[2023-06-30 11:12:40,439] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:12:40,441] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:12:40,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference
[2023-06-30 11:12:41,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:12:41,595] [INFO] Task started: Prodigal
[2023-06-30 11:12:41,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8082932-c686-4afb-8d9b-c4ae51f24467/GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna.gz | prodigal -d GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/cds.fna -a GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:12:44,665] [INFO] Task succeeded: Prodigal
[2023-06-30 11:12:44,666] [INFO] Task started: HMMsearch
[2023-06-30 11:12:44,666] [INFO] Running command: hmmsearch --tblout GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/reference_markers.hmm GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:12:44,825] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:12:44,825] [INFO] Found 6/6 markers.
[2023-06-30 11:12:44,842] [INFO] Query marker FASTA was written to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/markers.fasta
[2023-06-30 11:12:44,842] [INFO] Task started: Blastn
[2023-06-30 11:12:44,842] [INFO] Running command: blastn -query GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/markers.fasta -db /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/reference_markers.fasta -out GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:12:45,453] [INFO] Task succeeded: Blastn
[2023-06-30 11:12:45,457] [INFO] Selected 30 target genomes.
[2023-06-30 11:12:45,458] [INFO] Target genome list was writen to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/target_genomes.txt
[2023-06-30 11:12:45,464] [INFO] Task started: fastANI
[2023-06-30 11:12:45,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8082932-c686-4afb-8d9b-c4ae51f24467/GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna.gz --refList GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/target_genomes.txt --output GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:13:05,539] [INFO] Task succeeded: fastANI
[2023-06-30 11:13:05,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:13:05,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:13:05,541] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:13:05,541] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:13:05,542] [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 11:13:05,543] [INFO] DFAST Taxonomy check result was written to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/tc_result.tsv
[2023-06-30 11:13:05,544] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:13:05,544] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:13:05,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/checkm_data
[2023-06-30 11:13:05,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:13:05,563] [INFO] Task started: CheckM
[2023-06-30 11:13:05,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/checkm_input GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/checkm_result
[2023-06-30 11:13:22,318] [INFO] Task succeeded: CheckM
[2023-06-30 11:13:22,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:13:22,343] [INFO] ===== Completeness check finished =====
[2023-06-30 11:13:22,343] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:13:22,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/markers.fasta)
[2023-06-30 11:13:22,343] [INFO] Task started: Blastn
[2023-06-30 11:13:22,344] [INFO] Running command: blastn -query GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/markers.fasta -db /var/lib/cwl/stgb968f143-900e-42f2-9587-4082e002a8ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:13:23,322] [INFO] Task succeeded: Blastn
[2023-06-30 11:13:23,326] [INFO] Selected 10 target genomes.
[2023-06-30 11:13:23,326] [INFO] Target genome list was writen to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:13:23,328] [INFO] Task started: fastANI
[2023-06-30 11:13:23,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8082932-c686-4afb-8d9b-c4ae51f24467/GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna.gz --refList GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/target_genomes_gtdb.txt --output GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:13:25,567] [INFO] Task succeeded: fastANI
[2023-06-30 11:13:25,574] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:13:25,574] [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_903821145.1	s__PALSA-747 sp903821145	99.4846	307	343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.30	98.98	0.89	0.82	16	conclusive
GCA_903843225.1	s__PALSA-747 sp903843225	80.4464	156	343	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_903895995.1	s__PALSA-747 sp903895995	80.2554	183	343	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_903953805.1	s__PALSA-747 sp903953805	79.7074	149	343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.20	99.17	0.84	0.84	5	-
GCA_903834515.1	s__PALSA-747 sp903834515	79.4736	144	343	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_903854185.1	s__PALSA-747 sp903854185	78.5028	73	343	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_903871555.1	s__AAA044-D11 sp903871555	77.6583	55	343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
--------------------------------------------------------------------------------
[2023-06-30 11:13:25,576] [INFO] GTDB search result was written to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/result_gtdb.tsv
[2023-06-30 11:13:25,577] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:13:25,579] [INFO] DFAST_QC result json was written to GCA_903830005.1_freshwater_MAG_---_Ki2-D3_bin-0013_genomic.fna/dqc_result.json
[2023-06-30 11:13:25,579] [INFO] DFAST_QC completed!
[2023-06-30 11:13:25,579] [INFO] Total running time: 0h0m45s