[2024-01-24 13:22:25,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,180] [INFO] DQC Reference Directory: /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference
[2024-01-24 13:22:26,620] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,621] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg298af0e7-b29b-45e0-ae75-707336b40132/GCF_002149015.1_ASM214901v1_genomic.fna.gz | prodigal -d GCF_002149015.1_ASM214901v1_genomic.fna/cds.fna -a GCF_002149015.1_ASM214901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:44,434] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:44,435] [INFO] Task started: HMMsearch
[2024-01-24 13:22:44,435] [INFO] Running command: hmmsearch --tblout GCF_002149015.1_ASM214901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/reference_markers.hmm GCF_002149015.1_ASM214901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:44,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:44,798] [INFO] Found 6/6 markers.
[2024-01-24 13:22:44,847] [INFO] Query marker FASTA was written to GCF_002149015.1_ASM214901v1_genomic.fna/markers.fasta
[2024-01-24 13:22:44,848] [INFO] Task started: Blastn
[2024-01-24 13:22:44,848] [INFO] Running command: blastn -query GCF_002149015.1_ASM214901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/reference_markers.fasta -out GCF_002149015.1_ASM214901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:46,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:46,118] [INFO] Selected 8 target genomes.
[2024-01-24 13:22:46,118] [INFO] Target genome list was writen to GCF_002149015.1_ASM214901v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:46,124] [INFO] Task started: fastANI
[2024-01-24 13:22:46,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg298af0e7-b29b-45e0-ae75-707336b40132/GCF_002149015.1_ASM214901v1_genomic.fna.gz --refList GCF_002149015.1_ASM214901v1_genomic.fna/target_genomes.txt --output GCF_002149015.1_ASM214901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:58,281] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:58,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:58,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:58,290] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:58,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:58,290] [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	100.0	1868	1879	95	conclusive
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	91.7797	1578	1879	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_000716975.1	2055	2055	suspected-type	True	91.7532	1578	1879	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	91.7244	1598	1879	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	91.6828	1551	1879	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	83.4268	1217	1879	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_014041935.1	2758710	2758710	type	True	83.4225	1216	1879	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	83.0101	1151	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:58,292] [INFO] DFAST Taxonomy check result was written to GCF_002149015.1_ASM214901v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:58,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:58,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:58,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/checkm_data
[2024-01-24 13:22:58,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:58,348] [INFO] Task started: CheckM
[2024-01-24 13:22:58,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002149015.1_ASM214901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002149015.1_ASM214901v1_genomic.fna/checkm_input GCF_002149015.1_ASM214901v1_genomic.fna/checkm_result
[2024-01-24 13:24:02,443] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:02,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:02,462] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:02,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:02,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002149015.1_ASM214901v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:02,463] [INFO] Task started: Blastn
[2024-01-24 13:24:02,463] [INFO] Running command: blastn -query GCF_002149015.1_ASM214901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9189bc5-ba8c-4ac0-8905-c0e44fc20149/dqc_reference/reference_markers_gtdb.fasta -out GCF_002149015.1_ASM214901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:04,165] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:04,169] [INFO] Selected 9 target genomes.
[2024-01-24 13:24:04,169] [INFO] Target genome list was writen to GCF_002149015.1_ASM214901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:04,199] [INFO] Task started: fastANI
[2024-01-24 13:24:04,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg298af0e7-b29b-45e0-ae75-707336b40132/GCF_002149015.1_ASM214901v1_genomic.fna.gz --refList GCF_002149015.1_ASM214901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002149015.1_ASM214901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:16,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:16,513] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:16,514] [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_002149015.1	s__Gordonia lacunae	100.0	1868	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001698225.1	s__Gordonia terrae	91.7353	1597	1879	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	90.1815	1518	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_011290605.1	s__Gordonia sp002009645	89.074	1497	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCA_014041935.1	s__Gordonia sp014041935	83.4261	1216	1879	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	83.0046	1152	1879	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	82.8692	1150	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000332995.1	s__Gordonia amicalis	82.866	1140	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_000327325.1	s__Gordonia rubripertincta	82.8278	1173	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:16,515] [INFO] GTDB search result was written to GCF_002149015.1_ASM214901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:16,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:16,519] [INFO] DFAST_QC result json was written to GCF_002149015.1_ASM214901v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:16,519] [INFO] DFAST_QC completed!
[2024-01-24 13:24:16,519] [INFO] Total running time: 0h1m51s