[2023-06-30 00:38:45,018] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:38:45,021] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:38:45,022] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference
[2023-06-30 00:38:47,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:38:47,115] [INFO] Task started: Prodigal
[2023-06-30 00:38:47,116] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfe06106-f2fb-4b61-bb86-654564b420fe/GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna.gz | prodigal -d GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/cds.fna -a GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:38:49,759] [INFO] Task succeeded: Prodigal
[2023-06-30 00:38:49,760] [INFO] Task started: HMMsearch
[2023-06-30 00:38:49,760] [INFO] Running command: hmmsearch --tblout GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/reference_markers.hmm GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:38:50,020] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:38:50,022] [INFO] Found 6/6 markers.
[2023-06-30 00:38:50,039] [INFO] Query marker FASTA was written to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/markers.fasta
[2023-06-30 00:38:50,040] [INFO] Task started: Blastn
[2023-06-30 00:38:50,040] [INFO] Running command: blastn -query GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/reference_markers.fasta -out GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:38:51,125] [INFO] Task succeeded: Blastn
[2023-06-30 00:38:51,130] [INFO] Selected 20 target genomes.
[2023-06-30 00:38:51,130] [INFO] Target genome list was writen to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/target_genomes.txt
[2023-06-30 00:38:51,135] [INFO] Task started: fastANI
[2023-06-30 00:38:51,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe06106-f2fb-4b61-bb86-654564b420fe/GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna.gz --refList GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/target_genomes.txt --output GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:39:01,544] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:01,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:39:01,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:39:01,548] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:39:01,549] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:39:01,549] [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 00:39:01,551] [INFO] DFAST Taxonomy check result was written to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/tc_result.tsv
[2023-06-30 00:39:01,552] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:39:01,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:39:01,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/checkm_data
[2023-06-30 00:39:01,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:39:01,573] [INFO] Task started: CheckM
[2023-06-30 00:39:01,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/checkm_input GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/checkm_result
[2023-06-30 00:39:18,452] [INFO] Task succeeded: CheckM
[2023-06-30 00:39:18,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 7.24%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-30 00:39:18,479] [INFO] ===== Completeness check finished =====
[2023-06-30 00:39:18,480] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:39:18,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/markers.fasta)
[2023-06-30 00:39:18,480] [INFO] Task started: Blastn
[2023-06-30 00:39:18,480] [INFO] Running command: blastn -query GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa60834-0694-424e-86cc-b31654f7d960/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:39:19,664] [INFO] Task succeeded: Blastn
[2023-06-30 00:39:19,668] [INFO] Selected 10 target genomes.
[2023-06-30 00:39:19,669] [INFO] Target genome list was writen to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:39:19,675] [INFO] Task started: fastANI
[2023-06-30 00:39:19,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe06106-f2fb-4b61-bb86-654564b420fe/GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna.gz --refList GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/target_genomes_gtdb.txt --output GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:39:22,208] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:22,216] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:39:22,217] [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_903871555.1	s__AAA044-D11 sp903871555	99.6555	313	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	conclusive
GCA_007280395.1	s__AAA044-D11 sp007280395	82.3301	206	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000485495.1	s__AAA044-D11 sp000485495	82.1187	181	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701575.1	s__AAA044-D11 sp009701575	81.8393	220	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726125.1	s__AAA044-D11 sp009726125	81.7035	248	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_009705075.1	s__AAA044-D11 sp009705075	81.1574	131	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.34	98.34	0.77	0.77	2	-
GCA_009702205.1	s__AAA044-D11 sp009702205	80.4325	165	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701525.1	s__AAA044-D11 sp009701525	80.3929	169	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367715.1	s__AAA044-D11 sp002367715	79.4616	155	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.65	98.65	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 00:39:22,219] [INFO] GTDB search result was written to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/result_gtdb.tsv
[2023-06-30 00:39:22,219] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:39:22,222] [INFO] DFAST_QC result json was written to GCA_903830205.1_freshwater_MAG_---_KT2_bin-903_genomic.fna/dqc_result.json
[2023-06-30 00:39:22,222] [INFO] DFAST_QC completed!
[2023-06-30 00:39:22,222] [INFO] Total running time: 0h0m37s