[2023-06-28 18:41:22,354] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:22,357] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:22,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference
[2023-06-28 18:41:23,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:23,978] [INFO] Task started: Prodigal
[2023-06-28 18:41:23,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc747b9f-304a-4423-b1e7-6d92333f05be/GCA_017621985.1_ASM1762198v1_genomic.fna.gz | prodigal -d GCA_017621985.1_ASM1762198v1_genomic.fna/cds.fna -a GCA_017621985.1_ASM1762198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:29,641] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:29,642] [INFO] Task started: HMMsearch
[2023-06-28 18:41:29,642] [INFO] Running command: hmmsearch --tblout GCA_017621985.1_ASM1762198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/reference_markers.hmm GCA_017621985.1_ASM1762198v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:29,887] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:29,889] [INFO] Found 6/6 markers.
[2023-06-28 18:41:29,925] [INFO] Query marker FASTA was written to GCA_017621985.1_ASM1762198v1_genomic.fna/markers.fasta
[2023-06-28 18:41:29,925] [INFO] Task started: Blastn
[2023-06-28 18:41:29,926] [INFO] Running command: blastn -query GCA_017621985.1_ASM1762198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/reference_markers.fasta -out GCA_017621985.1_ASM1762198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:30,519] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:30,524] [INFO] Selected 23 target genomes.
[2023-06-28 18:41:30,524] [INFO] Target genome list was writen to GCA_017621985.1_ASM1762198v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:30,531] [INFO] Task started: fastANI
[2023-06-28 18:41:30,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc747b9f-304a-4423-b1e7-6d92333f05be/GCA_017621985.1_ASM1762198v1_genomic.fna.gz --refList GCA_017621985.1_ASM1762198v1_genomic.fna/target_genomes.txt --output GCA_017621985.1_ASM1762198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:43,321] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:43,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:43,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:43,324] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:43,324] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:41:43,324] [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 18:41:43,326] [INFO] DFAST Taxonomy check result was written to GCA_017621985.1_ASM1762198v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:43,327] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:43,327] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:43,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/checkm_data
[2023-06-28 18:41:43,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:43,361] [INFO] Task started: CheckM
[2023-06-28 18:41:43,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621985.1_ASM1762198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621985.1_ASM1762198v1_genomic.fna/checkm_input GCA_017621985.1_ASM1762198v1_genomic.fna/checkm_result
[2023-06-28 18:42:07,676] [INFO] Task succeeded: CheckM
[2023-06-28 18:42:07,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:42:07,698] [INFO] ===== Completeness check finished =====
[2023-06-28 18:42:07,698] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:42:07,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621985.1_ASM1762198v1_genomic.fna/markers.fasta)
[2023-06-28 18:42:07,699] [INFO] Task started: Blastn
[2023-06-28 18:42:07,699] [INFO] Running command: blastn -query GCA_017621985.1_ASM1762198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95eb3d0-e3e5-4602-bb9e-4f71f90852bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621985.1_ASM1762198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:42:08,523] [INFO] Task succeeded: Blastn
[2023-06-28 18:42:08,528] [INFO] Selected 22 target genomes.
[2023-06-28 18:42:08,528] [INFO] Target genome list was writen to GCA_017621985.1_ASM1762198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:42:08,548] [INFO] Task started: fastANI
[2023-06-28 18:42:08,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc747b9f-304a-4423-b1e7-6d92333f05be/GCA_017621985.1_ASM1762198v1_genomic.fna.gz --refList GCA_017621985.1_ASM1762198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621985.1_ASM1762198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:42:20,847] [INFO] Task succeeded: fastANI
[2023-06-28 18:42:20,869] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:42:20,870] [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_910584875.1	s__Eubacterium_F sp910584875	98.2374	668	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.24	98.24	0.92	0.92	2	conclusive
GCA_910574015.1	s__Eubacterium_F sp910574015	79.3088	341	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	99.61	98.86	0.93	0.82	4	-
GCA_910575665.1	s__Eubacterium_F sp910575665	77.4328	85	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.59	95.46	0.90	0.84	7	-
GCA_910577295.1	s__Eubacterium_F sp910577295	77.364	79	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002362575.1	s__Eubacterium_F sp002362575	77.2677	114	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	99.97	99.97	0.97	0.97	2	-
GCA_910589595.1	s__Eubacterium_F sp910589595	77.211	82	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583555.1	s__Eubacterium_F sp910583555	77.1888	90	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584645.1	s__Eubacterium_F sp910584645	77.0996	99	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477605.1	s__Eubacterium_F sp003491505	76.8238	88	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.02	96.96	0.87	0.69	18	-
GCA_002431395.1	s__Eubacterium_F sp002431395	76.7845	53	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433735.1	s__Eubacterium_F sp000433735	76.7418	97	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.51	97.83	0.95	0.95	3	-
GCA_002490465.1	s__Eubacterium_F sp002490465	76.7011	84	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:42:20,872] [INFO] GTDB search result was written to GCA_017621985.1_ASM1762198v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:42:20,873] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:42:20,875] [INFO] DFAST_QC result json was written to GCA_017621985.1_ASM1762198v1_genomic.fna/dqc_result.json
[2023-06-28 18:42:20,876] [INFO] DFAST_QC completed!
[2023-06-28 18:42:20,876] [INFO] Total running time: 0h0m59s