[2023-06-28 01:52:36,678] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:52:36,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:52:36,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference
[2023-06-28 01:52:38,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:52:38,863] [INFO] Task started: Prodigal
[2023-06-28 01:52:38,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg2052b0a2-65c9-40b0-8dcd-8d24dcf190a3/GCA_026169755.1_ASM2616975v1_genomic.fna.gz | prodigal -d GCA_026169755.1_ASM2616975v1_genomic.fna/cds.fna -a GCA_026169755.1_ASM2616975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:52:42,812] [INFO] Task succeeded: Prodigal
[2023-06-28 01:52:42,812] [INFO] Task started: HMMsearch
[2023-06-28 01:52:42,812] [INFO] Running command: hmmsearch --tblout GCA_026169755.1_ASM2616975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/reference_markers.hmm GCA_026169755.1_ASM2616975v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:52:43,038] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:52:43,039] [INFO] Found 6/6 markers.
[2023-06-28 01:52:43,058] [INFO] Query marker FASTA was written to GCA_026169755.1_ASM2616975v1_genomic.fna/markers.fasta
[2023-06-28 01:52:43,059] [INFO] Task started: Blastn
[2023-06-28 01:52:43,059] [INFO] Running command: blastn -query GCA_026169755.1_ASM2616975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/reference_markers.fasta -out GCA_026169755.1_ASM2616975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:52:43,678] [INFO] Task succeeded: Blastn
[2023-06-28 01:52:43,682] [INFO] Selected 19 target genomes.
[2023-06-28 01:52:43,682] [INFO] Target genome list was writen to GCA_026169755.1_ASM2616975v1_genomic.fna/target_genomes.txt
[2023-06-28 01:52:43,687] [INFO] Task started: fastANI
[2023-06-28 01:52:43,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg2052b0a2-65c9-40b0-8dcd-8d24dcf190a3/GCA_026169755.1_ASM2616975v1_genomic.fna.gz --refList GCA_026169755.1_ASM2616975v1_genomic.fna/target_genomes.txt --output GCA_026169755.1_ASM2616975v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:52:53,484] [INFO] Task succeeded: fastANI
[2023-06-28 01:52:53,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:52:53,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:52:53,492] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:52:53,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:52:53,493] [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 coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	77.1681	76	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:52:53,495] [INFO] DFAST Taxonomy check result was written to GCA_026169755.1_ASM2616975v1_genomic.fna/tc_result.tsv
[2023-06-28 01:52:53,496] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:52:53,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:52:53,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/checkm_data
[2023-06-28 01:52:53,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:52:53,522] [INFO] Task started: CheckM
[2023-06-28 01:52:53,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026169755.1_ASM2616975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026169755.1_ASM2616975v1_genomic.fna/checkm_input GCA_026169755.1_ASM2616975v1_genomic.fna/checkm_result
[2023-06-28 01:53:12,887] [INFO] Task succeeded: CheckM
[2023-06-28 01:53:12,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:53:12,909] [INFO] ===== Completeness check finished =====
[2023-06-28 01:53:12,909] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:53:12,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026169755.1_ASM2616975v1_genomic.fna/markers.fasta)
[2023-06-28 01:53:12,910] [INFO] Task started: Blastn
[2023-06-28 01:53:12,910] [INFO] Running command: blastn -query GCA_026169755.1_ASM2616975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd7d6ac-acc4-468c-9752-84fd94ddb9cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_026169755.1_ASM2616975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:53:13,907] [INFO] Task succeeded: Blastn
[2023-06-28 01:53:13,912] [INFO] Selected 21 target genomes.
[2023-06-28 01:53:13,913] [INFO] Target genome list was writen to GCA_026169755.1_ASM2616975v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:53:13,929] [INFO] Task started: fastANI
[2023-06-28 01:53:13,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg2052b0a2-65c9-40b0-8dcd-8d24dcf190a3/GCA_026169755.1_ASM2616975v1_genomic.fna.gz --refList GCA_026169755.1_ASM2616975v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026169755.1_ASM2616975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:53:20,807] [INFO] Task succeeded: fastANI
[2023-06-28 01:53:20,820] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:53:20,820] [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_900540085.1	s__Scybalenecus sp900540085	99.171	523	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Scybalenecus	95.0	98.41	97.48	0.93	0.88	5	conclusive
GCA_015655975.1	s__Scybalenecus sp015655975	87.344	463	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Scybalenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436835.1	s__Eubacterium_R sp000436835	77.7643	84	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.32	97.52	0.92	0.86	14	-
GCA_003526845.1	s__Eubacterium_R sp003526845	77.7103	76	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.76	98.46	0.93	0.92	8	-
GCA_900539325.1	s__Eubacterium_R sp900539325	77.6117	71	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.44	97.34	0.90	0.87	4	-
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	77.1681	76	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	-
GCA_014465955.1	s__Eubacterium_R sp014465955	77.1618	96	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540235.1	s__Eubacterium_R sp900540235	77.1564	84	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.09	96.24	0.90	0.86	3	-
GCA_002493595.1	s__Eubacterium_R sp002493595	76.8821	56	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761545.1	s__Eubacterium_R sp900761545	76.6638	63	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:53:20,822] [INFO] GTDB search result was written to GCA_026169755.1_ASM2616975v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:53:20,822] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:53:20,825] [INFO] DFAST_QC result json was written to GCA_026169755.1_ASM2616975v1_genomic.fna/dqc_result.json
[2023-06-28 01:53:20,826] [INFO] DFAST_QC completed!
[2023-06-28 01:53:20,826] [INFO] Total running time: 0h0m44s