[2024-01-24 15:26:39,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference
[2024-01-24 15:26:41,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,072] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,072] [INFO] Running command: gunzip -c /var/lib/cwl/stga0dc36b8-96dd-4351-800d-fc9f0fe14875/GCF_012396225.1_ASM1239622v1_genomic.fna.gz | prodigal -d GCF_012396225.1_ASM1239622v1_genomic.fna/cds.fna -a GCF_012396225.1_ASM1239622v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:59,450] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:59,451] [INFO] Task started: HMMsearch
[2024-01-24 15:26:59,451] [INFO] Running command: hmmsearch --tblout GCF_012396225.1_ASM1239622v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/reference_markers.hmm GCF_012396225.1_ASM1239622v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:59,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:59,783] [INFO] Found 6/6 markers.
[2024-01-24 15:26:59,837] [INFO] Query marker FASTA was written to GCF_012396225.1_ASM1239622v1_genomic.fna/markers.fasta
[2024-01-24 15:26:59,838] [INFO] Task started: Blastn
[2024-01-24 15:26:59,838] [INFO] Running command: blastn -query GCF_012396225.1_ASM1239622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/reference_markers.fasta -out GCF_012396225.1_ASM1239622v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:01,273] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:01,279] [INFO] Selected 7 target genomes.
[2024-01-24 15:27:01,280] [INFO] Target genome list was writen to GCF_012396225.1_ASM1239622v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:01,285] [INFO] Task started: fastANI
[2024-01-24 15:27:01,285] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dc36b8-96dd-4351-800d-fc9f0fe14875/GCF_012396225.1_ASM1239622v1_genomic.fna.gz --refList GCF_012396225.1_ASM1239622v1_genomic.fna/target_genomes.txt --output GCF_012396225.1_ASM1239622v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:11,773] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:11,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:11,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:11,781] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:11,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:11,781] [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 rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	100.0	1772	1876	95	conclusive
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	99.9701	1638	1876	95	conclusive
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	92.8376	1386	1876	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	92.5974	1398	1876	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	89.3718	1426	1876	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	88.667	1336	1876	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	88.6612	1346	1876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:11,783] [INFO] DFAST Taxonomy check result was written to GCF_012396225.1_ASM1239622v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:11,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:11,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:11,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/checkm_data
[2024-01-24 15:27:11,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:11,841] [INFO] Task started: CheckM
[2024-01-24 15:27:11,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396225.1_ASM1239622v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396225.1_ASM1239622v1_genomic.fna/checkm_input GCF_012396225.1_ASM1239622v1_genomic.fna/checkm_result
[2024-01-24 15:28:11,029] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:11,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 25.00%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:11,055] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:11,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:11,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396225.1_ASM1239622v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:11,056] [INFO] Task started: Blastn
[2024-01-24 15:28:11,057] [INFO] Running command: blastn -query GCF_012396225.1_ASM1239622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb200a8-a4fe-4299-9397-9fd85089ddcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396225.1_ASM1239622v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:13,175] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:13,178] [INFO] Selected 6 target genomes.
[2024-01-24 15:28:13,178] [INFO] Target genome list was writen to GCF_012396225.1_ASM1239622v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:13,184] [INFO] Task started: fastANI
[2024-01-24 15:28:13,184] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dc36b8-96dd-4351-800d-fc9f0fe14875/GCF_012396225.1_ASM1239622v1_genomic.fna.gz --refList GCF_012396225.1_ASM1239622v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396225.1_ASM1239622v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:21,875] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:21,882] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:21,882] [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_000327325.1	s__Gordonia rubripertincta	99.9701	1638	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	conclusive
GCF_000225505.1	s__Gordonia alkanivorans	92.8376	1386	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000298235.1	s__Gordonia namibiensis	92.5904	1399	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_900105725.1	s__Gordonia westfalica	89.3521	1430	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332995.1	s__Gordonia amicalis	88.652	1338	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_011290605.1	s__Gordonia sp002009645	83.1547	1159	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:21,883] [INFO] GTDB search result was written to GCF_012396225.1_ASM1239622v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:21,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:21,887] [INFO] DFAST_QC result json was written to GCF_012396225.1_ASM1239622v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:21,887] [INFO] DFAST_QC completed!
[2024-01-24 15:28:21,887] [INFO] Total running time: 0h1m42s