[2023-03-16 08:50:58,989] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:58,990] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:58,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference
[2023-03-16 08:51:00,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,089] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,089] [INFO] Running command: cat /var/lib/cwl/stg6169079d-3ec8-41a4-bd20-0bc3ead34493/OceanDNA-b42519.fa | prodigal -d OceanDNA-b42519/cds.fna -a OceanDNA-b42519/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:03,701] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:03,701] [INFO] Task started: HMMsearch
[2023-03-16 08:51:03,702] [INFO] Running command: hmmsearch --tblout OceanDNA-b42519/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/reference_markers.hmm OceanDNA-b42519/protein.faa > /dev/null
[2023-03-16 08:51:03,893] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:03,894] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6169079d-3ec8-41a4-bd20-0bc3ead34493/OceanDNA-b42519.fa]
[2023-03-16 08:51:03,906] [INFO] Query marker FASTA was written to OceanDNA-b42519/markers.fasta
[2023-03-16 08:51:03,907] [INFO] Task started: Blastn
[2023-03-16 08:51:03,907] [INFO] Running command: blastn -query OceanDNA-b42519/markers.fasta -db /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/reference_markers.fasta -out OceanDNA-b42519/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:04,408] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:04,410] [INFO] Selected 15 target genomes.
[2023-03-16 08:51:04,410] [INFO] Target genome list was writen to OceanDNA-b42519/target_genomes.txt
[2023-03-16 08:51:04,437] [INFO] Task started: fastANI
[2023-03-16 08:51:04,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg6169079d-3ec8-41a4-bd20-0bc3ead34493/OceanDNA-b42519.fa --refList OceanDNA-b42519/target_genomes.txt --output OceanDNA-b42519/fastani_result.tsv --threads 1
[2023-03-16 08:51:11,227] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:11,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:11,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:11,227] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:11,227] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:11,227] [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
--------------------------------------------------------------------------------
[2023-03-16 08:51:11,228] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42519/tc_result.tsv
[2023-03-16 08:51:11,229] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:11,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:11,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/checkm_data
[2023-03-16 08:51:11,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:11,236] [INFO] Task started: CheckM
[2023-03-16 08:51:11,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42519/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42519/checkm_input OceanDNA-b42519/checkm_result
[2023-03-16 08:51:26,890] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:26,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:26,898] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:26,898] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:26,898] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42519/markers.fasta)
[2023-03-16 08:51:26,899] [INFO] Task started: Blastn
[2023-03-16 08:51:26,899] [INFO] Running command: blastn -query OceanDNA-b42519/markers.fasta -db /var/lib/cwl/stg94c4d05c-17eb-466f-a17a-bcd5973eb497/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42519/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:27,618] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:27,621] [INFO] Selected 14 target genomes.
[2023-03-16 08:51:27,621] [INFO] Target genome list was writen to OceanDNA-b42519/target_genomes_gtdb.txt
[2023-03-16 08:51:27,656] [INFO] Task started: fastANI
[2023-03-16 08:51:27,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg6169079d-3ec8-41a4-bd20-0bc3ead34493/OceanDNA-b42519.fa --refList OceanDNA-b42519/target_genomes_gtdb.txt --output OceanDNA-b42519/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:31,335] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:31,338] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:51:31,338] [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_001628005.1	s__AEGEAN-183 sp001628005	94.1137	172	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	99.32	99.31	0.88	0.87	3	-
GCA_012965075.1	s__AEGEAN-183 sp012965075	80.1973	116	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	98.73	98.73	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:51:31,341] [INFO] GTDB search result was written to OceanDNA-b42519/result_gtdb.tsv
[2023-03-16 08:51:31,344] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:31,346] [INFO] DFAST_QC result json was written to OceanDNA-b42519/dqc_result.json
[2023-03-16 08:51:31,347] [INFO] DFAST_QC completed!
[2023-03-16 08:51:31,347] [INFO] Total running time: 0h0m32s