[2024-01-25 17:39:35,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference
[2024-01-25 17:39:36,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,827] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e8d1e77-222b-4cf3-bbaa-773f23bb6807/GCF_943169635.2_ASM94316963v2_genomic.fna.gz | prodigal -d GCF_943169635.2_ASM94316963v2_genomic.fna/cds.fna -a GCF_943169635.2_ASM94316963v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:39,689] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:39,689] [INFO] Task started: HMMsearch
[2024-01-25 17:39:39,690] [INFO] Running command: hmmsearch --tblout GCF_943169635.2_ASM94316963v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/reference_markers.hmm GCF_943169635.2_ASM94316963v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:39,874] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:39,875] [INFO] Found 6/6 markers.
[2024-01-25 17:39:39,893] [INFO] Query marker FASTA was written to GCF_943169635.2_ASM94316963v2_genomic.fna/markers.fasta
[2024-01-25 17:39:39,894] [INFO] Task started: Blastn
[2024-01-25 17:39:39,894] [INFO] Running command: blastn -query GCF_943169635.2_ASM94316963v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/reference_markers.fasta -out GCF_943169635.2_ASM94316963v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:40,447] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:40,449] [INFO] Selected 8 target genomes.
[2024-01-25 17:39:40,450] [INFO] Target genome list was writen to GCF_943169635.2_ASM94316963v2_genomic.fna/target_genomes.txt
[2024-01-25 17:39:40,461] [INFO] Task started: fastANI
[2024-01-25 17:39:40,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8d1e77-222b-4cf3-bbaa-773f23bb6807/GCF_943169635.2_ASM94316963v2_genomic.fna.gz --refList GCF_943169635.2_ASM94316963v2_genomic.fna/target_genomes.txt --output GCF_943169635.2_ASM94316963v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:44,676] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:44,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:44,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:44,680] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:44,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:44,680] [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
Fenollaria sporofastidiosus	strain=EMRHCC_24	GCA_943169635.1	2811778	2811778	type	True	100.0	543	543	95	conclusive
Fenollaria massiliensis	strain=9401234	GCA_000312505.3	938288	938288	type	True	87.017	438	543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:44,681] [INFO] DFAST Taxonomy check result was written to GCF_943169635.2_ASM94316963v2_genomic.fna/tc_result.tsv
[2024-01-25 17:39:44,682] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:44,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:44,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/checkm_data
[2024-01-25 17:39:44,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:44,702] [INFO] Task started: CheckM
[2024-01-25 17:39:44,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943169635.2_ASM94316963v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943169635.2_ASM94316963v2_genomic.fna/checkm_input GCF_943169635.2_ASM94316963v2_genomic.fna/checkm_result
[2024-01-25 17:39:59,779] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:59,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:59,802] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:59,802] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:59,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943169635.2_ASM94316963v2_genomic.fna/markers.fasta)
[2024-01-25 17:39:59,803] [INFO] Task started: Blastn
[2024-01-25 17:39:59,803] [INFO] Running command: blastn -query GCF_943169635.2_ASM94316963v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb41dfb6-4ecb-4134-9c52-be278469e2a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_943169635.2_ASM94316963v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:00,608] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:00,612] [INFO] Selected 5 target genomes.
[2024-01-25 17:40:00,612] [INFO] Target genome list was writen to GCF_943169635.2_ASM94316963v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:00,627] [INFO] Task started: fastANI
[2024-01-25 17:40:00,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8d1e77-222b-4cf3-bbaa-773f23bb6807/GCF_943169635.2_ASM94316963v2_genomic.fna.gz --refList GCF_943169635.2_ASM94316963v2_genomic.fna/target_genomes_gtdb.txt --output GCF_943169635.2_ASM94316963v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:02,813] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:02,818] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:02,818] [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_905332505.2	s__Fenollaria sp905332505	100.0	543	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Fenollaria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000312505.2	s__Fenollaria massiliensis	87.0397	437	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Fenollaria	95.0	96.81	96.74	0.87	0.86	4	-
GCF_001457835.1	s__Fenollaria timonensis	85.959	390	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Fenollaria	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900539225.1	s__Fenollaria sp900539225	85.7048	376	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Fenollaria	95.0	95.44	95.44	0.91	0.91	2	-
GCA_900539725.1	s__Fenollaria sp900539725	85.6234	387	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Fenollaria	95.0	95.17	95.17	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:02,820] [INFO] GTDB search result was written to GCF_943169635.2_ASM94316963v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:02,820] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:02,822] [INFO] DFAST_QC result json was written to GCF_943169635.2_ASM94316963v2_genomic.fna/dqc_result.json
[2024-01-25 17:40:02,822] [INFO] DFAST_QC completed!
[2024-01-25 17:40:02,823] [INFO] Total running time: 0h0m27s