[2023-06-30 20:25:34,952] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:25:34,954] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:25:34,954] [INFO] DQC Reference Directory: /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference
[2023-06-30 20:25:36,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:25:36,289] [INFO] Task started: Prodigal
[2023-06-30 20:25:36,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg3baad429-f52d-4575-af15-4aeaeff8c7d4/GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna.gz | prodigal -d GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/cds.fna -a GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:25:45,620] [INFO] Task succeeded: Prodigal
[2023-06-30 20:25:45,620] [INFO] Task started: HMMsearch
[2023-06-30 20:25:45,620] [INFO] Running command: hmmsearch --tblout GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/reference_markers.hmm GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:25:45,940] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:25:45,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3baad429-f52d-4575-af15-4aeaeff8c7d4/GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna.gz]
[2023-06-30 20:25:45,986] [INFO] Query marker FASTA was written to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/markers.fasta
[2023-06-30 20:25:45,986] [INFO] Task started: Blastn
[2023-06-30 20:25:45,987] [INFO] Running command: blastn -query GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/markers.fasta -db /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/reference_markers.fasta -out GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:25:46,556] [INFO] Task succeeded: Blastn
[2023-06-30 20:25:46,575] [INFO] Selected 15 target genomes.
[2023-06-30 20:25:46,576] [INFO] Target genome list was writen to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/target_genomes.txt
[2023-06-30 20:25:46,578] [INFO] Task started: fastANI
[2023-06-30 20:25:46,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baad429-f52d-4575-af15-4aeaeff8c7d4/GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna.gz --refList GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/target_genomes.txt --output GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:25:59,414] [INFO] Task succeeded: fastANI
[2023-06-30 20:25:59,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:25:59,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:25:59,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:25:59,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:25:59,416] [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 20:25:59,418] [INFO] DFAST Taxonomy check result was written to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/tc_result.tsv
[2023-06-30 20:25:59,419] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:25:59,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:25:59,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/checkm_data
[2023-06-30 20:25:59,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:25:59,478] [INFO] Task started: CheckM
[2023-06-30 20:25:59,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/checkm_input GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/checkm_result
[2023-06-30 20:26:33,296] [INFO] Task succeeded: CheckM
[2023-06-30 20:26:33,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.34%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 20:26:33,321] [INFO] ===== Completeness check finished =====
[2023-06-30 20:26:33,322] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:26:33,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/markers.fasta)
[2023-06-30 20:26:33,323] [INFO] Task started: Blastn
[2023-06-30 20:26:33,323] [INFO] Running command: blastn -query GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/markers.fasta -db /var/lib/cwl/stge72ca570-48c6-43b6-8791-0bafa8649af5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:26:34,124] [INFO] Task succeeded: Blastn
[2023-06-30 20:26:34,128] [INFO] Selected 12 target genomes.
[2023-06-30 20:26:34,129] [INFO] Target genome list was writen to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:26:34,136] [INFO] Task started: fastANI
[2023-06-30 20:26:34,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baad429-f52d-4575-af15-4aeaeff8c7d4/GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna.gz --refList GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/target_genomes_gtdb.txt --output GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:26:47,467] [INFO] Task succeeded: fastANI
[2023-06-30 20:26:47,489] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:26:47,489] [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_903819605.1	s__Pseudanabaena sp903819605	97.3301	920	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	97.61	97.57	0.80	0.79	3	conclusive
GCA_003242085.1	s__Pseudanabaena frigida	84.4675	896	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251945.1	s__Pseudanabaena sp002251945	81.2038	757	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967015.1	s__Pseudanabaena sp003967015	81.179	748	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002914585.1	s__Pseudanabaena sp002914585	81.107	776	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696925.1	s__Pseudanabaena sp014696925	81.0678	747	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006937785.1	s__Pseudanabaena sp006937785	81.0092	726	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584665.1	s__Pseudanabaena sp016584665	80.8259	782	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249035.1	s__Pseudanabaena sp003249035	80.4462	651	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325645.1	s__Pseudanabaena sp002325645	80.3786	605	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696355.1	s__Pseudanabaena sp014696355	80.1507	603	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696345.1	s__Pseudanabaena sp014696345	78.6247	366	1322	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:26:47,491] [INFO] GTDB search result was written to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/result_gtdb.tsv
[2023-06-30 20:26:47,492] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:26:47,495] [INFO] DFAST_QC result json was written to GCA_903844015.1_freshwater_MAG_---_T7-5_bin-036_genomic.fna/dqc_result.json
[2023-06-30 20:26:47,495] [INFO] DFAST_QC completed!
[2023-06-30 20:26:47,495] [INFO] Total running time: 0h1m13s