[2024-01-24 15:26:55,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference
[2024-01-24 15:26:56,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,579] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,580] [INFO] Running command: gunzip -c /var/lib/cwl/stg98418867-55a3-4f89-ac4f-0e9fa2172ea0/GCF_004121315.1_ASM412131v1_genomic.fna.gz | prodigal -d GCF_004121315.1_ASM412131v1_genomic.fna/cds.fna -a GCF_004121315.1_ASM412131v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:07,570] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:07,570] [INFO] Task started: HMMsearch
[2024-01-24 15:27:07,571] [INFO] Running command: hmmsearch --tblout GCF_004121315.1_ASM412131v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/reference_markers.hmm GCF_004121315.1_ASM412131v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:07,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:07,829] [INFO] Found 6/6 markers.
[2024-01-24 15:27:07,865] [INFO] Query marker FASTA was written to GCF_004121315.1_ASM412131v1_genomic.fna/markers.fasta
[2024-01-24 15:27:07,865] [INFO] Task started: Blastn
[2024-01-24 15:27:07,866] [INFO] Running command: blastn -query GCF_004121315.1_ASM412131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/reference_markers.fasta -out GCF_004121315.1_ASM412131v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:09,164] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:09,168] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:09,168] [INFO] Target genome list was writen to GCF_004121315.1_ASM412131v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:09,191] [INFO] Task started: fastANI
[2024-01-24 15:27:09,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg98418867-55a3-4f89-ac4f-0e9fa2172ea0/GCF_004121315.1_ASM412131v1_genomic.fna.gz --refList GCF_004121315.1_ASM412131v1_genomic.fna/target_genomes.txt --output GCF_004121315.1_ASM412131v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:18,028] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:18,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:18,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:18,037] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:18,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:18,037] [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 turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	100.0	1329	1329	95	conclusive
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	99.9887	1318	1329	95	conclusive
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	94.4611	1180	1329	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	92.2106	1183	1329	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	90.0463	1101	1329	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	89.0663	1089	1329	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.5612	582	1329	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.2172	589	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:18,046] [INFO] DFAST Taxonomy check result was written to GCF_004121315.1_ASM412131v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:18,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:18,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:18,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/checkm_data
[2024-01-24 15:27:18,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:18,098] [INFO] Task started: CheckM
[2024-01-24 15:27:18,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004121315.1_ASM412131v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004121315.1_ASM412131v1_genomic.fna/checkm_input GCF_004121315.1_ASM412131v1_genomic.fna/checkm_result
[2024-01-24 15:28:13,846] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:13,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:13,874] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:13,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:13,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004121315.1_ASM412131v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:13,875] [INFO] Task started: Blastn
[2024-01-24 15:28:13,875] [INFO] Running command: blastn -query GCF_004121315.1_ASM412131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004a1c47-9937-43d7-9231-ccb04e327fe0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004121315.1_ASM412131v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:15,960] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:15,963] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:15,963] [INFO] Target genome list was writen to GCF_004121315.1_ASM412131v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:15,967] [INFO] Task started: fastANI
[2024-01-24 15:28:15,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg98418867-55a3-4f89-ac4f-0e9fa2172ea0/GCF_004121315.1_ASM412131v1_genomic.fna.gz --refList GCF_004121315.1_ASM412131v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004121315.1_ASM412131v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:24,087] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:24,101] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:24,101] [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_000718325.1	s__Oerskovia turbata	99.9887	1318	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	conclusive
GCF_005937995.2	s__Oerskovia sp005937995	94.729	1193	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_016907365.1	s__Oerskovia paurometabola	92.9615	1169	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_016907235.1	s__Oerskovia jenensis	92.2106	1183	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015142735.1	s__Oerskovia sp015142735	90.0603	1100	1329	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	89.3133	1088	1329	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	89.0798	1088	1329	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 15:28:24,104] [INFO] GTDB search result was written to GCF_004121315.1_ASM412131v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:24,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:24,107] [INFO] DFAST_QC result json was written to GCF_004121315.1_ASM412131v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:24,108] [INFO] DFAST_QC completed!
[2024-01-24 15:28:24,108] [INFO] Total running time: 0h1m29s