[2023-06-05 05:03:04,957] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:03:04,971] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:03:04,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference
[2023-06-05 05:03:06,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:03:06,626] [INFO] Task started: Prodigal
[2023-06-05 05:03:06,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg706c87b4-a1fd-4472-9068-0e83c11be151/GCA_934487215.1_ERR7746688_bin.427_genomic.fna.gz | prodigal -d GCA_934487215.1_ERR7746688_bin.427_genomic.fna/cds.fna -a GCA_934487215.1_ERR7746688_bin.427_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:03:10,779] [INFO] Task succeeded: Prodigal
[2023-06-05 05:03:10,779] [INFO] Task started: HMMsearch
[2023-06-05 05:03:10,779] [INFO] Running command: hmmsearch --tblout GCA_934487215.1_ERR7746688_bin.427_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/reference_markers.hmm GCA_934487215.1_ERR7746688_bin.427_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:03:11,024] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:03:11,026] [INFO] Found 6/6 markers.
[2023-06-05 05:03:11,052] [INFO] Query marker FASTA was written to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/markers.fasta
[2023-06-05 05:03:11,052] [INFO] Task started: Blastn
[2023-06-05 05:03:11,052] [INFO] Running command: blastn -query GCA_934487215.1_ERR7746688_bin.427_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/reference_markers.fasta -out GCA_934487215.1_ERR7746688_bin.427_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:11,662] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:11,666] [INFO] Selected 18 target genomes.
[2023-06-05 05:03:11,667] [INFO] Target genome list was writen to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/target_genomes.txt
[2023-06-05 05:03:11,669] [INFO] Task started: fastANI
[2023-06-05 05:03:11,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg706c87b4-a1fd-4472-9068-0e83c11be151/GCA_934487215.1_ERR7746688_bin.427_genomic.fna.gz --refList GCA_934487215.1_ERR7746688_bin.427_genomic.fna/target_genomes.txt --output GCA_934487215.1_ERR7746688_bin.427_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:03:18,868] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:18,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:03:18,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:03:18,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:03:18,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:03:18,872] [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
--------------------------------------------------------------------------------
[2023-06-05 05:03:18,874] [INFO] DFAST Taxonomy check result was written to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/tc_result.tsv
[2023-06-05 05:03:18,874] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:03:18,875] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:03:18,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/checkm_data
[2023-06-05 05:03:18,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:03:18,904] [INFO] Task started: CheckM
[2023-06-05 05:03:18,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934487215.1_ERR7746688_bin.427_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934487215.1_ERR7746688_bin.427_genomic.fna/checkm_input GCA_934487215.1_ERR7746688_bin.427_genomic.fna/checkm_result
[2023-06-05 05:03:38,857] [INFO] Task succeeded: CheckM
[2023-06-05 05:03:38,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:03:38,880] [INFO] ===== Completeness check finished =====
[2023-06-05 05:03:38,881] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:03:38,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934487215.1_ERR7746688_bin.427_genomic.fna/markers.fasta)
[2023-06-05 05:03:38,881] [INFO] Task started: Blastn
[2023-06-05 05:03:38,882] [INFO] Running command: blastn -query GCA_934487215.1_ERR7746688_bin.427_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d24fe92-2d79-4688-9d51-6168b5f00b70/dqc_reference/reference_markers_gtdb.fasta -out GCA_934487215.1_ERR7746688_bin.427_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:39,916] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:39,922] [INFO] Selected 24 target genomes.
[2023-06-05 05:03:39,922] [INFO] Target genome list was writen to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:03:39,931] [INFO] Task started: fastANI
[2023-06-05 05:03:39,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg706c87b4-a1fd-4472-9068-0e83c11be151/GCA_934487215.1_ERR7746688_bin.427_genomic.fna.gz --refList GCA_934487215.1_ERR7746688_bin.427_genomic.fna/target_genomes_gtdb.txt --output GCA_934487215.1_ERR7746688_bin.427_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:03:48,850] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:48,866] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:03:48,867] [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_900770195.1	s__Ruminococcus_C sp900770195	98.7074	577	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900554975.1	s__UBA1394 sp900554975	77.489	51	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	98.07	98.05	0.85	0.82	3	-
GCA_015066715.1	s__UBA1394 sp015066715	77.3005	70	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438605.1	s__Ruminococcus sp002438605	77.1274	99	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.60	98.45	0.90	0.84	7	-
GCA_900551505.1	s__UBA5884 sp900551505	77.069	50	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884	95.0	99.59	99.59	0.90	0.90	2	-
GCA_017523285.1	s__Ruminococcus sp017523285	77.0596	88	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.29	98.01	0.84	0.78	3	-
GCA_902362965.1	s__UBA1394 sp900066845	76.9603	69	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	98.61	98.18	0.90	0.86	6	-
GCA_002431975.1	s__UBA5884 sp002431975	76.7639	79	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884	95.0	99.32	99.20	0.85	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-05 05:03:48,869] [INFO] GTDB search result was written to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/result_gtdb.tsv
[2023-06-05 05:03:48,870] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:03:48,873] [INFO] DFAST_QC result json was written to GCA_934487215.1_ERR7746688_bin.427_genomic.fna/dqc_result.json
[2023-06-05 05:03:48,874] [INFO] DFAST_QC completed!
[2023-06-05 05:03:48,874] [INFO] Total running time: 0h0m44s