[2024-01-24 14:31:01,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:01,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:01,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference
[2024-01-24 14:31:04,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:04,073] [INFO] Task started: Prodigal
[2024-01-24 14:31:04,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac8b793-841c-41be-9d39-dd6fe73ac037/GCF_014836745.1_ASM1483674v1_genomic.fna.gz | prodigal -d GCF_014836745.1_ASM1483674v1_genomic.fna/cds.fna -a GCF_014836745.1_ASM1483674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:16,046] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:16,047] [INFO] Task started: HMMsearch
[2024-01-24 14:31:16,047] [INFO] Running command: hmmsearch --tblout GCF_014836745.1_ASM1483674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/reference_markers.hmm GCF_014836745.1_ASM1483674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:16,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:16,386] [INFO] Found 6/6 markers.
[2024-01-24 14:31:16,432] [INFO] Query marker FASTA was written to GCF_014836745.1_ASM1483674v1_genomic.fna/markers.fasta
[2024-01-24 14:31:16,432] [INFO] Task started: Blastn
[2024-01-24 14:31:16,432] [INFO] Running command: blastn -query GCF_014836745.1_ASM1483674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/reference_markers.fasta -out GCF_014836745.1_ASM1483674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:17,856] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:17,859] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:17,859] [INFO] Target genome list was writen to GCF_014836745.1_ASM1483674v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:17,863] [INFO] Task started: fastANI
[2024-01-24 14:31:17,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac8b793-841c-41be-9d39-dd6fe73ac037/GCF_014836745.1_ASM1483674v1_genomic.fna.gz --refList GCF_014836745.1_ASM1483674v1_genomic.fna/target_genomes.txt --output GCF_014836745.1_ASM1483674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:29,511] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:29,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:29,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:29,528] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:29,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:29,528] [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	93.9088	1246	1401	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	93.498	1272	1401	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	92.9047	1174	1401	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	92.8935	1170	1401	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	90.4225	1139	1401	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	89.7213	1171	1401	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	89.4151	1169	1401	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.363	592	1401	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.0693	603	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:29,531] [INFO] DFAST Taxonomy check result was written to GCF_014836745.1_ASM1483674v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:29,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:29,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:29,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/checkm_data
[2024-01-24 14:31:29,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:29,592] [INFO] Task started: CheckM
[2024-01-24 14:31:29,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836745.1_ASM1483674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836745.1_ASM1483674v1_genomic.fna/checkm_input GCF_014836745.1_ASM1483674v1_genomic.fna/checkm_result
[2024-01-24 14:32:29,678] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:29,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:29,702] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:29,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:29,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836745.1_ASM1483674v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:29,703] [INFO] Task started: Blastn
[2024-01-24 14:32:29,703] [INFO] Running command: blastn -query GCF_014836745.1_ASM1483674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48af7f75-40a7-4fed-8f07-128ea818b201/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836745.1_ASM1483674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:31,698] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:31,701] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:31,702] [INFO] Target genome list was writen to GCF_014836745.1_ASM1483674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:31,708] [INFO] Task started: fastANI
[2024-01-24 14:32:31,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac8b793-841c-41be-9d39-dd6fe73ac037/GCF_014836745.1_ASM1483674v1_genomic.fna.gz --refList GCF_014836745.1_ASM1483674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836745.1_ASM1483674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:40,822] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:40,832] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:40,832] [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	99.1969	1363	1401	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	93.7995	1258	1401	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	93.498	1272	1401	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	92.8779	1171	1401	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	90.4176	1139	1401	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	89.7395	1169	1401	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	89.4151	1169	1401	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 14:32:40,834] [INFO] GTDB search result was written to GCF_014836745.1_ASM1483674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:40,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:40,838] [INFO] DFAST_QC result json was written to GCF_014836745.1_ASM1483674v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:40,838] [INFO] DFAST_QC completed!
[2024-01-24 14:32:40,838] [INFO] Total running time: 0h1m39s