[2023-06-30 00:55:30,206] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:30,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:30,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference
[2023-06-30 00:55:31,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:31,517] [INFO] Task started: Prodigal
[2023-06-30 00:55:31,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dd0757d-7b3f-4f8d-87b4-401f1c5b0761/GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna.gz | prodigal -d GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/cds.fna -a GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:39,692] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:39,692] [INFO] Task started: HMMsearch
[2023-06-30 00:55:39,693] [INFO] Running command: hmmsearch --tblout GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/reference_markers.hmm GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:39,883] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:39,885] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5dd0757d-7b3f-4f8d-87b4-401f1c5b0761/GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna.gz]
[2023-06-30 00:55:39,907] [INFO] Query marker FASTA was written to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/markers.fasta
[2023-06-30 00:55:39,907] [INFO] Task started: Blastn
[2023-06-30 00:55:39,907] [INFO] Running command: blastn -query GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/markers.fasta -db /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/reference_markers.fasta -out GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:40,425] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:40,429] [INFO] Selected 10 target genomes.
[2023-06-30 00:55:40,429] [INFO] Target genome list was writen to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/target_genomes.txt
[2023-06-30 00:55:40,430] [INFO] Task started: fastANI
[2023-06-30 00:55:40,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dd0757d-7b3f-4f8d-87b4-401f1c5b0761/GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna.gz --refList GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/target_genomes.txt --output GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:55:45,449] [INFO] Task succeeded: fastANI
[2023-06-30 00:55:45,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:55:45,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:55:45,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:55:45,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:55:45,454] [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 00:55:45,456] [INFO] DFAST Taxonomy check result was written to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/tc_result.tsv
[2023-06-30 00:55:45,457] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:55:45,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:55:45,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/checkm_data
[2023-06-30 00:55:45,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:55:45,481] [INFO] Task started: CheckM
[2023-06-30 00:55:45,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/checkm_input GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/checkm_result
[2023-06-30 00:56:14,239] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:14,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 28.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:14,258] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:14,259] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:14,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/markers.fasta)
[2023-06-30 00:56:14,260] [INFO] Task started: Blastn
[2023-06-30 00:56:14,260] [INFO] Running command: blastn -query GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/markers.fasta -db /var/lib/cwl/stg6589c1db-87df-42b3-aae4-5d82c50dcb92/dqc_reference/reference_markers_gtdb.fasta -out GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:14,807] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:14,811] [INFO] Selected 11 target genomes.
[2023-06-30 00:56:14,811] [INFO] Target genome list was writen to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:14,817] [INFO] Task started: fastANI
[2023-06-30 00:56:14,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dd0757d-7b3f-4f8d-87b4-401f1c5b0761/GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna.gz --refList GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/target_genomes_gtdb.txt --output GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:56:20,478] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:20,489] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:56:20,490] [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_903934745.1	s__Cyanobium sp903934745	98.1007	128	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	98.56	98.31	0.81	0.80	4	conclusive
GCA_903823115.1	s__Cyanobium sp903823115	86.5803	131	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.94	99.88	0.97	0.96	6	-
GCA_903831165.1	s__Cyanobium sp903831165	82.1988	96	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.25	99.25	0.81	0.81	2	-
GCA_903882285.1	s__Cyanobium sp903882285	80.3991	102	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
GCF_015840715.1	s__Cyanobium sp015840715	80.1118	98	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252705.1	s__Vulcanococcus limneticus	79.7629	98	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038415.1	s__Cyanobium sp019038415	79.6332	99	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000708525.1	s__Cyanobium sp000708525	79.555	97	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191755.1	s__Cyanobium sp014191755	79.2963	86	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882415.1	s__Vulcanococcus sp016882415	79.165	58	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280235.1	s__NIES-981 sp014280235	78.9176	95	135	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	97.33	97.33	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 00:56:20,492] [INFO] GTDB search result was written to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/result_gtdb.tsv
[2023-06-30 00:56:20,492] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:56:20,495] [INFO] DFAST_QC result json was written to GCA_903945295.1_freshwater_MAG_---_Loc090907-8-6m_bin-196_genomic.fna/dqc_result.json
[2023-06-30 00:56:20,495] [INFO] DFAST_QC completed!
[2023-06-30 00:56:20,495] [INFO] Total running time: 0h0m50s