[2024-01-24 14:06:06,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference
[2024-01-24 14:06:08,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,008] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5aa9f16-4a53-451b-a3a5-cfb188140a3a/GCF_014284475.1_ASM1428447v1_genomic.fna.gz | prodigal -d GCF_014284475.1_ASM1428447v1_genomic.fna/cds.fna -a GCF_014284475.1_ASM1428447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,456] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,456] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,457] [INFO] Running command: hmmsearch --tblout GCF_014284475.1_ASM1428447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/reference_markers.hmm GCF_014284475.1_ASM1428447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,824] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,854] [INFO] Query marker FASTA was written to GCF_014284475.1_ASM1428447v1_genomic.fna/markers.fasta
[2024-01-24 14:06:16,854] [INFO] Task started: Blastn
[2024-01-24 14:06:16,854] [INFO] Running command: blastn -query GCF_014284475.1_ASM1428447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/reference_markers.fasta -out GCF_014284475.1_ASM1428447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,477] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,485] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:17,485] [INFO] Target genome list was writen to GCF_014284475.1_ASM1428447v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,492] [INFO] Task started: fastANI
[2024-01-24 14:06:17,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5aa9f16-4a53-451b-a3a5-cfb188140a3a/GCF_014284475.1_ASM1428447v1_genomic.fna.gz --refList GCF_014284475.1_ASM1428447v1_genomic.fna/target_genomes.txt --output GCF_014284475.1_ASM1428447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:28,672] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:28,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:28,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:28,680] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:28,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:28,681] [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
Acetobacterium paludosum	strain=DSM 8237	GCA_008086595.1	52693	52693	type	True	80.9893	561	1041	95	below_threshold
Acetobacterium dehalogenans	strain=DSM 11527	GCA_000472665.1	82116	82116	type	True	79.5691	368	1041	95	below_threshold
Acetobacterium bakii	strain=DSM 8239	GCA_001263355.1	52689	52689	type	True	78.6608	302	1041	95	below_threshold
Acetobacterium wieringae	strain=DSM 1911	GCA_001766835.1	52694	52694	type	True	78.6226	333	1041	95	below_threshold
Acetobacterium bakii	strain=DSM 8239	GCA_008086625.1	52689	52689	type	True	78.6051	306	1041	95	below_threshold
Acetobacterium woodii	strain=DSM 1030	GCA_000247605.1	33952	33952	type	True	78.3441	280	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:28,684] [INFO] DFAST Taxonomy check result was written to GCF_014284475.1_ASM1428447v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:28,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:28,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:28,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/checkm_data
[2024-01-24 14:06:28,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:28,719] [INFO] Task started: CheckM
[2024-01-24 14:06:28,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284475.1_ASM1428447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284475.1_ASM1428447v1_genomic.fna/checkm_input GCF_014284475.1_ASM1428447v1_genomic.fna/checkm_result
[2024-01-24 14:06:59,512] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:59,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,535] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:59,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:59,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284475.1_ASM1428447v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:59,536] [INFO] Task started: Blastn
[2024-01-24 14:06:59,536] [INFO] Running command: blastn -query GCF_014284475.1_ASM1428447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2dc9a2d-c740-4615-ac57-6f6fc87c1ef8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284475.1_ASM1428447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:00,351] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:00,358] [INFO] Selected 16 target genomes.
[2024-01-24 14:07:00,358] [INFO] Target genome list was writen to GCF_014284475.1_ASM1428447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:00,402] [INFO] Task started: fastANI
[2024-01-24 14:07:00,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5aa9f16-4a53-451b-a3a5-cfb188140a3a/GCF_014284475.1_ASM1428447v1_genomic.fna.gz --refList GCF_014284475.1_ASM1428447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284475.1_ASM1428447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:10,510] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:10,523] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:10,523] [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_014284475.1	s__Acetobacterium fimetarium	100.0	1036	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008086595.1	s__Acetobacterium paludosum	80.9604	564	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008086615.1	s__Acetobacterium tundrae	80.6844	537	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000472665.1	s__Acetobacterium dehalogenans	79.5503	366	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	96.75	96.75	0.83	0.83	2	-
GCA_016213825.1	s__Acetobacterium woodii_A	79.118	336	1041	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_001263355.1	s__Acetobacterium bakii	78.6593	302	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001766835.1	s__Acetobacterium wieringae	78.6476	330	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	97.41	97.27	0.88	0.86	5	-
GCA_002841405.1	s__Acetobacterium sp002841405	78.4032	279	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650045.1	s__Acetobacterium sp016650045	78.3816	159	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:10,526] [INFO] GTDB search result was written to GCF_014284475.1_ASM1428447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:10,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:10,529] [INFO] DFAST_QC result json was written to GCF_014284475.1_ASM1428447v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:10,529] [INFO] DFAST_QC completed!
[2024-01-24 14:07:10,529] [INFO] Total running time: 0h1m4s