reference_markers.fasta -out GCF_023078355.1_ASM2307835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:50,285] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:50,289] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:50,289] [INFO] Target genome list was writen to GCF_023078355.1_ASM2307835v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:50,310] [INFO] Task started: fastANI
[2024-01-24 10:48:50,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0e12b7-e5d6-4e97-be6d-e636fcda77d0/GCF_023078355.1_ASM2307835v1_genomic.fna.gz --refList GCF_023078355.1_ASM2307835v1_genomic.fna/target_genomes.txt --output GCF_023078355.1_ASM2307835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:08,509] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:08,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:08,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:08,529] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:49:08,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:49:08,530] [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
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	89.1047	1471	1802	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	88.8343	1493	1802	95	below_threshold
Gordonia terrae	strain=NCTC10669	GCA_901542405.1	2055	2055	suspected-type	True	88.8312	1491	1802	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	88.8167	1492	1802	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_000716975.1	2055	2055	suspected-type	True	88.7793	1460	1802	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	88.6524	1460	1802	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	83.4643	1166	1802	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	83.3673	1247	1802	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	83.0919	1158	1802	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	83.0842	1128	1802	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	83.0196	1174	1802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:08,540] [INFO] DFAST Taxonomy check result was written to GCF_023078355.1_ASM2307835v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:08,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:08,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:08,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/checkm_data
[2024-01-24 10:49:08,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:08,604] [INFO] Task started: CheckM
[2024-01-24 10:49:08,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078355.1_ASM2307835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078355.1_ASM2307835v1_genomic.fna/checkm_input GCF_023078355.1_ASM2307835v1_genomic.fna/checkm_result
[2024-01-24 10:50:40,833] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:40,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:40,856] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:40,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:40,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078355.1_ASM2307835v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:40,857] [INFO] Task started: Blastn
[2024-01-24 10:50:40,857] [INFO] Running command: blastn -query GCF_023078355.1_ASM2307835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c91d9a2-8158-41da-80dd-f0734ada7ab0/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078355.1_ASM2307835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:42,667] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:42,671] [INFO] Selected 9 target genomes.
[2024-01-24 10:50:42,672] [INFO] Target genome list was writen to GCF_023078355.1_ASM2307835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:42,678] [INFO] Task started: fastANI
[2024-01-24 10:50:42,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0e12b7-e5d6-4e97-be6d-e636fcda77d0/GCF_023078355.1_ASM2307835v1_genomic.fna.gz --refList GCF_023078355.1_ASM2307835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078355.1_ASM2307835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:57,193] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:57,209] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:57,211] [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_011290605.1	s__Gordonia sp002009645	97.7075	1607	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	conclusive
GCF_002149015.1	s__Gordonia lacunae	89.0861	1473	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698225.1	s__Gordonia terrae	88.8228	1493	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCF_000143885.2	s__Gordonia sp000143885	88.5926	1469	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCA_014041935.1	s__Gordonia sp014041935	83.5885	1176	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	-
GCF_000225505.1	s__Gordonia alkanivorans	83.4861	1163	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_900105725.1	s__Gordonia westfalica	83.3815	1247	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	83.1063	1156	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000298235.1	s__Gordonia namibiensis	83.0806	1129	1802	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:57,213] [INFO] GTDB search result was written to GCF_023078355.1_ASM2307835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:57,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:57,217] [INFO] DFAST_QC result json was written to GCF_023078355.1_ASM2307835v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:57,218] [INFO] DFAST_QC completed!
[2024-01-24 10:50:57,218] [INFO] Total running time: 0h2m48s