[2023-06-04 18:00:17,608] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:17,611] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:17,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference
[2023-06-04 18:00:18,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:18,873] [INFO] Task started: Prodigal
[2023-06-04 18:00:18,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d7690ba-3b5b-4b12-ad81-6eb6c3700a66/GCA_934539595.1_ERR7745890_bin.274_genomic.fna.gz | prodigal -d GCA_934539595.1_ERR7745890_bin.274_genomic.fna/cds.fna -a GCA_934539595.1_ERR7745890_bin.274_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:23,050] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:23,051] [INFO] Task started: HMMsearch
[2023-06-04 18:00:23,051] [INFO] Running command: hmmsearch --tblout GCA_934539595.1_ERR7745890_bin.274_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/reference_markers.hmm GCA_934539595.1_ERR7745890_bin.274_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:23,290] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:23,292] [INFO] Found 6/6 markers.
[2023-06-04 18:00:23,317] [INFO] Query marker FASTA was written to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/markers.fasta
[2023-06-04 18:00:23,318] [INFO] Task started: Blastn
[2023-06-04 18:00:23,318] [INFO] Running command: blastn -query GCA_934539595.1_ERR7745890_bin.274_genomic.fna/markers.fasta -db /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/reference_markers.fasta -out GCA_934539595.1_ERR7745890_bin.274_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:23,960] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:23,965] [INFO] Selected 22 target genomes.
[2023-06-04 18:00:23,965] [INFO] Target genome list was writen to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/target_genomes.txt
[2023-06-04 18:00:25,408] [INFO] Task started: fastANI
[2023-06-04 18:00:25,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d7690ba-3b5b-4b12-ad81-6eb6c3700a66/GCA_934539595.1_ERR7745890_bin.274_genomic.fna.gz --refList GCA_934539595.1_ERR7745890_bin.274_genomic.fna/target_genomes.txt --output GCA_934539595.1_ERR7745890_bin.274_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:37,847] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:37,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:37,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:37,852] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:37,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:00:37,852] [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	77.9814	143	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:00:37,855] [INFO] DFAST Taxonomy check result was written to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/tc_result.tsv
[2023-06-04 18:00:37,855] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:37,856] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:37,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/checkm_data
[2023-06-04 18:00:37,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:37,894] [INFO] Task started: CheckM
[2023-06-04 18:00:37,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934539595.1_ERR7745890_bin.274_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934539595.1_ERR7745890_bin.274_genomic.fna/checkm_input GCA_934539595.1_ERR7745890_bin.274_genomic.fna/checkm_result
[2023-06-04 18:00:57,881] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:57,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:57,903] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:57,903] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:57,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934539595.1_ERR7745890_bin.274_genomic.fna/markers.fasta)
[2023-06-04 18:00:57,904] [INFO] Task started: Blastn
[2023-06-04 18:00:57,904] [INFO] Running command: blastn -query GCA_934539595.1_ERR7745890_bin.274_genomic.fna/markers.fasta -db /var/lib/cwl/stg7033d92d-6ee7-46f9-88b5-9282e4afff27/dqc_reference/reference_markers_gtdb.fasta -out GCA_934539595.1_ERR7745890_bin.274_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:58,892] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:58,897] [INFO] Selected 14 target genomes.
[2023-06-04 18:00:58,897] [INFO] Target genome list was writen to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:58,941] [INFO] Task started: fastANI
[2023-06-04 18:00:58,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d7690ba-3b5b-4b12-ad81-6eb6c3700a66/GCA_934539595.1_ERR7745890_bin.274_genomic.fna.gz --refList GCA_934539595.1_ERR7745890_bin.274_genomic.fna/target_genomes_gtdb.txt --output GCA_934539595.1_ERR7745890_bin.274_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:01:04,129] [INFO] Task succeeded: fastANI
[2023-06-04 18:01:04,143] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:01:04,144] [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_000434995.1	s__Eubacterium_R sp000434995	98.0061	519	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.46	98.20	0.94	0.90	9	conclusive
GCA_000436835.1	s__Eubacterium_R sp000436835	83.0277	445	595	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_900540235.1	s__Eubacterium_R sp900540235	81.8022	408	595	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_900539325.1	s__Eubacterium_R sp900539325	78.4675	157	595	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	-
GCA_910577195.1	s__Eubacterium_R sp910577195	78.4563	188	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	96.35	96.35	0.82	0.82	2	-
GCA_900544515.1	s__Eubacterium_R sp900544515	78.193	142	595	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_900767025.1	s__Eubacterium_R sp900767025	77.9071	184	595	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_009774735.1	s__Eubacterium_R sp009774735	77.6878	142	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.57	98.57	0.83	0.83	2	-
GCA_002493325.1	s__Eubacterium_R sp002493325	77.4365	172	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.54	97.36	0.89	0.85	3	-
GCA_900764665.1	s__Eubacterium_R sp900764665	77.2675	116	595	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_900539425.1	s__Eubacterium_R sp900539425	76.7398	74	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.89	97.76	0.89	0.86	5	-
GCA_002329285.1	s__Eubacterium_R sp002329285	76.3025	61	595	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	-
--------------------------------------------------------------------------------
[2023-06-04 18:01:04,146] [INFO] GTDB search result was written to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/result_gtdb.tsv
[2023-06-04 18:01:04,146] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:01:04,149] [INFO] DFAST_QC result json was written to GCA_934539595.1_ERR7745890_bin.274_genomic.fna/dqc_result.json
[2023-06-04 18:01:04,150] [INFO] DFAST_QC completed!
[2023-06-04 18:01:04,150] [INFO] Total running time: 0h0m47s