[2023-06-30 13:15:39,977] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:15:39,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:15:39,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference
[2023-06-30 13:15:42,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:15:42,717] [INFO] Task started: Prodigal
[2023-06-30 13:15:42,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fb92937-46a9-4bbb-8a6c-d66af34b81d5/GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna.gz | prodigal -d GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/cds.fna -a GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:15:45,201] [INFO] Task succeeded: Prodigal
[2023-06-30 13:15:45,202] [INFO] Task started: HMMsearch
[2023-06-30 13:15:45,202] [INFO] Running command: hmmsearch --tblout GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/reference_markers.hmm GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:15:45,396] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:15:45,398] [INFO] Found 6/6 markers.
[2023-06-30 13:15:45,419] [INFO] Query marker FASTA was written to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/markers.fasta
[2023-06-30 13:15:45,420] [INFO] Task started: Blastn
[2023-06-30 13:15:45,420] [INFO] Running command: blastn -query GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/markers.fasta -db /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/reference_markers.fasta -out GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:15:46,060] [INFO] Task succeeded: Blastn
[2023-06-30 13:15:46,064] [INFO] Selected 22 target genomes.
[2023-06-30 13:15:46,065] [INFO] Target genome list was writen to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/target_genomes.txt
[2023-06-30 13:15:46,124] [INFO] Task started: fastANI
[2023-06-30 13:15:46,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb92937-46a9-4bbb-8a6c-d66af34b81d5/GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna.gz --refList GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/target_genomes.txt --output GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:15:55,375] [INFO] Task succeeded: fastANI
[2023-06-30 13:15:55,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:15:55,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:15:55,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:15:55,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:15:55,420] [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 13:15:55,423] [INFO] DFAST Taxonomy check result was written to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/tc_result.tsv
[2023-06-30 13:15:55,424] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:15:55,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:15:55,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/checkm_data
[2023-06-30 13:15:55,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:15:55,449] [INFO] Task started: CheckM
[2023-06-30 13:15:55,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/checkm_input GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/checkm_result
[2023-06-30 13:16:10,550] [INFO] Task succeeded: CheckM
[2023-06-30 13:16:10,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:16:10,573] [INFO] ===== Completeness check finished =====
[2023-06-30 13:16:10,573] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:16:10,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/markers.fasta)
[2023-06-30 13:16:10,574] [INFO] Task started: Blastn
[2023-06-30 13:16:10,574] [INFO] Running command: blastn -query GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/markers.fasta -db /var/lib/cwl/stg54259e0c-8a1d-4a16-8bfb-a08e6ccaef94/dqc_reference/reference_markers_gtdb.fasta -out GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:16:11,479] [INFO] Task succeeded: Blastn
[2023-06-30 13:16:11,483] [INFO] Selected 21 target genomes.
[2023-06-30 13:16:11,484] [INFO] Target genome list was writen to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:16:11,495] [INFO] Task started: fastANI
[2023-06-30 13:16:11,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb92937-46a9-4bbb-8a6c-d66af34b81d5/GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna.gz --refList GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/target_genomes_gtdb.txt --output GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:16:15,856] [INFO] Task succeeded: fastANI
[2023-06-30 13:16:15,867] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:16:15,867] [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_903878415.1	s__UBA7398 sp903878415	99.467	310	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA7398	95.0	99.37	98.92	0.94	0.90	19	conclusive
GCA_014190155.1	s__UBA7398 sp014190155	87.6115	277	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA7398	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205455.1	s__UBA7398 sp013205455	86.8671	178	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA7398	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470135.1	s__UBA7398 sp002470135	86.148	253	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA7398	95.0	99.27	98.46	0.86	0.77	4	-
GCA_009927575.1	s__UBA7398 sp009927575	76.5639	76	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA7398	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:16:15,870] [INFO] GTDB search result was written to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/result_gtdb.tsv
[2023-06-30 13:16:15,870] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:16:15,873] [INFO] DFAST_QC result json was written to GCA_903900645.1_freshwater_MAG_---_LJ-3-4m_bin-0914_genomic.fna/dqc_result.json
[2023-06-30 13:16:15,873] [INFO] DFAST_QC completed!
[2023-06-30 13:16:15,873] [INFO] Total running time: 0h0m36s