[2023-06-05 07:10:31,688] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:10:31,691] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:10:31,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference
[2023-06-05 07:10:32,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:10:32,981] [INFO] Task started: Prodigal
[2023-06-05 07:10:32,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg5da47b78-df58-4a41-b41d-0ca3463ea7fd/GCA_934561045.1_ERR7738560_bin.162_genomic.fna.gz | prodigal -d GCA_934561045.1_ERR7738560_bin.162_genomic.fna/cds.fna -a GCA_934561045.1_ERR7738560_bin.162_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:10:37,564] [INFO] Task succeeded: Prodigal
[2023-06-05 07:10:37,565] [INFO] Task started: HMMsearch
[2023-06-05 07:10:37,565] [INFO] Running command: hmmsearch --tblout GCA_934561045.1_ERR7738560_bin.162_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/reference_markers.hmm GCA_934561045.1_ERR7738560_bin.162_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:10:37,836] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:10:37,838] [INFO] Found 6/6 markers.
[2023-06-05 07:10:37,857] [INFO] Query marker FASTA was written to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/markers.fasta
[2023-06-05 07:10:37,857] [INFO] Task started: Blastn
[2023-06-05 07:10:37,857] [INFO] Running command: blastn -query GCA_934561045.1_ERR7738560_bin.162_genomic.fna/markers.fasta -db /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/reference_markers.fasta -out GCA_934561045.1_ERR7738560_bin.162_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:38,485] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:38,490] [INFO] Selected 22 target genomes.
[2023-06-05 07:10:38,490] [INFO] Target genome list was writen to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/target_genomes.txt
[2023-06-05 07:10:38,494] [INFO] Task started: fastANI
[2023-06-05 07:10:38,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg5da47b78-df58-4a41-b41d-0ca3463ea7fd/GCA_934561045.1_ERR7738560_bin.162_genomic.fna.gz --refList GCA_934561045.1_ERR7738560_bin.162_genomic.fna/target_genomes.txt --output GCA_934561045.1_ERR7738560_bin.162_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:10:48,566] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:48,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:10:48,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:10:48,574] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:10:48,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:10:48,574] [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	89.8241	472	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:10:48,577] [INFO] DFAST Taxonomy check result was written to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/tc_result.tsv
[2023-06-05 07:10:48,578] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:10:48,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:10:48,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/checkm_data
[2023-06-05 07:10:48,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:10:48,600] [INFO] Task started: CheckM
[2023-06-05 07:10:48,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934561045.1_ERR7738560_bin.162_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934561045.1_ERR7738560_bin.162_genomic.fna/checkm_input GCA_934561045.1_ERR7738560_bin.162_genomic.fna/checkm_result
[2023-06-05 07:11:09,630] [INFO] Task succeeded: CheckM
[2023-06-05 07:11:09,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:11:09,653] [INFO] ===== Completeness check finished =====
[2023-06-05 07:11:09,653] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:11:09,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934561045.1_ERR7738560_bin.162_genomic.fna/markers.fasta)
[2023-06-05 07:11:09,654] [INFO] Task started: Blastn
[2023-06-05 07:11:09,654] [INFO] Running command: blastn -query GCA_934561045.1_ERR7738560_bin.162_genomic.fna/markers.fasta -db /var/lib/cwl/stg4156124a-5ad4-49db-9acf-1dceac27032e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934561045.1_ERR7738560_bin.162_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:11:10,705] [INFO] Task succeeded: Blastn
[2023-06-05 07:11:10,709] [INFO] Selected 12 target genomes.
[2023-06-05 07:11:10,710] [INFO] Target genome list was writen to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:11:10,718] [INFO] Task started: fastANI
[2023-06-05 07:11:10,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg5da47b78-df58-4a41-b41d-0ca3463ea7fd/GCA_934561045.1_ERR7738560_bin.162_genomic.fna.gz --refList GCA_934561045.1_ERR7738560_bin.162_genomic.fna/target_genomes_gtdb.txt --output GCA_934561045.1_ERR7738560_bin.162_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:11:14,950] [INFO] Task succeeded: fastANI
[2023-06-05 07:11:14,964] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:11:14,965] [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_900539325.1	s__Eubacterium_R sp900539325	97.3764	544	586	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	conclusive
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	89.8133	472	586	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_900766895.1	s__Eubacterium_R sp900766895	81.0773	292	586	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_900772705.1	s__Eubacterium_R sp900772705	80.0586	184	586	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_900539165.1	s__Eubacterium_R sp900539165	79.7903	263	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900542875.1	s__Eubacterium_R sp900542875	79.4947	245	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.37	97.10	0.91	0.86	6	-
GCA_003526845.1	s__Eubacterium_R sp003526845	78.3787	227	586	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_017445905.1	s__Eubacterium_R sp017445905	77.5084	114	586	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_017514345.1	s__Eubacterium_R sp017514345	77.4069	126	586	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_015065505.1	s__Eubacterium_R sp015065505	77.3969	136	586	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_017543415.1	s__Eubacterium_R sp017543415	77.0524	68	586	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	-
--------------------------------------------------------------------------------
[2023-06-05 07:11:14,967] [INFO] GTDB search result was written to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/result_gtdb.tsv
[2023-06-05 07:11:14,968] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:11:14,971] [INFO] DFAST_QC result json was written to GCA_934561045.1_ERR7738560_bin.162_genomic.fna/dqc_result.json
[2023-06-05 07:11:14,971] [INFO] DFAST_QC completed!
[2023-06-05 07:11:14,971] [INFO] Total running time: 0h0m43s