[2023-03-18 23:48:46,612] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:48:46,612] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:48:46,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference
[2023-03-18 23:48:47,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:48:47,709] [INFO] Task started: Prodigal
[2023-03-18 23:48:47,710] [INFO] Running command: cat /var/lib/cwl/stg0e920425-abad-4c97-8567-45edd47e759c/OceanDNA-b30746.fa | prodigal -d OceanDNA-b30746/cds.fna -a OceanDNA-b30746/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:49:01,966] [INFO] Task succeeded: Prodigal
[2023-03-18 23:49:01,967] [INFO] Task started: HMMsearch
[2023-03-18 23:49:01,967] [INFO] Running command: hmmsearch --tblout OceanDNA-b30746/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/reference_markers.hmm OceanDNA-b30746/protein.faa > /dev/null
[2023-03-18 23:49:02,152] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:49:02,152] [INFO] Found 6/6 markers.
[2023-03-18 23:49:02,172] [INFO] Query marker FASTA was written to OceanDNA-b30746/markers.fasta
[2023-03-18 23:49:02,173] [INFO] Task started: Blastn
[2023-03-18 23:49:02,173] [INFO] Running command: blastn -query OceanDNA-b30746/markers.fasta -db /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/reference_markers.fasta -out OceanDNA-b30746/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:02,740] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:02,741] [INFO] Selected 25 target genomes.
[2023-03-18 23:49:02,741] [INFO] Target genome list was writen to OceanDNA-b30746/target_genomes.txt
[2023-03-18 23:49:02,795] [INFO] Task started: fastANI
[2023-03-18 23:49:02,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e920425-abad-4c97-8567-45edd47e759c/OceanDNA-b30746.fa --refList OceanDNA-b30746/target_genomes.txt --output OceanDNA-b30746/fastani_result.tsv --threads 1
[2023-03-18 23:49:19,635] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:19,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:49:19,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:49:19,636] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:49:19,636] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:49:19,636] [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 23:49:19,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30746/tc_result.tsv
[2023-03-18 23:49:19,637] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:49:19,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:49:19,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/checkm_data
[2023-03-18 23:49:19,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:49:19,644] [INFO] Task started: CheckM
[2023-03-18 23:49:19,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30746/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30746/checkm_input OceanDNA-b30746/checkm_result
[2023-03-18 23:49:58,074] [INFO] Task succeeded: CheckM
[2023-03-18 23:49:58,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:49:58,116] [INFO] ===== Completeness check finished =====
[2023-03-18 23:49:58,116] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:49:58,116] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30746/markers.fasta)
[2023-03-18 23:49:58,117] [INFO] Task started: Blastn
[2023-03-18 23:49:58,117] [INFO] Running command: blastn -query OceanDNA-b30746/markers.fasta -db /var/lib/cwl/stgecee2dbb-a9a7-407a-9a9c-bf9dace02fff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30746/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:58,994] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:59,011] [INFO] Selected 22 target genomes.
[2023-03-18 23:49:59,011] [INFO] Target genome list was writen to OceanDNA-b30746/target_genomes_gtdb.txt
[2023-03-18 23:49:59,077] [INFO] Task started: fastANI
[2023-03-18 23:49:59,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e920425-abad-4c97-8567-45edd47e759c/OceanDNA-b30746.fa --refList OceanDNA-b30746/target_genomes_gtdb.txt --output OceanDNA-b30746/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:50:12,271] [INFO] Task succeeded: fastANI
[2023-03-18 23:50:12,272] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:50:12,273] [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_018660465.1	s__JABJKH01 sp018660465	82.8952	624	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JABJKH01;g__JABJKH01	95.0	99.88	99.82	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-18 23:50:12,273] [INFO] GTDB search result was written to OceanDNA-b30746/result_gtdb.tsv
[2023-03-18 23:50:12,273] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:50:12,274] [INFO] DFAST_QC result json was written to OceanDNA-b30746/dqc_result.json
[2023-03-18 23:50:12,274] [INFO] DFAST_QC completed!
[2023-03-18 23:50:12,274] [INFO] Total running time: 0h1m26s