[2023-06-30 13:27:47,712] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:27:47,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:27:47,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference
[2023-06-30 13:27:49,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:27:49,165] [INFO] Task started: Prodigal
[2023-06-30 13:27:49,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg787758f2-ee34-4878-a0b9-aa24db82eee1/GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna.gz | prodigal -d GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/cds.fna -a GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:27:55,504] [INFO] Task succeeded: Prodigal
[2023-06-30 13:27:55,505] [INFO] Task started: HMMsearch
[2023-06-30 13:27:55,505] [INFO] Running command: hmmsearch --tblout GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/reference_markers.hmm GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:27:55,746] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:27:55,747] [INFO] Found 6/6 markers.
[2023-06-30 13:27:55,767] [INFO] Query marker FASTA was written to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/markers.fasta
[2023-06-30 13:27:55,768] [INFO] Task started: Blastn
[2023-06-30 13:27:55,768] [INFO] Running command: blastn -query GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/markers.fasta -db /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/reference_markers.fasta -out GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:27:56,437] [INFO] Task succeeded: Blastn
[2023-06-30 13:27:56,442] [INFO] Selected 22 target genomes.
[2023-06-30 13:27:56,443] [INFO] Target genome list was writen to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/target_genomes.txt
[2023-06-30 13:27:56,450] [INFO] Task started: fastANI
[2023-06-30 13:27:56,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg787758f2-ee34-4878-a0b9-aa24db82eee1/GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna.gz --refList GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/target_genomes.txt --output GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:28:06,070] [INFO] Task succeeded: fastANI
[2023-06-30 13:28:06,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:28:06,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:28:06,073] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:28:06,073] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:28:06,073] [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
--------------------------------------------------------------------------------
[2023-06-30 13:28:06,075] [INFO] DFAST Taxonomy check result was written to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/tc_result.tsv
[2023-06-30 13:28:06,075] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:28:06,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:28:06,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/checkm_data
[2023-06-30 13:28:06,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:28:06,102] [INFO] Task started: CheckM
[2023-06-30 13:28:06,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/checkm_input GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/checkm_result
[2023-06-30 13:28:31,351] [INFO] Task succeeded: CheckM
[2023-06-30 13:28:31,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:28:31,373] [INFO] ===== Completeness check finished =====
[2023-06-30 13:28:31,373] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:28:31,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/markers.fasta)
[2023-06-30 13:28:31,374] [INFO] Task started: Blastn
[2023-06-30 13:28:31,374] [INFO] Running command: blastn -query GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/markers.fasta -db /var/lib/cwl/stg09aed1ad-7d1f-4e9d-9ed4-a0756edd2f9f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:28:32,231] [INFO] Task succeeded: Blastn
[2023-06-30 13:28:32,236] [INFO] Selected 9 target genomes.
[2023-06-30 13:28:32,236] [INFO] Target genome list was writen to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:28:32,243] [INFO] Task started: fastANI
[2023-06-30 13:28:32,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg787758f2-ee34-4878-a0b9-aa24db82eee1/GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna.gz --refList GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/target_genomes_gtdb.txt --output GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:28:35,048] [INFO] Task succeeded: fastANI
[2023-06-30 13:28:35,060] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:28:35,061] [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_903937405.1	s__UBA2645 sp903937405	99.9947	497	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.33	98.10	0.93	0.79	16	conclusive
GCA_903879805.1	s__UBA2645 sp903879805	79.0625	236	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898475.1	s__UBA2645 sp903898475	78.8501	193	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.93	99.93	0.95	0.95	2	-
GCA_017999675.1	s__UBA2645 sp017999675	78.7582	217	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359655.1	s__UBA2645 sp002359655	78.3422	188	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.96	99.93	0.97	0.95	3	-
GCA_018969185.1	s__UBA2645 sp018969185	77.5297	156	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882165.1	s__UBA2645 sp016882165	77.0244	91	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959715.1	s__SYAR01 sp903959715	76.5441	87	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:28:35,063] [INFO] GTDB search result was written to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/result_gtdb.tsv
[2023-06-30 13:28:35,064] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:28:35,066] [INFO] DFAST_QC result json was written to GCA_903953375.1_freshwater_MAG_---_Loc080925-5m_bin-0951_genomic.fna/dqc_result.json
[2023-06-30 13:28:35,067] [INFO] DFAST_QC completed!
[2023-06-30 13:28:35,067] [INFO] Total running time: 0h0m47s