[2023-03-18 04:04:53,880] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg402ba12a-01d7-4af4-ace8-9b9316afc063/OceanDNA-a839.fa | prodigal -d OceanDNA-a839/cds.fna -a OceanDNA-a839/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:04,677] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:04,677] [INFO] Task started: HMMsearch
[2023-03-18 04:05:04,677] [INFO] Running command: hmmsearch --tblout OceanDNA-a839/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/reference_markers.hmm OceanDNA-a839/protein.faa > /dev/null
[2023-03-18 04:05:04,798] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:04,799] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg402ba12a-01d7-4af4-ace8-9b9316afc063/OceanDNA-a839.fa]
[2023-03-18 04:05:04,809] [INFO] Query marker FASTA was written to OceanDNA-a839/markers.fasta
[2023-03-18 04:05:04,809] [INFO] Task started: Blastn
[2023-03-18 04:05:04,809] [INFO] Running command: blastn -query OceanDNA-a839/markers.fasta -db /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/reference_markers.fasta -out OceanDNA-a839/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:05,221] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:05,224] [INFO] Selected 2 target genomes.
[2023-03-18 04:05:05,224] [INFO] Target genome list was writen to OceanDNA-a839/target_genomes.txt
[2023-03-18 04:05:05,226] [INFO] Task started: fastANI
[2023-03-18 04:05:05,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg402ba12a-01d7-4af4-ace8-9b9316afc063/OceanDNA-a839.fa --refList OceanDNA-a839/target_genomes.txt --output OceanDNA-a839/fastani_result.tsv --threads 1
[2023-03-18 04:05:05,895] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:05,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:05,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:05,896] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:05,896] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:05:05,896] [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 04:05:05,896] [INFO] DFAST Taxonomy check result was written to OceanDNA-a839/tc_result.tsv
[2023-03-18 04:05:05,897] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:05,897] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:05,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/checkm_data
[2023-03-18 04:05:05,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:06,007] [INFO] Task started: CheckM
[2023-03-18 04:05:06,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a839/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a839/checkm_input OceanDNA-a839/checkm_result
[2023-03-18 04:05:35,259] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:35,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:35,287] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:35,287] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:35,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a839/markers.fasta)
[2023-03-18 04:05:35,287] [INFO] Task started: Blastn
[2023-03-18 04:05:35,287] [INFO] Running command: blastn -query OceanDNA-a839/markers.fasta -db /var/lib/cwl/stg26f92aa2-9f2d-44b7-842d-67d67d980e4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a839/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:35,682] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:35,687] [INFO] Selected 5 target genomes.
[2023-03-18 04:05:35,687] [INFO] Target genome list was writen to OceanDNA-a839/target_genomes_gtdb.txt
[2023-03-18 04:05:35,778] [INFO] Task started: fastANI
[2023-03-18 04:05:35,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg402ba12a-01d7-4af4-ace8-9b9316afc063/OceanDNA-a839.fa --refList OceanDNA-a839/target_genomes_gtdb.txt --output OceanDNA-a839/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:05:37,632] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:37,634] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:05:37,634] [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_002495315.1	s__UBA141 sp002495315	92.0241	389	448	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA141;g__UBA141	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:05:37,634] [INFO] GTDB search result was written to OceanDNA-a839/result_gtdb.tsv
[2023-03-18 04:05:37,634] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:05:37,635] [INFO] DFAST_QC result json was written to OceanDNA-a839/dqc_result.json
[2023-03-18 04:05:37,635] [INFO] DFAST_QC completed!
[2023-03-18 04:05:37,635] [INFO] Total running time: 0h0m44s