[2024-01-24 14:05:34,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference
[2024-01-24 14:05:35,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,306] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f85f035-a8aa-4fbe-a674-9a8dcc79cf23/GCF_016907365.1_ASM1690736v1_genomic.fna.gz | prodigal -d GCF_016907365.1_ASM1690736v1_genomic.fna/cds.fna -a GCF_016907365.1_ASM1690736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:47,328] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:47,328] [INFO] Task started: HMMsearch
[2024-01-24 14:05:47,329] [INFO] Running command: hmmsearch --tblout GCF_016907365.1_ASM1690736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/reference_markers.hmm GCF_016907365.1_ASM1690736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:47,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:47,672] [INFO] Found 6/6 markers.
[2024-01-24 14:05:47,712] [INFO] Query marker FASTA was written to GCF_016907365.1_ASM1690736v1_genomic.fna/markers.fasta
[2024-01-24 14:05:47,713] [INFO] Task started: Blastn
[2024-01-24 14:05:47,713] [INFO] Running command: blastn -query GCF_016907365.1_ASM1690736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/reference_markers.fasta -out GCF_016907365.1_ASM1690736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,008] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,011] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:49,011] [INFO] Target genome list was writen to GCF_016907365.1_ASM1690736v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,015] [INFO] Task started: fastANI
[2024-01-24 14:05:49,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f85f035-a8aa-4fbe-a674-9a8dcc79cf23/GCF_016907365.1_ASM1690736v1_genomic.fna.gz --refList GCF_016907365.1_ASM1690736v1_genomic.fna/target_genomes.txt --output GCF_016907365.1_ASM1690736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:59,376] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:59,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:59,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:59,386] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:59,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:59,386] [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
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	93.8822	1250	1442	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	93.3794	1309	1442	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	92.9542	1171	1442	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	92.9123	1165	1442	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	90.2989	1154	1442	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	89.7642	1183	1442	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	89.4429	1164	1442	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.5927	614	1442	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.9343	619	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:59,388] [INFO] DFAST Taxonomy check result was written to GCF_016907365.1_ASM1690736v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:59,389] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:59,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:59,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/checkm_data
[2024-01-24 14:05:59,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:59,435] [INFO] Task started: CheckM
[2024-01-24 14:05:59,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907365.1_ASM1690736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907365.1_ASM1690736v1_genomic.fna/checkm_input GCF_016907365.1_ASM1690736v1_genomic.fna/checkm_result
[2024-01-24 14:07:15,626] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:15,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:15,653] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:15,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:15,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907365.1_ASM1690736v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:15,654] [INFO] Task started: Blastn
[2024-01-24 14:07:15,654] [INFO] Running command: blastn -query GCF_016907365.1_ASM1690736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf16a172a-9ee6-46ce-b461-1c8a64631092/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907365.1_ASM1690736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:17,683] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:17,686] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:17,687] [INFO] Target genome list was writen to GCF_016907365.1_ASM1690736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:17,693] [INFO] Task started: fastANI
[2024-01-24 14:07:17,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f85f035-a8aa-4fbe-a674-9a8dcc79cf23/GCF_016907365.1_ASM1690736v1_genomic.fna.gz --refList GCF_016907365.1_ASM1690736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907365.1_ASM1690736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:26,200] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:26,214] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:26,214] [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_016907365.1	s__Oerskovia paurometabola	100.0	1440	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	conclusive
GCF_005937995.2	s__Oerskovia sp005937995	93.8113	1286	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_016907235.1	s__Oerskovia jenensis	93.3794	1309	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718325.1	s__Oerskovia turbata	92.9036	1165	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCF_015142735.1	s__Oerskovia sp015142735	90.3126	1153	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692445.1	s__Oerskovia enterophila	89.7642	1183	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_014836755.1	s__Oerskovia sp014836755	89.4429	1164	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,216] [INFO] GTDB search result was written to GCF_016907365.1_ASM1690736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:26,217] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:26,221] [INFO] DFAST_QC result json was written to GCF_016907365.1_ASM1690736v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:26,221] [INFO] DFAST_QC completed!
[2024-01-24 14:07:26,222] [INFO] Total running time: 0h1m52s