[2023-06-29 11:51:49,866] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:51:49,871] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:51:49,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference
[2023-06-29 11:51:52,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:51:52,472] [INFO] Task started: Prodigal
[2023-06-29 11:51:52,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgff5aebd1-03c9-4a8e-8bed-96d8acdf35c6/GCA_020025055.1_ASM2002505v1_genomic.fna.gz | prodigal -d GCA_020025055.1_ASM2002505v1_genomic.fna/cds.fna -a GCA_020025055.1_ASM2002505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:51:54,707] [INFO] Task succeeded: Prodigal
[2023-06-29 11:51:54,707] [INFO] Task started: HMMsearch
[2023-06-29 11:51:54,707] [INFO] Running command: hmmsearch --tblout GCA_020025055.1_ASM2002505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/reference_markers.hmm GCA_020025055.1_ASM2002505v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:51:55,091] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:51:55,093] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgff5aebd1-03c9-4a8e-8bed-96d8acdf35c6/GCA_020025055.1_ASM2002505v1_genomic.fna.gz]
[2023-06-29 11:51:55,127] [INFO] Query marker FASTA was written to GCA_020025055.1_ASM2002505v1_genomic.fna/markers.fasta
[2023-06-29 11:51:55,132] [INFO] Task started: Blastn
[2023-06-29 11:51:55,133] [INFO] Running command: blastn -query GCA_020025055.1_ASM2002505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/reference_markers.fasta -out GCA_020025055.1_ASM2002505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:51:57,919] [INFO] Task succeeded: Blastn
[2023-06-29 11:51:57,923] [INFO] Selected 24 target genomes.
[2023-06-29 11:51:57,923] [INFO] Target genome list was writen to GCA_020025055.1_ASM2002505v1_genomic.fna/target_genomes.txt
[2023-06-29 11:51:57,972] [INFO] Task started: fastANI
[2023-06-29 11:51:57,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5aebd1-03c9-4a8e-8bed-96d8acdf35c6/GCA_020025055.1_ASM2002505v1_genomic.fna.gz --refList GCA_020025055.1_ASM2002505v1_genomic.fna/target_genomes.txt --output GCA_020025055.1_ASM2002505v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:52:12,787] [INFO] Task succeeded: fastANI
[2023-06-29 11:52:12,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:52:12,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:52:12,793] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:52:12,793] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:52:12,793] [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
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	78.701	111	387	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	78.0418	116	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:52:12,796] [INFO] DFAST Taxonomy check result was written to GCA_020025055.1_ASM2002505v1_genomic.fna/tc_result.tsv
[2023-06-29 11:52:12,797] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:52:12,797] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:52:12,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/checkm_data
[2023-06-29 11:52:12,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:52:12,816] [INFO] Task started: CheckM
[2023-06-29 11:52:12,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025055.1_ASM2002505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025055.1_ASM2002505v1_genomic.fna/checkm_input GCA_020025055.1_ASM2002505v1_genomic.fna/checkm_result
[2023-06-29 11:52:28,852] [INFO] Task succeeded: CheckM
[2023-06-29 11:52:28,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:52:28,883] [INFO] ===== Completeness check finished =====
[2023-06-29 11:52:28,884] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:52:28,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025055.1_ASM2002505v1_genomic.fna/markers.fasta)
[2023-06-29 11:52:28,885] [INFO] Task started: Blastn
[2023-06-29 11:52:28,885] [INFO] Running command: blastn -query GCA_020025055.1_ASM2002505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06312156-81b7-4b76-a533-0eef6cabb2a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025055.1_ASM2002505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:52:29,741] [INFO] Task succeeded: Blastn
[2023-06-29 11:52:29,746] [INFO] Selected 22 target genomes.
[2023-06-29 11:52:29,746] [INFO] Target genome list was writen to GCA_020025055.1_ASM2002505v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:52:29,769] [INFO] Task started: fastANI
[2023-06-29 11:52:29,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5aebd1-03c9-4a8e-8bed-96d8acdf35c6/GCA_020025055.1_ASM2002505v1_genomic.fna.gz --refList GCA_020025055.1_ASM2002505v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025055.1_ASM2002505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:52:37,432] [INFO] Task succeeded: fastANI
[2023-06-29 11:52:37,440] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:52:37,440] [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_010537335.1	s__Amedibacterium intestinale	78.701	111	387	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCA_904395785.1	s__Amedibacterium sp904395785	78.3183	108	387	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341945.1	s__Longicatena caecimuris	78.0458	118	387	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	-
--------------------------------------------------------------------------------
[2023-06-29 11:52:37,443] [INFO] GTDB search result was written to GCA_020025055.1_ASM2002505v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:52:37,443] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:52:37,446] [INFO] DFAST_QC result json was written to GCA_020025055.1_ASM2002505v1_genomic.fna/dqc_result.json
[2023-06-29 11:52:37,446] [INFO] DFAST_QC completed!
[2023-06-29 11:52:37,446] [INFO] Total running time: 0h0m48s