[2023-06-30 07:45:12,803] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:45:12,823] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:45:12,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference
[2023-06-30 07:45:14,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:45:14,759] [INFO] Task started: Prodigal
[2023-06-30 07:45:14,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d07358e-c3ba-488d-8ca7-8d82cd8a2589/GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna.gz | prodigal -d GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/cds.fna -a GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:45:16,625] [INFO] Task succeeded: Prodigal
[2023-06-30 07:45:16,626] [INFO] Task started: HMMsearch
[2023-06-30 07:45:16,626] [INFO] Running command: hmmsearch --tblout GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/reference_markers.hmm GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:45:16,848] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:45:16,849] [INFO] Found 6/6 markers.
[2023-06-30 07:45:16,889] [INFO] Query marker FASTA was written to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/markers.fasta
[2023-06-30 07:45:16,890] [INFO] Task started: Blastn
[2023-06-30 07:45:16,890] [INFO] Running command: blastn -query GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/reference_markers.fasta -out GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:45:18,882] [INFO] Task succeeded: Blastn
[2023-06-30 07:45:18,887] [INFO] Selected 29 target genomes.
[2023-06-30 07:45:18,887] [INFO] Target genome list was writen to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/target_genomes.txt
[2023-06-30 07:45:18,920] [INFO] Task started: fastANI
[2023-06-30 07:45:18,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d07358e-c3ba-488d-8ca7-8d82cd8a2589/GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna.gz --refList GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/target_genomes.txt --output GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:45:29,376] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:29,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:45:29,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:45:29,378] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:45:29,378] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 07:45:29,378] [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 07:45:29,380] [INFO] DFAST Taxonomy check result was written to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/tc_result.tsv
[2023-06-30 07:45:29,380] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:45:29,381] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:45:29,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/checkm_data
[2023-06-30 07:45:29,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:45:29,402] [INFO] Task started: CheckM
[2023-06-30 07:45:29,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/checkm_input GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/checkm_result
[2023-06-30 07:45:44,008] [INFO] Task succeeded: CheckM
[2023-06-30 07:45:44,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 3.65%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-30 07:45:44,033] [INFO] ===== Completeness check finished =====
[2023-06-30 07:45:44,033] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:45:44,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/markers.fasta)
[2023-06-30 07:45:44,034] [INFO] Task started: Blastn
[2023-06-30 07:45:44,035] [INFO] Running command: blastn -query GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d21a90-64ed-4b2a-8391-e69d7da74333/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:45:45,079] [INFO] Task succeeded: Blastn
[2023-06-30 07:45:45,085] [INFO] Selected 14 target genomes.
[2023-06-30 07:45:45,085] [INFO] Target genome list was writen to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:45:45,110] [INFO] Task started: fastANI
[2023-06-30 07:45:45,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d07358e-c3ba-488d-8ca7-8d82cd8a2589/GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna.gz --refList GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/target_genomes_gtdb.txt --output GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:45:47,917] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:47,931] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:45:47,932] [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_903897475.1	s__Nanopelagicus sp903897475	99.0612	207	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.94	98.64	0.81	0.80	6	conclusive
GCA_010030895.1	s__Nanopelagicus sp010030895	83.0899	178	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.34	97.93	0.89	0.87	8	-
GCA_009700155.1	s__Nanopelagicus sp009700155	82.7227	150	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.43	98.37	0.82	0.81	3	-
GCA_001437855.1	s__Nanopelagicus sp001437855	80.6315	117	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	96.40	95.11	0.72	0.67	12	-
GCA_016870895.1	s__Nanopelagicus sp016870895	80.1145	119	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383815.1	s__Nanopelagicus sp000383815	80.0353	103	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287885.2	s__Nanopelagicus limnes	80.0155	141	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288305.1	s__Nanopelagicus abundans	79.7259	130	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	79.4147	124	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
GCA_000378865.1	s__Nanopelagicus sp000378865	79.2395	92	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462445.1	s__Nanopelagicus sp016462445	79.0023	117	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704285.1	s__Nanopelagicus sp009704285	78.2367	68	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702465.1	s__Nanopelagicus sp009702465	77.4259	64	263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:45:47,934] [INFO] GTDB search result was written to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/result_gtdb.tsv
[2023-06-30 07:45:47,934] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:45:47,937] [INFO] DFAST_QC result json was written to GCA_903830075.1_freshwater_MAG_---_LaPlata-5m-a_bin-072_genomic.fna/dqc_result.json
[2023-06-30 07:45:47,938] [INFO] DFAST_QC completed!
[2023-06-30 07:45:47,938] [INFO] Total running time: 0h0m35s