[2024-01-25 19:02:35,576] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:35,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:35,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference
[2024-01-25 19:02:36,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:36,720] [INFO] Task started: Prodigal
[2024-01-25 19:02:36,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdf7da32-379a-4656-830f-818b0b1786ae/GCF_001027545.1_ASM102754v1_genomic.fna.gz | prodigal -d GCF_001027545.1_ASM102754v1_genomic.fna/cds.fna -a GCF_001027545.1_ASM102754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:39,759] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:39,759] [INFO] Task started: HMMsearch
[2024-01-25 19:02:39,759] [INFO] Running command: hmmsearch --tblout GCF_001027545.1_ASM102754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/reference_markers.hmm GCF_001027545.1_ASM102754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:39,921] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:39,922] [INFO] Found 6/6 markers.
[2024-01-25 19:02:39,939] [INFO] Query marker FASTA was written to GCF_001027545.1_ASM102754v1_genomic.fna/markers.fasta
[2024-01-25 19:02:39,939] [INFO] Task started: Blastn
[2024-01-25 19:02:39,939] [INFO] Running command: blastn -query GCF_001027545.1_ASM102754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/reference_markers.fasta -out GCF_001027545.1_ASM102754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:40,475] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:40,478] [INFO] Selected 13 target genomes.
[2024-01-25 19:02:40,478] [INFO] Target genome list was writen to GCF_001027545.1_ASM102754v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:40,509] [INFO] Task started: fastANI
[2024-01-25 19:02:40,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf7da32-379a-4656-830f-818b0b1786ae/GCF_001027545.1_ASM102754v1_genomic.fna.gz --refList GCF_001027545.1_ASM102754v1_genomic.fna/target_genomes.txt --output GCF_001027545.1_ASM102754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:47,927] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:47,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:47,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:47,931] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:47,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:47,931] [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
Endomicrobium proavitum	strain=Rsa215	GCA_001027545.1	1408281	1408281	type	True	100.0	529	529	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:02:47,934] [INFO] DFAST Taxonomy check result was written to GCF_001027545.1_ASM102754v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:47,935] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:47,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:47,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/checkm_data
[2024-01-25 19:02:47,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:47,954] [INFO] Task started: CheckM
[2024-01-25 19:02:47,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001027545.1_ASM102754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001027545.1_ASM102754v1_genomic.fna/checkm_input GCF_001027545.1_ASM102754v1_genomic.fna/checkm_result
[2024-01-25 19:03:03,200] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:03,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:03,242] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:03,242] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:03,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001027545.1_ASM102754v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:03,243] [INFO] Task started: Blastn
[2024-01-25 19:03:03,243] [INFO] Running command: blastn -query GCF_001027545.1_ASM102754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12559a3f-9fbb-4b02-b509-c5769a22f930/dqc_reference/reference_markers_gtdb.fasta -out GCF_001027545.1_ASM102754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:04,046] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:04,050] [INFO] Selected 15 target genomes.
[2024-01-25 19:03:04,050] [INFO] Target genome list was writen to GCF_001027545.1_ASM102754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:04,071] [INFO] Task started: fastANI
[2024-01-25 19:03:04,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf7da32-379a-4656-830f-818b0b1786ae/GCF_001027545.1_ASM102754v1_genomic.fna.gz --refList GCF_001027545.1_ASM102754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001027545.1_ASM102754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:11,360] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:11,365] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:11,365] [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_001027545.1	s__Endomicrobium proavitum	100.0	529	529	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009778965.1	s__Endomicrobium sp009778965	77.6893	136	529	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.87	99.87	0.94	0.94	2	-
GCA_009781315.1	s__Endomicrobium sp009781315	77.5115	161	529	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.96	99.96	1.00	1.00	2	-
GCA_009778325.1	s__Endomicrobium sp009778325	77.1626	120	529	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:11,366] [INFO] GTDB search result was written to GCF_001027545.1_ASM102754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:11,367] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:11,369] [INFO] DFAST_QC result json was written to GCF_001027545.1_ASM102754v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:11,369] [INFO] DFAST_QC completed!
[2024-01-25 19:03:11,369] [INFO] Total running time: 0h0m36s