[2023-06-28 12:49:24,093] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:24,096] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:24,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference
[2023-06-28 12:49:25,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:25,416] [INFO] Task started: Prodigal
[2023-06-28 12:49:25,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8f1b433-a1e4-4b0c-811f-79c6e366d2f4/GCA_944385015.1_BRZ_AR_bin84_genomic.fna.gz | prodigal -d GCA_944385015.1_BRZ_AR_bin84_genomic.fna/cds.fna -a GCA_944385015.1_BRZ_AR_bin84_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:30,589] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:30,590] [INFO] Task started: HMMsearch
[2023-06-28 12:49:30,590] [INFO] Running command: hmmsearch --tblout GCA_944385015.1_BRZ_AR_bin84_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/reference_markers.hmm GCA_944385015.1_BRZ_AR_bin84_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:30,851] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:30,853] [INFO] Found 6/6 markers.
[2023-06-28 12:49:30,875] [INFO] Query marker FASTA was written to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/markers.fasta
[2023-06-28 12:49:30,875] [INFO] Task started: Blastn
[2023-06-28 12:49:30,876] [INFO] Running command: blastn -query GCA_944385015.1_BRZ_AR_bin84_genomic.fna/markers.fasta -db /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/reference_markers.fasta -out GCA_944385015.1_BRZ_AR_bin84_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:31,519] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:31,523] [INFO] Selected 21 target genomes.
[2023-06-28 12:49:31,523] [INFO] Target genome list was writen to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/target_genomes.txt
[2023-06-28 12:49:31,525] [INFO] Task started: fastANI
[2023-06-28 12:49:31,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8f1b433-a1e4-4b0c-811f-79c6e366d2f4/GCA_944385015.1_BRZ_AR_bin84_genomic.fna.gz --refList GCA_944385015.1_BRZ_AR_bin84_genomic.fna/target_genomes.txt --output GCA_944385015.1_BRZ_AR_bin84_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:40,676] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:40,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:40,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:40,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:40,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:49:40,679] [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
--------------------------------------------------------------------------------
[2023-06-28 12:49:40,681] [INFO] DFAST Taxonomy check result was written to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/tc_result.tsv
[2023-06-28 12:49:40,682] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:40,682] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:40,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/checkm_data
[2023-06-28 12:49:40,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:40,712] [INFO] Task started: CheckM
[2023-06-28 12:49:40,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385015.1_BRZ_AR_bin84_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385015.1_BRZ_AR_bin84_genomic.fna/checkm_input GCA_944385015.1_BRZ_AR_bin84_genomic.fna/checkm_result
[2023-06-28 12:50:03,180] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:03,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:03,208] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:03,209] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:03,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385015.1_BRZ_AR_bin84_genomic.fna/markers.fasta)
[2023-06-28 12:50:03,210] [INFO] Task started: Blastn
[2023-06-28 12:50:03,210] [INFO] Running command: blastn -query GCA_944385015.1_BRZ_AR_bin84_genomic.fna/markers.fasta -db /var/lib/cwl/stg5146ab78-997d-4670-a8de-c2ef2bc83a81/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385015.1_BRZ_AR_bin84_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:04,264] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:04,268] [INFO] Selected 12 target genomes.
[2023-06-28 12:50:04,268] [INFO] Target genome list was writen to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:04,271] [INFO] Task started: fastANI
[2023-06-28 12:50:04,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8f1b433-a1e4-4b0c-811f-79c6e366d2f4/GCA_944385015.1_BRZ_AR_bin84_genomic.fna.gz --refList GCA_944385015.1_BRZ_AR_bin84_genomic.fna/target_genomes_gtdb.txt --output GCA_944385015.1_BRZ_AR_bin84_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:08,782] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:08,801] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:08,801] [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_900546785.1	s__Eubacterium_R faecipullorum	97.5483	543	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.03	98.11	0.88	0.82	3	conclusive
GCA_000431535.1	s__Eubacterium_R faecale	81.643	439	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.79	98.10	0.92	0.82	9	-
GCA_900539845.1	s__Eubacterium_R faecavium	80.0082	357	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.18	98.52	0.94	0.90	5	-
GCA_900539425.1	s__Eubacterium_R sp900539425	79.6326	330	671	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_900547915.1	s__Eubacterium_R sp900547915	79.4684	195	671	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_000433975.1	s__Eubacterium_R sp000433975	78.1195	212	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.06	97.98	0.95	0.88	9	-
GCA_900539775.1	s__Eubacterium_R sp900539775	77.9957	181	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.81	98.50	0.97	0.95	6	-
GCA_900539325.1	s__Eubacterium_R sp900539325	77.6511	54	671	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_902797915.1	s__Eubacterium_R sp902797915	77.4995	97	671	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_003526845.1	s__Eubacterium_R sp003526845	77.0881	59	671	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	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:08,805] [INFO] GTDB search result was written to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:08,805] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:08,808] [INFO] DFAST_QC result json was written to GCA_944385015.1_BRZ_AR_bin84_genomic.fna/dqc_result.json
[2023-06-28 12:50:08,808] [INFO] DFAST_QC completed!
[2023-06-28 12:50:08,808] [INFO] Total running time: 0h0m45s