[2023-07-01 01:28:41,749] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:28:41,752] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:28:41,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference
[2023-07-01 01:28:43,021] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:28:43,022] [INFO] Task started: Prodigal
[2023-07-01 01:28:43,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e4309e5-ad82-4b70-b75a-cee75dc420f3/GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna.gz | prodigal -d GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/cds.fna -a GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:28:53,307] [INFO] Task succeeded: Prodigal
[2023-07-01 01:28:53,307] [INFO] Task started: HMMsearch
[2023-07-01 01:28:53,307] [INFO] Running command: hmmsearch --tblout GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/reference_markers.hmm GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:28:53,601] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:28:53,603] [INFO] Found 6/6 markers.
[2023-07-01 01:28:53,661] [INFO] Query marker FASTA was written to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/markers.fasta
[2023-07-01 01:28:53,662] [INFO] Task started: Blastn
[2023-07-01 01:28:53,662] [INFO] Running command: blastn -query GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/markers.fasta -db /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/reference_markers.fasta -out GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:28:54,240] [INFO] Task succeeded: Blastn
[2023-07-01 01:28:54,279] [INFO] Selected 14 target genomes.
[2023-07-01 01:28:54,280] [INFO] Target genome list was writen to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/target_genomes.txt
[2023-07-01 01:28:54,286] [INFO] Task started: fastANI
[2023-07-01 01:28:54,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4309e5-ad82-4b70-b75a-cee75dc420f3/GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna.gz --refList GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/target_genomes.txt --output GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:29:04,104] [INFO] Task succeeded: fastANI
[2023-07-01 01:29:04,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:29:04,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:29:04,107] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:29:04,108] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 01:29:04,108] [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
--------------------------------------------------------------------------------
[2023-07-01 01:29:04,114] [INFO] DFAST Taxonomy check result was written to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/tc_result.tsv
[2023-07-01 01:29:04,115] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:29:04,115] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:29:04,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/checkm_data
[2023-07-01 01:29:04,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:29:04,171] [INFO] Task started: CheckM
[2023-07-01 01:29:04,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/checkm_input GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/checkm_result
[2023-07-01 01:29:38,789] [INFO] Task succeeded: CheckM
[2023-07-01 01:29:38,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.23%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:29:38,813] [INFO] ===== Completeness check finished =====
[2023-07-01 01:29:38,814] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:29:38,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/markers.fasta)
[2023-07-01 01:29:38,814] [INFO] Task started: Blastn
[2023-07-01 01:29:38,815] [INFO] Running command: blastn -query GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/markers.fasta -db /var/lib/cwl/stgff42d8d2-55c3-4016-a421-470b21715ad4/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:29:39,595] [INFO] Task succeeded: Blastn
[2023-07-01 01:29:39,600] [INFO] Selected 18 target genomes.
[2023-07-01 01:29:39,600] [INFO] Target genome list was writen to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:29:39,618] [INFO] Task started: fastANI
[2023-07-01 01:29:39,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4309e5-ad82-4b70-b75a-cee75dc420f3/GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna.gz --refList GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/target_genomes_gtdb.txt --output GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:29:53,032] [INFO] Task succeeded: fastANI
[2023-07-01 01:29:53,039] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:29:53,039] [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_903821495.1	s__CAIJLM01 sp903821495	99.8467	1160	1230	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__Chthonomonadaceae;g__CAIJLM01	95.0	99.85	99.85	0.94	0.93	3	conclusive
GCA_900299305.1	s__CAIJLM01 sp900299305	77.0969	393	1230	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__Chthonomonadaceae;g__CAIJLM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:29:53,041] [INFO] GTDB search result was written to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/result_gtdb.tsv
[2023-07-01 01:29:53,042] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:29:53,044] [INFO] DFAST_QC result json was written to GCA_903894435.1_freshwater_MAG_---_Umea1p3_bin-478_genomic.fna/dqc_result.json
[2023-07-01 01:29:53,044] [INFO] DFAST_QC completed!
[2023-07-01 01:29:53,044] [INFO] Total running time: 0h1m11s