[2024-01-25 17:37:05,558] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference
[2024-01-25 17:37:06,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,694] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e2773a-ac95-4396-9580-afd1c65584f2/GCF_014836755.1_ASM1483675v1_genomic.fna.gz | prodigal -d GCF_014836755.1_ASM1483675v1_genomic.fna/cds.fna -a GCF_014836755.1_ASM1483675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:17,335] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:17,336] [INFO] Task started: HMMsearch
[2024-01-25 17:37:17,336] [INFO] Running command: hmmsearch --tblout GCF_014836755.1_ASM1483675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/reference_markers.hmm GCF_014836755.1_ASM1483675v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:17,569] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:17,570] [INFO] Found 6/6 markers.
[2024-01-25 17:37:17,608] [INFO] Query marker FASTA was written to GCF_014836755.1_ASM1483675v1_genomic.fna/markers.fasta
[2024-01-25 17:37:17,608] [INFO] Task started: Blastn
[2024-01-25 17:37:17,608] [INFO] Running command: blastn -query GCF_014836755.1_ASM1483675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/reference_markers.fasta -out GCF_014836755.1_ASM1483675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:18,883] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:18,885] [INFO] Selected 9 target genomes.
[2024-01-25 17:37:18,886] [INFO] Target genome list was writen to GCF_014836755.1_ASM1483675v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:18,896] [INFO] Task started: fastANI
[2024-01-25 17:37:18,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e2773a-ac95-4396-9580-afd1c65584f2/GCF_014836755.1_ASM1483675v1_genomic.fna.gz --refList GCF_014836755.1_ASM1483675v1_genomic.fna/target_genomes.txt --output GCF_014836755.1_ASM1483675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:29,593] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:29,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:29,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:29,601] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:29,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:29,601] [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 merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	100.0	1474	1475	95	conclusive
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	94.4706	1247	1475	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	89.9499	1159	1475	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	89.3549	1166	1475	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	89.2519	1184	1475	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	89.0529	1105	1475	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	89.0299	1095	1475	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.2843	609	1475	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.8018	561	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:29,602] [INFO] DFAST Taxonomy check result was written to GCF_014836755.1_ASM1483675v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:29,603] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:29,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:29,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/checkm_data
[2024-01-25 17:37:29,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:29,646] [INFO] Task started: CheckM
[2024-01-25 17:37:29,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836755.1_ASM1483675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836755.1_ASM1483675v1_genomic.fna/checkm_input GCF_014836755.1_ASM1483675v1_genomic.fna/checkm_result
[2024-01-25 17:38:27,569] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:27,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:27,596] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:27,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:27,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836755.1_ASM1483675v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:27,598] [INFO] Task started: Blastn
[2024-01-25 17:38:27,598] [INFO] Running command: blastn -query GCF_014836755.1_ASM1483675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d4ba7d3-1bec-440a-86aa-df6477d2ad43/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836755.1_ASM1483675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:29,712] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:29,715] [INFO] Selected 7 target genomes.
[2024-01-25 17:38:29,715] [INFO] Target genome list was writen to GCF_014836755.1_ASM1483675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:29,719] [INFO] Task started: fastANI
[2024-01-25 17:38:29,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e2773a-ac95-4396-9580-afd1c65584f2/GCF_014836755.1_ASM1483675v1_genomic.fna.gz --refList GCF_014836755.1_ASM1483675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836755.1_ASM1483675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:38,122] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:38,128] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:38,128] [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_014836755.1	s__Oerskovia sp014836755	100.0	1474	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001692445.1	s__Oerskovia enterophila	94.4706	1247	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_015142735.1	s__Oerskovia sp015142735	89.9349	1160	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907365.1	s__Oerskovia paurometabola	89.4189	1157	1475	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	89.2644	1183	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937995.2	s__Oerskovia sp005937995	89.1647	1167	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_000718325.1	s__Oerskovia turbata	89.0299	1095	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:38,129] [INFO] GTDB search result was written to GCF_014836755.1_ASM1483675v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:38,130] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:38,132] [INFO] DFAST_QC result json was written to GCF_014836755.1_ASM1483675v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:38,132] [INFO] DFAST_QC completed!
[2024-01-25 17:38:38,132] [INFO] Total running time: 0h1m33s