[2023-06-30 03:32:50,071] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:32:50,075] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:32:50,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference
[2023-06-30 03:32:51,330] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:32:51,331] [INFO] Task started: Prodigal
[2023-06-30 03:32:51,331] [INFO] Running command: gunzip -c /var/lib/cwl/stg5643b076-f92a-457d-885f-069d01b6d442/GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna.gz | prodigal -d GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/cds.fna -a GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:32:54,567] [INFO] Task succeeded: Prodigal
[2023-06-30 03:32:54,568] [INFO] Task started: HMMsearch
[2023-06-30 03:32:54,568] [INFO] Running command: hmmsearch --tblout GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/reference_markers.hmm GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:32:54,804] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:32:54,805] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5643b076-f92a-457d-885f-069d01b6d442/GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna.gz]
[2023-06-30 03:32:54,826] [INFO] Query marker FASTA was written to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/markers.fasta
[2023-06-30 03:32:54,827] [INFO] Task started: Blastn
[2023-06-30 03:32:54,827] [INFO] Running command: blastn -query GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/markers.fasta -db /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/reference_markers.fasta -out GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:32:55,427] [INFO] Task succeeded: Blastn
[2023-06-30 03:32:55,431] [INFO] Selected 20 target genomes.
[2023-06-30 03:32:55,431] [INFO] Target genome list was writen to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/target_genomes.txt
[2023-06-30 03:32:55,436] [INFO] Task started: fastANI
[2023-06-30 03:32:55,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg5643b076-f92a-457d-885f-069d01b6d442/GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna.gz --refList GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/target_genomes.txt --output GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:05,897] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:05,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:05,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:05,900] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:05,900] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 03:33:05,900] [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 03:33:05,902] [INFO] DFAST Taxonomy check result was written to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/tc_result.tsv
[2023-06-30 03:33:05,903] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:05,903] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:05,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/checkm_data
[2023-06-30 03:33:05,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:05,939] [INFO] Task started: CheckM
[2023-06-30 03:33:05,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/checkm_input GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/checkm_result
[2023-06-30 03:33:23,540] [INFO] Task succeeded: CheckM
[2023-06-30 03:33:23,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:33:23,561] [INFO] ===== Completeness check finished =====
[2023-06-30 03:33:23,562] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:33:23,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/markers.fasta)
[2023-06-30 03:33:23,563] [INFO] Task started: Blastn
[2023-06-30 03:33:23,563] [INFO] Running command: blastn -query GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/markers.fasta -db /var/lib/cwl/stgffae0e52-5867-4e03-a337-fe4bd04f32f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:24,393] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:24,397] [INFO] Selected 9 target genomes.
[2023-06-30 03:33:24,397] [INFO] Target genome list was writen to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:33:24,413] [INFO] Task started: fastANI
[2023-06-30 03:33:24,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg5643b076-f92a-457d-885f-069d01b6d442/GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna.gz --refList GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/target_genomes_gtdb.txt --output GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:33:26,686] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:26,694] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:33:26,695] [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_903953805.1	s__PALSA-747 sp903953805	99.219	286	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.20	99.17	0.84	0.84	5	conclusive
GCA_903895995.1	s__PALSA-747 sp903895995	79.9899	165	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.95	98.41	0.92	0.88	16	-
GCA_903821145.1	s__PALSA-747 sp903821145	79.606	155	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.30	98.98	0.89	0.82	16	-
GCA_903834515.1	s__PALSA-747 sp903834515	79.3144	158	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.03	97.42	0.96	0.95	4	-
GCA_903843225.1	s__PALSA-747 sp903843225	78.9176	152	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.35	99.04	0.93	0.89	10	-
GCA_903854185.1	s__PALSA-747 sp903854185	77.362	68	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838035.1	s__AAA044-D11 sp903838035	77.3083	55	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.47	98.88	0.87	0.84	8	-
GCA_903919375.1	s__AAA044-D11 sp903919375	77.1529	63	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.04	98.97	0.88	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-30 03:33:26,697] [INFO] GTDB search result was written to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/result_gtdb.tsv
[2023-06-30 03:33:26,698] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:33:26,701] [INFO] DFAST_QC result json was written to GCA_903939455.1_freshwater_MAG_---_E-2_bin-023_genomic.fna/dqc_result.json
[2023-06-30 03:33:26,701] [INFO] DFAST_QC completed!
[2023-06-30 03:33:26,701] [INFO] Total running time: 0h0m37s