[2023-03-16 09:23:09,047] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,047] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference
[2023-03-16 09:23:10,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:10,144] [INFO] Task started: Prodigal
[2023-03-16 09:23:10,145] [INFO] Running command: cat /var/lib/cwl/stg2024054a-f759-4d2d-a7e8-d725d0e38312/OceanDNA-b21258.fa | prodigal -d OceanDNA-b21258/cds.fna -a OceanDNA-b21258/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:23:15,659] [INFO] Task succeeded: Prodigal
[2023-03-16 09:23:15,660] [INFO] Task started: HMMsearch
[2023-03-16 09:23:15,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b21258/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/reference_markers.hmm OceanDNA-b21258/protein.faa > /dev/null
[2023-03-16 09:23:15,808] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:23:15,809] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2024054a-f759-4d2d-a7e8-d725d0e38312/OceanDNA-b21258.fa]
[2023-03-16 09:23:15,820] [INFO] Query marker FASTA was written to OceanDNA-b21258/markers.fasta
[2023-03-16 09:23:15,821] [INFO] Task started: Blastn
[2023-03-16 09:23:15,821] [INFO] Running command: blastn -query OceanDNA-b21258/markers.fasta -db /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/reference_markers.fasta -out OceanDNA-b21258/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:16,318] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:16,318] [INFO] Selected 10 target genomes.
[2023-03-16 09:23:16,318] [INFO] Target genome list was writen to OceanDNA-b21258/target_genomes.txt
[2023-03-16 09:23:16,325] [INFO] Task started: fastANI
[2023-03-16 09:23:16,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg2024054a-f759-4d2d-a7e8-d725d0e38312/OceanDNA-b21258.fa --refList OceanDNA-b21258/target_genomes.txt --output OceanDNA-b21258/fastani_result.tsv --threads 1
[2023-03-16 09:23:21,687] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:21,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:23:21,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:23:21,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:23:21,688] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:23:21,688] [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 09:23:21,688] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21258/tc_result.tsv
[2023-03-16 09:23:21,688] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:23:21,689] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:23:21,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/checkm_data
[2023-03-16 09:23:21,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:23:21,695] [INFO] Task started: CheckM
[2023-03-16 09:23:21,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21258/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21258/checkm_input OceanDNA-b21258/checkm_result
[2023-03-16 09:23:41,444] [INFO] Task succeeded: CheckM
[2023-03-16 09:23:41,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.50%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 09:23:41,446] [INFO] ===== Completeness check finished =====
[2023-03-16 09:23:41,446] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:23:41,446] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21258/markers.fasta)
[2023-03-16 09:23:41,447] [INFO] Task started: Blastn
[2023-03-16 09:23:41,447] [INFO] Running command: blastn -query OceanDNA-b21258/markers.fasta -db /var/lib/cwl/stg6eb9ba9f-fe74-485c-bc01-d222e1d2d8be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21258/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:42,136] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:42,136] [INFO] Selected 12 target genomes.
[2023-03-16 09:23:42,137] [INFO] Target genome list was writen to OceanDNA-b21258/target_genomes_gtdb.txt
[2023-03-16 09:23:42,168] [INFO] Task started: fastANI
[2023-03-16 09:23:42,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg2024054a-f759-4d2d-a7e8-d725d0e38312/OceanDNA-b21258.fa --refList OceanDNA-b21258/target_genomes_gtdb.txt --output OceanDNA-b21258/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:23:47,764] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:47,767] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:23:47,767] [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_000372225.1	s__Nitromaritima sp000372225	84.1882	201	318	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018697205.1	s__Nitromaritima sp018697205	81.7418	238	318	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
GCA_018647025.1	s__Nitromaritima sp018647025	80.327	156	318	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	-
--------------------------------------------------------------------------------
[2023-03-16 09:23:47,767] [INFO] GTDB search result was written to OceanDNA-b21258/result_gtdb.tsv
[2023-03-16 09:23:47,767] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:23:47,767] [INFO] DFAST_QC result json was written to OceanDNA-b21258/dqc_result.json
[2023-03-16 09:23:47,768] [INFO] DFAST_QC completed!
[2023-03-16 09:23:47,768] [INFO] Total running time: 0h0m39s