[2023-06-05 04:42:50,847] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:42:50,853] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:42:50,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference
[2023-06-05 04:42:52,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:42:52,115] [INFO] Task started: Prodigal
[2023-06-05 04:42:52,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg734b7481-0fc7-4b6d-a13e-c156a83ae8ce/GCA_934464875.1_ERR7738185_bin.154_genomic.fna.gz | prodigal -d GCA_934464875.1_ERR7738185_bin.154_genomic.fna/cds.fna -a GCA_934464875.1_ERR7738185_bin.154_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:42:57,557] [INFO] Task succeeded: Prodigal
[2023-06-05 04:42:57,558] [INFO] Task started: HMMsearch
[2023-06-05 04:42:57,558] [INFO] Running command: hmmsearch --tblout GCA_934464875.1_ERR7738185_bin.154_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/reference_markers.hmm GCA_934464875.1_ERR7738185_bin.154_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:42:57,800] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:42:57,801] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg734b7481-0fc7-4b6d-a13e-c156a83ae8ce/GCA_934464875.1_ERR7738185_bin.154_genomic.fna.gz]
[2023-06-05 04:42:57,824] [INFO] Query marker FASTA was written to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/markers.fasta
[2023-06-05 04:42:57,824] [INFO] Task started: Blastn
[2023-06-05 04:42:57,824] [INFO] Running command: blastn -query GCA_934464875.1_ERR7738185_bin.154_genomic.fna/markers.fasta -db /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/reference_markers.fasta -out GCA_934464875.1_ERR7738185_bin.154_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:42:58,404] [INFO] Task succeeded: Blastn
[2023-06-05 04:42:58,409] [INFO] Selected 18 target genomes.
[2023-06-05 04:42:58,409] [INFO] Target genome list was writen to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/target_genomes.txt
[2023-06-05 04:42:58,438] [INFO] Task started: fastANI
[2023-06-05 04:42:58,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg734b7481-0fc7-4b6d-a13e-c156a83ae8ce/GCA_934464875.1_ERR7738185_bin.154_genomic.fna.gz --refList GCA_934464875.1_ERR7738185_bin.154_genomic.fna/target_genomes.txt --output GCA_934464875.1_ERR7738185_bin.154_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:43:08,813] [INFO] Task succeeded: fastANI
[2023-06-05 04:43:08,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:43:08,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:43:08,818] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:43:08,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:43:08,818] [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
Ruminococcus callidus	strain=ATCC 27760	GCA_000468015.1	40519	40519	type	True	77.9456	124	558	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:43:08,820] [INFO] DFAST Taxonomy check result was written to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/tc_result.tsv
[2023-06-05 04:43:08,821] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:43:08,821] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:43:08,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/checkm_data
[2023-06-05 04:43:08,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:43:08,847] [INFO] Task started: CheckM
[2023-06-05 04:43:08,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934464875.1_ERR7738185_bin.154_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934464875.1_ERR7738185_bin.154_genomic.fna/checkm_input GCA_934464875.1_ERR7738185_bin.154_genomic.fna/checkm_result
[2023-06-05 04:43:31,937] [INFO] Task succeeded: CheckM
[2023-06-05 04:43:31,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:43:31,960] [INFO] ===== Completeness check finished =====
[2023-06-05 04:43:31,960] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:43:31,961] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934464875.1_ERR7738185_bin.154_genomic.fna/markers.fasta)
[2023-06-05 04:43:31,961] [INFO] Task started: Blastn
[2023-06-05 04:43:31,961] [INFO] Running command: blastn -query GCA_934464875.1_ERR7738185_bin.154_genomic.fna/markers.fasta -db /var/lib/cwl/stg57f744f9-7c4a-4be4-9570-2af0b22d47b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_934464875.1_ERR7738185_bin.154_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:43:32,794] [INFO] Task succeeded: Blastn
[2023-06-05 04:43:32,799] [INFO] Selected 19 target genomes.
[2023-06-05 04:43:32,799] [INFO] Target genome list was writen to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:43:32,945] [INFO] Task started: fastANI
[2023-06-05 04:43:32,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg734b7481-0fc7-4b6d-a13e-c156a83ae8ce/GCA_934464875.1_ERR7738185_bin.154_genomic.fna.gz --refList GCA_934464875.1_ERR7738185_bin.154_genomic.fna/target_genomes_gtdb.txt --output GCA_934464875.1_ERR7738185_bin.154_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:43:41,411] [INFO] Task succeeded: fastANI
[2023-06-05 04:43:41,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:43:41,421] [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_000437255.1	s__Ruminococcus_C sp000437255	98.6802	530	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	99.16	99.04	0.92	0.92	3	conclusive
GCA_000433635.1	s__Ruminococcus_C sp000433635	78.606	137	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.33	97.52	0.89	0.86	9	-
GCA_900545285.1	s__Ruminococcus_C sp900545285	78.3593	119	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.99	98.98	0.87	0.83	3	-
GCA_000980705.1	s__Ruminococcus_C sp000980705	78.3569	113	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.76	98.57	0.85	0.78	6	-
GCF_000468015.1	s__Ruminococcus_C callidus	77.9456	124	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	97.99	97.28	0.85	0.77	9	-
GCA_000437175.1	s__Ruminococcus_C sp000437175	77.8776	120	558	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.59	98.57	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-05 04:43:41,425] [INFO] GTDB search result was written to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/result_gtdb.tsv
[2023-06-05 04:43:41,425] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:43:41,428] [INFO] DFAST_QC result json was written to GCA_934464875.1_ERR7738185_bin.154_genomic.fna/dqc_result.json
[2023-06-05 04:43:41,428] [INFO] DFAST_QC completed!
[2023-06-05 04:43:41,428] [INFO] Total running time: 0h0m51s