[2023-06-19 03:25:54,997] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:25:54,999] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:25:54,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference
[2023-06-19 03:25:56,506] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:25:56,507] [INFO] Task started: Prodigal
[2023-06-19 03:25:56,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f5e74e0-2bdd-425e-85de-0bdf473b3f46/GCA_029554505.1_ASM2955450v1_genomic.fna.gz | prodigal -d GCA_029554505.1_ASM2955450v1_genomic.fna/cds.fna -a GCA_029554505.1_ASM2955450v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:26:02,698] [INFO] Task succeeded: Prodigal
[2023-06-19 03:26:02,699] [INFO] Task started: HMMsearch
[2023-06-19 03:26:02,699] [INFO] Running command: hmmsearch --tblout GCA_029554505.1_ASM2955450v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/reference_markers.hmm GCA_029554505.1_ASM2955450v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:26:02,941] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:26:02,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f5e74e0-2bdd-425e-85de-0bdf473b3f46/GCA_029554505.1_ASM2955450v1_genomic.fna.gz]
[2023-06-19 03:26:02,980] [INFO] Query marker FASTA was written to GCA_029554505.1_ASM2955450v1_genomic.fna/markers.fasta
[2023-06-19 03:26:02,981] [INFO] Task started: Blastn
[2023-06-19 03:26:02,981] [INFO] Running command: blastn -query GCA_029554505.1_ASM2955450v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/reference_markers.fasta -out GCA_029554505.1_ASM2955450v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:26:03,710] [INFO] Task succeeded: Blastn
[2023-06-19 03:26:03,714] [INFO] Selected 24 target genomes.
[2023-06-19 03:26:03,715] [INFO] Target genome list was writen to GCA_029554505.1_ASM2955450v1_genomic.fna/target_genomes.txt
[2023-06-19 03:26:03,719] [INFO] Task started: fastANI
[2023-06-19 03:26:03,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5e74e0-2bdd-425e-85de-0bdf473b3f46/GCA_029554505.1_ASM2955450v1_genomic.fna.gz --refList GCA_029554505.1_ASM2955450v1_genomic.fna/target_genomes.txt --output GCA_029554505.1_ASM2955450v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:26:17,279] [INFO] Task succeeded: fastANI
[2023-06-19 03:26:17,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:26:17,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:26:17,284] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:26:17,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:26:17,284] [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
Sphaerochaeta associata	strain=GLS2T	GCA_022869165.1	1129264	1129264	type	True	76.642	62	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:26:17,288] [INFO] DFAST Taxonomy check result was written to GCA_029554505.1_ASM2955450v1_genomic.fna/tc_result.tsv
[2023-06-19 03:26:17,289] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:26:17,289] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:26:17,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/checkm_data
[2023-06-19 03:26:17,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:26:17,322] [INFO] Task started: CheckM
[2023-06-19 03:26:17,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029554505.1_ASM2955450v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029554505.1_ASM2955450v1_genomic.fna/checkm_input GCA_029554505.1_ASM2955450v1_genomic.fna/checkm_result
[2023-06-19 03:26:43,162] [INFO] Task succeeded: CheckM
[2023-06-19 03:26:43,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 9.72%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-19 03:26:43,189] [INFO] ===== Completeness check finished =====
[2023-06-19 03:26:43,189] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:26:43,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029554505.1_ASM2955450v1_genomic.fna/markers.fasta)
[2023-06-19 03:26:43,190] [INFO] Task started: Blastn
[2023-06-19 03:26:43,190] [INFO] Running command: blastn -query GCA_029554505.1_ASM2955450v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80fe0f31-fc58-494e-97ac-2056912bf5a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_029554505.1_ASM2955450v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:26:44,163] [INFO] Task succeeded: Blastn
[2023-06-19 03:26:44,168] [INFO] Selected 16 target genomes.
[2023-06-19 03:26:44,168] [INFO] Target genome list was writen to GCA_029554505.1_ASM2955450v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:26:44,176] [INFO] Task started: fastANI
[2023-06-19 03:26:44,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5e74e0-2bdd-425e-85de-0bdf473b3f46/GCA_029554505.1_ASM2955450v1_genomic.fna.gz --refList GCA_029554505.1_ASM2955450v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029554505.1_ASM2955450v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:26:51,541] [INFO] Task succeeded: fastANI
[2023-06-19 03:26:51,553] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:26:51,554] [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
GCA_004294855.1	s__Sphaerochaeta sp004294855	97.9068	387	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	97.83	97.73	0.85	0.79	4	conclusive
GCA_012519115.1	s__Sphaerochaeta sp012519115	86.6587	331	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012800465.1	s__Sphaerochaeta sp012800465	85.9373	222	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001604325.1	s__Sphaerochaeta sp001604325	77.8264	77	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.87	98.79	0.85	0.79	4	-
GCA_001603105.1	s__Sphaerochaeta sp001603105	77.0242	74	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432715.1	s__Sphaerochaeta sp002432715	76.7797	57	614	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
--------------------------------------------------------------------------------
[2023-06-19 03:26:51,556] [INFO] GTDB search result was written to GCA_029554505.1_ASM2955450v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:26:51,557] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:26:51,560] [INFO] DFAST_QC result json was written to GCA_029554505.1_ASM2955450v1_genomic.fna/dqc_result.json
[2023-06-19 03:26:51,560] [INFO] DFAST_QC completed!
[2023-06-19 03:26:51,561] [INFO] Total running time: 0h0m57s