[2023-06-30 01:12:06,880] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:12:06,882] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:12:06,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference
[2023-06-30 01:12:08,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:12:08,359] [INFO] Task started: Prodigal
[2023-06-30 01:12:08,359] [INFO] Running command: gunzip -c /var/lib/cwl/stgfed98904-7c89-4683-a6aa-1000a72d16b5/GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna.gz | prodigal -d GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/cds.fna -a GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:12:11,205] [INFO] Task succeeded: Prodigal
[2023-06-30 01:12:11,206] [INFO] Task started: HMMsearch
[2023-06-30 01:12:11,206] [INFO] Running command: hmmsearch --tblout GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/reference_markers.hmm GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:12:11,434] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:12:11,436] [INFO] Found 6/6 markers.
[2023-06-30 01:12:11,458] [INFO] Query marker FASTA was written to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/markers.fasta
[2023-06-30 01:12:11,459] [INFO] Task started: Blastn
[2023-06-30 01:12:11,459] [INFO] Running command: blastn -query GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/markers.fasta -db /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/reference_markers.fasta -out GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:12,120] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:12,124] [INFO] Selected 20 target genomes.
[2023-06-30 01:12:12,125] [INFO] Target genome list was writen to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/target_genomes.txt
[2023-06-30 01:12:12,130] [INFO] Task started: fastANI
[2023-06-30 01:12:12,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed98904-7c89-4683-a6aa-1000a72d16b5/GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna.gz --refList GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/target_genomes.txt --output GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:12:22,308] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:22,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:12:22,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:12:22,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:12:22,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:12:22,311] [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 01:12:22,313] [INFO] DFAST Taxonomy check result was written to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/tc_result.tsv
[2023-06-30 01:12:22,314] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:12:22,314] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:12:22,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/checkm_data
[2023-06-30 01:12:22,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:12:22,342] [INFO] Task started: CheckM
[2023-06-30 01:12:22,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/checkm_input GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/checkm_result
[2023-06-30 01:12:39,273] [INFO] Task succeeded: CheckM
[2023-06-30 01:12:39,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 01:12:39,294] [INFO] ===== Completeness check finished =====
[2023-06-30 01:12:39,295] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:12:39,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/markers.fasta)
[2023-06-30 01:12:39,296] [INFO] Task started: Blastn
[2023-06-30 01:12:39,296] [INFO] Running command: blastn -query GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/markers.fasta -db /var/lib/cwl/stgca4314c0-48c4-4a7f-8d7a-96d91dc3a9f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:40,276] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:40,280] [INFO] Selected 10 target genomes.
[2023-06-30 01:12:40,280] [INFO] Target genome list was writen to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:12:40,287] [INFO] Task started: fastANI
[2023-06-30 01:12:40,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed98904-7c89-4683-a6aa-1000a72d16b5/GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna.gz --refList GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/target_genomes_gtdb.txt --output GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:12:42,503] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:42,513] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:12:42,513] [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	99.3416	342	387	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	82.5045	230	387	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	82.0723	208	387	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	82.0298	279	387	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_009701575.1	s__AAA044-D11 sp009701575	82.0252	242	387	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_009705075.1	s__AAA044-D11 sp009705075	81.2869	150	387	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_009701525.1	s__AAA044-D11 sp009701525	80.8651	177	387	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_009702205.1	s__AAA044-D11 sp009702205	80.4318	180	387	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	79.7577	172	387	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.65	98.65	0.87	0.87	2	-
GCA_903821145.1	s__PALSA-747 sp903821145	77.56	56	387	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.30	98.98	0.89	0.82	16	-
--------------------------------------------------------------------------------
[2023-06-30 01:12:42,515] [INFO] GTDB search result was written to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/result_gtdb.tsv
[2023-06-30 01:12:42,516] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:12:42,521] [INFO] DFAST_QC result json was written to GCA_903852925.1_freshwater_MAG_---_Ki3-D4_bin-450_genomic.fna/dqc_result.json
[2023-06-30 01:12:42,521] [INFO] DFAST_QC completed!
[2023-06-30 01:12:42,521] [INFO] Total running time: 0h0m36s