[2023-06-05 00:14:23,717] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:23,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:23,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference
[2023-06-05 00:14:25,050] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:25,051] [INFO] Task started: Prodigal
[2023-06-05 00:14:25,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg16318c9f-da3b-4a55-bfca-818eed71ac89/GCA_934131005.1_ERR7746184_bin.254_genomic.fna.gz | prodigal -d GCA_934131005.1_ERR7746184_bin.254_genomic.fna/cds.fna -a GCA_934131005.1_ERR7746184_bin.254_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:27,076] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:27,076] [INFO] Task started: HMMsearch
[2023-06-05 00:14:27,076] [INFO] Running command: hmmsearch --tblout GCA_934131005.1_ERR7746184_bin.254_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/reference_markers.hmm GCA_934131005.1_ERR7746184_bin.254_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:27,342] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:27,344] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg16318c9f-da3b-4a55-bfca-818eed71ac89/GCA_934131005.1_ERR7746184_bin.254_genomic.fna.gz]
[2023-06-05 00:14:27,364] [INFO] Query marker FASTA was written to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/markers.fasta
[2023-06-05 00:14:27,365] [INFO] Task started: Blastn
[2023-06-05 00:14:27,365] [INFO] Running command: blastn -query GCA_934131005.1_ERR7746184_bin.254_genomic.fna/markers.fasta -db /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/reference_markers.fasta -out GCA_934131005.1_ERR7746184_bin.254_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:28,668] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:28,674] [INFO] Selected 25 target genomes.
[2023-06-05 00:14:28,674] [INFO] Target genome list was writen to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/target_genomes.txt
[2023-06-05 00:14:28,760] [INFO] Task started: fastANI
[2023-06-05 00:14:28,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg16318c9f-da3b-4a55-bfca-818eed71ac89/GCA_934131005.1_ERR7746184_bin.254_genomic.fna.gz --refList GCA_934131005.1_ERR7746184_bin.254_genomic.fna/target_genomes.txt --output GCA_934131005.1_ERR7746184_bin.254_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:37,278] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:37,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:37,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:37,281] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:37,281] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:14:37,281] [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 00:14:37,283] [INFO] DFAST Taxonomy check result was written to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/tc_result.tsv
[2023-06-05 00:14:37,284] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:37,284] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:37,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/checkm_data
[2023-06-05 00:14:37,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:37,309] [INFO] Task started: CheckM
[2023-06-05 00:14:37,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934131005.1_ERR7746184_bin.254_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934131005.1_ERR7746184_bin.254_genomic.fna/checkm_input GCA_934131005.1_ERR7746184_bin.254_genomic.fna/checkm_result
[2023-06-05 00:14:51,960] [INFO] Task succeeded: CheckM
[2023-06-05 00:14:51,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:14:52,001] [INFO] ===== Completeness check finished =====
[2023-06-05 00:14:52,001] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:14:52,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934131005.1_ERR7746184_bin.254_genomic.fna/markers.fasta)
[2023-06-05 00:14:52,002] [INFO] Task started: Blastn
[2023-06-05 00:14:52,002] [INFO] Running command: blastn -query GCA_934131005.1_ERR7746184_bin.254_genomic.fna/markers.fasta -db /var/lib/cwl/stg70009cc1-bdd9-437b-aafc-b6d013278815/dqc_reference/reference_markers_gtdb.fasta -out GCA_934131005.1_ERR7746184_bin.254_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:52,884] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:52,888] [INFO] Selected 25 target genomes.
[2023-06-05 00:14:52,888] [INFO] Target genome list was writen to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:14:52,899] [INFO] Task started: fastANI
[2023-06-05 00:14:52,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg16318c9f-da3b-4a55-bfca-818eed71ac89/GCA_934131005.1_ERR7746184_bin.254_genomic.fna.gz --refList GCA_934131005.1_ERR7746184_bin.254_genomic.fna/target_genomes_gtdb.txt --output GCA_934131005.1_ERR7746184_bin.254_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:14:57,557] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:57,566] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:14:57,567] [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_017432825.1	s__RUG11198 sp017432825	77.769	112	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409025.1	s__RUG705 sp017409025	76.3949	59	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG705	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	76.2808	55	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437895.1	s__CAG-914 sp000437895	76.1416	58	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-914	95.0	98.02	96.45	0.80	0.69	5	-
--------------------------------------------------------------------------------
[2023-06-05 00:14:57,569] [INFO] GTDB search result was written to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/result_gtdb.tsv
[2023-06-05 00:14:57,569] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:14:57,572] [INFO] DFAST_QC result json was written to GCA_934131005.1_ERR7746184_bin.254_genomic.fna/dqc_result.json
[2023-06-05 00:14:57,572] [INFO] DFAST_QC completed!
[2023-06-05 00:14:57,572] [INFO] Total running time: 0h0m34s