[2024-01-24 14:30:47,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference
[2024-01-24 14:30:48,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,478] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,478] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1cedb17-7f2c-4ddd-aef9-e5ffc157af88/GCF_002441855.2_ASM244185v2_genomic.fna.gz | prodigal -d GCF_002441855.2_ASM244185v2_genomic.fna/cds.fna -a GCF_002441855.2_ASM244185v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:59,909] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:59,909] [INFO] Task started: HMMsearch
[2024-01-24 14:30:59,909] [INFO] Running command: hmmsearch --tblout GCF_002441855.2_ASM244185v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/reference_markers.hmm GCF_002441855.2_ASM244185v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:00,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:00,228] [INFO] Found 6/6 markers.
[2024-01-24 14:31:00,271] [INFO] Query marker FASTA was written to GCF_002441855.2_ASM244185v2_genomic.fna/markers.fasta
[2024-01-24 14:31:00,272] [INFO] Task started: Blastn
[2024-01-24 14:31:00,272] [INFO] Running command: blastn -query GCF_002441855.2_ASM244185v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/reference_markers.fasta -out GCF_002441855.2_ASM244185v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:00,935] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:00,941] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:00,941] [INFO] Target genome list was writen to GCF_002441855.2_ASM244185v2_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,951] [INFO] Task started: fastANI
[2024-01-24 14:31:00,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cedb17-7f2c-4ddd-aef9-e5ffc157af88/GCF_002441855.2_ASM244185v2_genomic.fna.gz --refList GCF_002441855.2_ASM244185v2_genomic.fna/target_genomes.txt --output GCF_002441855.2_ASM244185v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:09,884] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:09,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:09,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:09,891] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:09,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:09,891] [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
Eubacterium maltosivorans	strain=YI	GCA_002441855.2	2041044	2041044	type	True	100.0	1443	1445	95	conclusive
Eubacterium callanderi	strain=FD	GCA_900142645.1	53442	53442	type	True	89.9458	1106	1445	95	below_threshold
Eubacterium limosum	strain=ATCC 8486	GCA_000807675.2	1736	1736	type	True	89.8383	1137	1445	95	below_threshold
Eubacterium barkeri	strain=VPI 5359	GCA_900107125.1	1528	1528	type	True	76.8947	82	1445	95	below_threshold
Eubacterium aggregans	strain=SR12	GCA_900107815.1	81409	81409	type	True	76.7007	82	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:09,893] [INFO] DFAST Taxonomy check result was written to GCF_002441855.2_ASM244185v2_genomic.fna/tc_result.tsv
[2024-01-24 14:31:09,893] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:09,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:09,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/checkm_data
[2024-01-24 14:31:09,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:09,935] [INFO] Task started: CheckM
[2024-01-24 14:31:09,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441855.2_ASM244185v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441855.2_ASM244185v2_genomic.fna/checkm_input GCF_002441855.2_ASM244185v2_genomic.fna/checkm_result
[2024-01-24 14:31:50,773] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:50,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:50,792] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:50,793] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:50,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441855.2_ASM244185v2_genomic.fna/markers.fasta)
[2024-01-24 14:31:50,794] [INFO] Task started: Blastn
[2024-01-24 14:31:50,794] [INFO] Running command: blastn -query GCF_002441855.2_ASM244185v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd979f-6e63-45eb-ad46-0878704aadda/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441855.2_ASM244185v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:51,661] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:51,666] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:51,666] [INFO] Target genome list was writen to GCF_002441855.2_ASM244185v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:51,674] [INFO] Task started: fastANI
[2024-01-24 14:31:51,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cedb17-7f2c-4ddd-aef9-e5ffc157af88/GCF_002441855.2_ASM244185v2_genomic.fna.gz --refList GCF_002441855.2_ASM244185v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002441855.2_ASM244185v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:02,386] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:02,394] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:02,394] [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_002441855.2	s__Eubacterium maltosivorans	100.0	1445	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Eubacterium	95.0	98.42	98.37	0.90	0.88	7	conclusive
GCF_900142645.1	s__Eubacterium callanderi	89.9291	1107	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Eubacterium	95.0	98.78	98.14	0.91	0.88	13	-
GCF_000807675.2	s__Eubacterium limosum	89.8414	1135	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Eubacterium	95.0	98.75	97.93	0.93	0.86	4	-
GCF_015547515.1	s__Eubacterium sp015547515	87.3191	1076	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Eubacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213825.1	s__Acetobacterium woodii_A	77.1447	56	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107815.1	s__Eubacterium_O aggregans	76.6664	83	1445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Eubacterium_O	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:02,396] [INFO] GTDB search result was written to GCF_002441855.2_ASM244185v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:02,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:02,400] [INFO] DFAST_QC result json was written to GCF_002441855.2_ASM244185v2_genomic.fna/dqc_result.json
[2024-01-24 14:32:02,400] [INFO] DFAST_QC completed!
[2024-01-24 14:32:02,400] [INFO] Total running time: 0h1m15s