[2024-01-24 11:26:38,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference
[2024-01-24 11:26:40,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,131] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e3b989d-411c-46c7-9b34-0da56afb0637/GCF_016405145.1_ASM1640514v1_genomic.fna.gz | prodigal -d GCF_016405145.1_ASM1640514v1_genomic.fna/cds.fna -a GCF_016405145.1_ASM1640514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:46,705] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:46,706] [INFO] Task started: HMMsearch
[2024-01-24 11:26:46,706] [INFO] Running command: hmmsearch --tblout GCF_016405145.1_ASM1640514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/reference_markers.hmm GCF_016405145.1_ASM1640514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:46,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:46,934] [INFO] Found 6/6 markers.
[2024-01-24 11:26:46,954] [INFO] Query marker FASTA was written to GCF_016405145.1_ASM1640514v1_genomic.fna/markers.fasta
[2024-01-24 11:26:46,954] [INFO] Task started: Blastn
[2024-01-24 11:26:46,955] [INFO] Running command: blastn -query GCF_016405145.1_ASM1640514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/reference_markers.fasta -out GCF_016405145.1_ASM1640514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:47,806] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:47,809] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:47,809] [INFO] Target genome list was writen to GCF_016405145.1_ASM1640514v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:47,830] [INFO] Task started: fastANI
[2024-01-24 11:26:47,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3b989d-411c-46c7-9b34-0da56afb0637/GCF_016405145.1_ASM1640514v1_genomic.fna.gz --refList GCF_016405145.1_ASM1640514v1_genomic.fna/target_genomes.txt --output GCF_016405145.1_ASM1640514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:59,828] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:59,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:59,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:59,853] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:59,853] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:59,853] [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
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	80.4689	325	730	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	78.6189	126	730	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.4759	145	730	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	78.4182	141	730	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.1203	136	730	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	77.6896	158	730	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	77.4236	117	730	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	77.4088	121	730	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	77.2693	95	730	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	77.2204	110	730	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	76.7205	70	730	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	76.6011	55	730	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.5381	60	730	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.3101	56	730	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.2323	82	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:59,856] [INFO] DFAST Taxonomy check result was written to GCF_016405145.1_ASM1640514v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:59,857] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:59,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:59,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/checkm_data
[2024-01-24 11:26:59,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:59,889] [INFO] Task started: CheckM
[2024-01-24 11:26:59,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016405145.1_ASM1640514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016405145.1_ASM1640514v1_genomic.fna/checkm_input GCF_016405145.1_ASM1640514v1_genomic.fna/checkm_result
[2024-01-24 11:27:24,898] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:24,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,927] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:24,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:24,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016405145.1_ASM1640514v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:24,928] [INFO] Task started: Blastn
[2024-01-24 11:27:24,928] [INFO] Running command: blastn -query GCF_016405145.1_ASM1640514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782c1573-0be3-4e5f-bfe3-60f8076e78fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016405145.1_ASM1640514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:26,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:26,203] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:26,203] [INFO] Target genome list was writen to GCF_016405145.1_ASM1640514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:26,230] [INFO] Task started: fastANI
[2024-01-24 11:27:26,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3b989d-411c-46c7-9b34-0da56afb0637/GCF_016405145.1_ASM1640514v1_genomic.fna.gz --refList GCF_016405145.1_ASM1640514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016405145.1_ASM1640514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:33,294] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,312] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:33,313] [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_016405145.1	s__Pauljensenia cardiffensis	100.0	727	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.37	97.30	0.94	0.93	4	conclusive
GCF_014208035.1	s__Pauljensenia hyovaginalis	80.5239	322	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCF_900155595.1	s__Pauljensenia mediterranea	80.5223	282	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900499005.1	s__Pauljensenia culturomici	80.0859	338	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420425.1	s__Pauljensenia vaccimaxillae	78.6504	125	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	78.5891	190	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_000411415.1	s__Pauljensenia sp000411415	78.5832	187	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_018986735.1	s__Pauljensenia sp018986735	78.5454	197	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001838165.1	s__Pauljensenia sp001838165	78.4901	185	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCA_018375675.1	s__Pauljensenia sp018375675	78.4645	174	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900445025.1	s__Pauljensenia odontolytica	78.4482	184	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001072465.1	s__Pauljensenia sp001072465	78.0876	203	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_900155435.1	s__Pauljensenia provencensis	77.6896	158	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	96.43	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,314] [INFO] GTDB search result was written to GCF_016405145.1_ASM1640514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:33,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:33,318] [INFO] DFAST_QC result json was written to GCF_016405145.1_ASM1640514v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:33,319] [INFO] DFAST_QC completed!
[2024-01-24 11:27:33,319] [INFO] Total running time: 0h0m54s