[2023-03-18 07:06:20,698] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,698] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference
[2023-03-18 07:06:22,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:22,303] [INFO] Task started: Prodigal
[2023-03-18 07:06:22,303] [INFO] Running command: cat /var/lib/cwl/stg247390a4-d088-48a4-b005-cb672cea3348/OceanDNA-a256.fa | prodigal -d OceanDNA-a256/cds.fna -a OceanDNA-a256/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:25,260] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:25,260] [INFO] Task started: HMMsearch
[2023-03-18 07:06:25,260] [INFO] Running command: hmmsearch --tblout OceanDNA-a256/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/reference_markers.hmm OceanDNA-a256/protein.faa > /dev/null
[2023-03-18 07:06:25,415] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:25,416] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg247390a4-d088-48a4-b005-cb672cea3348/OceanDNA-a256.fa]
[2023-03-18 07:06:25,421] [INFO] Query marker FASTA was written to OceanDNA-a256/markers.fasta
[2023-03-18 07:06:25,423] [INFO] Task started: Blastn
[2023-03-18 07:06:25,423] [INFO] Running command: blastn -query OceanDNA-a256/markers.fasta -db /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/reference_markers.fasta -out OceanDNA-a256/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:28,300] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:28,301] [INFO] Selected 2 target genomes.
[2023-03-18 07:06:28,301] [INFO] Target genome list was writen to OceanDNA-a256/target_genomes.txt
[2023-03-18 07:06:28,303] [INFO] Task started: fastANI
[2023-03-18 07:06:28,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg247390a4-d088-48a4-b005-cb672cea3348/OceanDNA-a256.fa --refList OceanDNA-a256/target_genomes.txt --output OceanDNA-a256/fastani_result.tsv --threads 1
[2023-03-18 07:06:28,824] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:28,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:28,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:28,825] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:28,825] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:28,825] [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
--------------------------------------------------------------------------------
[2023-03-18 07:06:28,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-a256/tc_result.tsv
[2023-03-18 07:06:28,825] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:28,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:28,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/checkm_data
[2023-03-18 07:06:28,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:28,927] [INFO] Task started: CheckM
[2023-03-18 07:06:28,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a256/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a256/checkm_input OceanDNA-a256/checkm_result
[2023-03-18 07:06:44,061] [INFO] Task succeeded: CheckM
[2023-03-18 07:06:44,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:06:44,063] [INFO] ===== Completeness check finished =====
[2023-03-18 07:06:44,063] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:06:44,063] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a256/markers.fasta)
[2023-03-18 07:06:44,065] [INFO] Task started: Blastn
[2023-03-18 07:06:44,065] [INFO] Running command: blastn -query OceanDNA-a256/markers.fasta -db /var/lib/cwl/stg37ea6dc2-4474-4a25-84ff-e64f94ef881e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a256/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:44,680] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:44,681] [INFO] Selected 5 target genomes.
[2023-03-18 07:06:44,681] [INFO] Target genome list was writen to OceanDNA-a256/target_genomes_gtdb.txt
[2023-03-18 07:06:44,934] [INFO] Task started: fastANI
[2023-03-18 07:06:44,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg247390a4-d088-48a4-b005-cb672cea3348/OceanDNA-a256.fa --refList OceanDNA-a256/target_genomes_gtdb.txt --output OceanDNA-a256/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:06:45,676] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:45,678] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:06:45,678] [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_002698885.1	s__Nitrosopelagicus sp002698885	80.3768	51	98	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:06:45,678] [INFO] GTDB search result was written to OceanDNA-a256/result_gtdb.tsv
[2023-03-18 07:06:45,678] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:06:45,679] [INFO] DFAST_QC result json was written to OceanDNA-a256/dqc_result.json
[2023-03-18 07:06:45,679] [INFO] DFAST_QC completed!
[2023-03-18 07:06:45,679] [INFO] Total running time: 0h0m25s