[2023-03-17 05:34:58,159] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,159] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,159] [INFO] DQC Reference Directory: /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference
[2023-03-17 05:34:59,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,269] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,269] [INFO] Running command: cat /var/lib/cwl/stg4df563e6-6aae-4886-8f79-6cc76fe9b64c/OceanDNA-b35649.fa | prodigal -d OceanDNA-b35649/cds.fna -a OceanDNA-b35649/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:02,401] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:02,401] [INFO] Task started: HMMsearch
[2023-03-17 05:35:02,401] [INFO] Running command: hmmsearch --tblout OceanDNA-b35649/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/reference_markers.hmm OceanDNA-b35649/protein.faa > /dev/null
[2023-03-17 05:35:02,574] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:02,574] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4df563e6-6aae-4886-8f79-6cc76fe9b64c/OceanDNA-b35649.fa]
[2023-03-17 05:35:02,592] [INFO] Query marker FASTA was written to OceanDNA-b35649/markers.fasta
[2023-03-17 05:35:02,594] [INFO] Task started: Blastn
[2023-03-17 05:35:02,594] [INFO] Running command: blastn -query OceanDNA-b35649/markers.fasta -db /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/reference_markers.fasta -out OceanDNA-b35649/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:03,268] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:03,272] [INFO] Selected 15 target genomes.
[2023-03-17 05:35:03,272] [INFO] Target genome list was writen to OceanDNA-b35649/target_genomes.txt
[2023-03-17 05:35:03,280] [INFO] Task started: fastANI
[2023-03-17 05:35:03,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg4df563e6-6aae-4886-8f79-6cc76fe9b64c/OceanDNA-b35649.fa --refList OceanDNA-b35649/target_genomes.txt --output OceanDNA-b35649/fastani_result.tsv --threads 1
[2023-03-17 05:35:09,527] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:09,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:09,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:09,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:35:09,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:35:09,528] [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
--------------------------------------------------------------------------------
[2023-03-17 05:35:09,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35649/tc_result.tsv
[2023-03-17 05:35:09,529] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:09,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:09,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/checkm_data
[2023-03-17 05:35:09,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:09,592] [INFO] Task started: CheckM
[2023-03-17 05:35:09,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35649/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35649/checkm_input OceanDNA-b35649/checkm_result
[2023-03-17 05:35:24,264] [INFO] Task succeeded: CheckM
[2023-03-17 05:35:24,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.40%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:35:24,324] [INFO] ===== Completeness check finished =====
[2023-03-17 05:35:24,324] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:35:24,325] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35649/markers.fasta)
[2023-03-17 05:35:24,326] [INFO] Task started: Blastn
[2023-03-17 05:35:24,326] [INFO] Running command: blastn -query OceanDNA-b35649/markers.fasta -db /var/lib/cwl/stge4d75c63-5c0c-4ab1-ad5f-dbf492c29115/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35649/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:25,168] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:25,170] [INFO] Selected 26 target genomes.
[2023-03-17 05:35:25,170] [INFO] Target genome list was writen to OceanDNA-b35649/target_genomes_gtdb.txt
[2023-03-17 05:35:25,306] [INFO] Task started: fastANI
[2023-03-17 05:35:25,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg4df563e6-6aae-4886-8f79-6cc76fe9b64c/OceanDNA-b35649.fa --refList OceanDNA-b35649/target_genomes_gtdb.txt --output OceanDNA-b35649/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:35:32,261] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:32,263] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:35:32,263] [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_002701705.1	s__GCA-2701705 sp002701705	78.8182	97	206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2701705	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:35:32,264] [INFO] GTDB search result was written to OceanDNA-b35649/result_gtdb.tsv
[2023-03-17 05:35:32,265] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:35:32,267] [INFO] DFAST_QC result json was written to OceanDNA-b35649/dqc_result.json
[2023-03-17 05:35:32,267] [INFO] DFAST_QC completed!
[2023-03-17 05:35:32,267] [INFO] Total running time: 0h0m34s