[2023-03-17 03:50:13,767] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference
[2023-03-17 03:50:15,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,140] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,140] [INFO] Running command: cat /var/lib/cwl/stged2ede6a-ea34-48cc-84b1-c0594c0facb8/OceanDNA-b12882.fa | prodigal -d OceanDNA-b12882/cds.fna -a OceanDNA-b12882/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:42,979] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:42,979] [INFO] Task started: HMMsearch
[2023-03-17 03:50:42,979] [INFO] Running command: hmmsearch --tblout OceanDNA-b12882/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/reference_markers.hmm OceanDNA-b12882/protein.faa > /dev/null
[2023-03-17 03:50:43,196] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:43,197] [INFO] Found 6/6 markers.
[2023-03-17 03:50:43,216] [INFO] Query marker FASTA was written to OceanDNA-b12882/markers.fasta
[2023-03-17 03:50:43,216] [INFO] Task started: Blastn
[2023-03-17 03:50:43,216] [INFO] Running command: blastn -query OceanDNA-b12882/markers.fasta -db /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/reference_markers.fasta -out OceanDNA-b12882/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:43,741] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:43,742] [INFO] Selected 31 target genomes.
[2023-03-17 03:50:43,742] [INFO] Target genome list was writen to OceanDNA-b12882/target_genomes.txt
[2023-03-17 03:50:43,757] [INFO] Task started: fastANI
[2023-03-17 03:50:43,757] [INFO] Running command: fastANI --query /var/lib/cwl/stged2ede6a-ea34-48cc-84b1-c0594c0facb8/OceanDNA-b12882.fa --refList OceanDNA-b12882/target_genomes.txt --output OceanDNA-b12882/fastani_result.tsv --threads 1
[2023-03-17 03:51:09,264] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:09,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:51:09,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:51:09,265] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:51:09,265] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:51:09,265] [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 03:51:09,331] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12882/tc_result.tsv
[2023-03-17 03:51:09,331] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:51:09,331] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:51:09,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/checkm_data
[2023-03-17 03:51:09,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:51:09,539] [INFO] Task started: CheckM
[2023-03-17 03:51:09,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12882/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12882/checkm_input OceanDNA-b12882/checkm_result
[2023-03-17 03:52:17,789] [INFO] Task succeeded: CheckM
[2023-03-17 03:52:17,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:52:17,791] [INFO] ===== Completeness check finished =====
[2023-03-17 03:52:17,791] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:52:17,792] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12882/markers.fasta)
[2023-03-17 03:52:17,792] [INFO] Task started: Blastn
[2023-03-17 03:52:17,792] [INFO] Running command: blastn -query OceanDNA-b12882/markers.fasta -db /var/lib/cwl/stg8535e742-17b0-4e8c-836f-e34707496c62/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12882/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:52:18,495] [INFO] Task succeeded: Blastn
[2023-03-17 03:52:18,496] [INFO] Selected 30 target genomes.
[2023-03-17 03:52:18,496] [INFO] Target genome list was writen to OceanDNA-b12882/target_genomes_gtdb.txt
[2023-03-17 03:52:19,066] [INFO] Task started: fastANI
[2023-03-17 03:52:19,066] [INFO] Running command: fastANI --query /var/lib/cwl/stged2ede6a-ea34-48cc-84b1-c0594c0facb8/OceanDNA-b12882.fa --refList OceanDNA-b12882/target_genomes_gtdb.txt --output OceanDNA-b12882/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:52:39,384] [INFO] Task succeeded: fastANI
[2023-03-17 03:52:39,387] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:52:39,387] [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_013824115.1	s__PNNG01 sp013824115	78.273	259	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__PNNG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483345.1	s__UBA7662 sp002483345	76.4723	93	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__UBA7662	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:52:39,387] [INFO] GTDB search result was written to OceanDNA-b12882/result_gtdb.tsv
[2023-03-17 03:52:39,387] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:52:39,387] [INFO] DFAST_QC result json was written to OceanDNA-b12882/dqc_result.json
[2023-03-17 03:52:39,388] [INFO] DFAST_QC completed!
[2023-03-17 03:52:39,388] [INFO] Total running time: 0h2m26s