[2024-01-24 14:15:34,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference
[2024-01-24 14:15:35,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,807] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,807] [INFO] Running command: gunzip -c /var/lib/cwl/stga94fffb1-f130-4a44-ba0a-ebdefb136576/GCF_000332995.1_ASM33299v1_genomic.fna.gz | prodigal -d GCF_000332995.1_ASM33299v1_genomic.fna/cds.fna -a GCF_000332995.1_ASM33299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:53,611] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:53,611] [INFO] Task started: HMMsearch
[2024-01-24 14:15:53,611] [INFO] Running command: hmmsearch --tblout GCF_000332995.1_ASM33299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/reference_markers.hmm GCF_000332995.1_ASM33299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:53,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:53,967] [INFO] Found 6/6 markers.
[2024-01-24 14:15:54,022] [INFO] Query marker FASTA was written to GCF_000332995.1_ASM33299v1_genomic.fna/markers.fasta
[2024-01-24 14:15:54,022] [INFO] Task started: Blastn
[2024-01-24 14:15:54,022] [INFO] Running command: blastn -query GCF_000332995.1_ASM33299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/reference_markers.fasta -out GCF_000332995.1_ASM33299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:55,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:55,260] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:55,260] [INFO] Target genome list was writen to GCF_000332995.1_ASM33299v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:55,264] [INFO] Task started: fastANI
[2024-01-24 14:15:55,264] [INFO] Running command: fastANI --query /var/lib/cwl/stga94fffb1-f130-4a44-ba0a-ebdefb136576/GCF_000332995.1_ASM33299v1_genomic.fna.gz --refList GCF_000332995.1_ASM33299v1_genomic.fna/target_genomes.txt --output GCF_000332995.1_ASM33299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:04,769] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:04,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:04,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:04,782] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:04,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:04,782] [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 amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	100.0	1586	1589	95	conclusive
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	99.9944	1589	1589	95	conclusive
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	89.6602	1403	1589	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	89.0225	1319	1589	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	88.6925	1319	1589	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	88.5743	1326	1589	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	88.3683	1327	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:04,784] [INFO] DFAST Taxonomy check result was written to GCF_000332995.1_ASM33299v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:04,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:04,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:04,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/checkm_data
[2024-01-24 14:16:04,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:04,839] [INFO] Task started: CheckM
[2024-01-24 14:16:04,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000332995.1_ASM33299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000332995.1_ASM33299v1_genomic.fna/checkm_input GCF_000332995.1_ASM33299v1_genomic.fna/checkm_result
[2024-01-24 14:17:06,656] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:06,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:06,685] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:06,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:06,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000332995.1_ASM33299v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:06,687] [INFO] Task started: Blastn
[2024-01-24 14:17:06,687] [INFO] Running command: blastn -query GCF_000332995.1_ASM33299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8ea3943-3007-4206-a211-075d207469bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000332995.1_ASM33299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:08,558] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:08,562] [INFO] Selected 6 target genomes.
[2024-01-24 14:17:08,562] [INFO] Target genome list was writen to GCF_000332995.1_ASM33299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:08,566] [INFO] Task started: fastANI
[2024-01-24 14:17:08,567] [INFO] Running command: fastANI --query /var/lib/cwl/stga94fffb1-f130-4a44-ba0a-ebdefb136576/GCF_000332995.1_ASM33299v1_genomic.fna.gz --refList GCF_000332995.1_ASM33299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000332995.1_ASM33299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:16,877] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:16,889] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:16,890] [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_000332995.1	s__Gordonia amicalis	100.0	1586	1589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	conclusive
GCF_900105725.1	s__Gordonia westfalica	89.6512	1404	1589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225505.1	s__Gordonia alkanivorans	89.0336	1318	1589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000327325.1	s__Gordonia rubripertincta	88.7015	1318	1589	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	88.3683	1327	1589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000344155.1	s__Gordonia paraffinivorans	84.0066	1140	1589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:16,892] [INFO] GTDB search result was written to GCF_000332995.1_ASM33299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:16,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:16,895] [INFO] DFAST_QC result json was written to GCF_000332995.1_ASM33299v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:16,895] [INFO] DFAST_QC completed!
[2024-01-24 14:17:16,895] [INFO] Total running time: 0h1m43s