[2023-03-18 08:55:50,587] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference
[2023-03-18 08:55:51,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,823] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,823] [INFO] Running command: cat /var/lib/cwl/stg10846cc1-5018-42dc-b356-aa6bcfa6fdca/OceanDNA-b33661.fa | prodigal -d OceanDNA-b33661/cds.fna -a OceanDNA-b33661/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:56,929] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:56,929] [INFO] Task started: HMMsearch
[2023-03-18 08:55:56,929] [INFO] Running command: hmmsearch --tblout OceanDNA-b33661/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/reference_markers.hmm OceanDNA-b33661/protein.faa > /dev/null
[2023-03-18 08:55:57,094] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:57,094] [INFO] Found 6/6 markers.
[2023-03-18 08:55:57,103] [INFO] Query marker FASTA was written to OceanDNA-b33661/markers.fasta
[2023-03-18 08:55:57,105] [INFO] Task started: Blastn
[2023-03-18 08:55:57,106] [INFO] Running command: blastn -query OceanDNA-b33661/markers.fasta -db /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/reference_markers.fasta -out OceanDNA-b33661/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:57,633] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:57,634] [INFO] Selected 18 target genomes.
[2023-03-18 08:55:57,634] [INFO] Target genome list was writen to OceanDNA-b33661/target_genomes.txt
[2023-03-18 08:55:57,648] [INFO] Task started: fastANI
[2023-03-18 08:55:57,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg10846cc1-5018-42dc-b356-aa6bcfa6fdca/OceanDNA-b33661.fa --refList OceanDNA-b33661/target_genomes.txt --output OceanDNA-b33661/fastani_result.tsv --threads 1
[2023-03-18 08:56:06,275] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:06,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:06,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:06,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:06,276] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:06,276] [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 08:56:06,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33661/tc_result.tsv
[2023-03-18 08:56:06,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:06,277] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:06,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/checkm_data
[2023-03-18 08:56:06,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:06,285] [INFO] Task started: CheckM
[2023-03-18 08:56:06,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33661/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33661/checkm_input OceanDNA-b33661/checkm_result
[2023-03-18 08:56:25,074] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:25,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:25,077] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:25,077] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:25,078] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33661/markers.fasta)
[2023-03-18 08:56:25,079] [INFO] Task started: Blastn
[2023-03-18 08:56:25,079] [INFO] Running command: blastn -query OceanDNA-b33661/markers.fasta -db /var/lib/cwl/stg31565f2d-d000-41b3-97ff-7c23c603473b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33661/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:25,808] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:25,809] [INFO] Selected 23 target genomes.
[2023-03-18 08:56:25,809] [INFO] Target genome list was writen to OceanDNA-b33661/target_genomes_gtdb.txt
[2023-03-18 08:56:25,838] [INFO] Task started: fastANI
[2023-03-18 08:56:25,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg10846cc1-5018-42dc-b356-aa6bcfa6fdca/OceanDNA-b33661.fa --refList OceanDNA-b33661/target_genomes_gtdb.txt --output OceanDNA-b33661/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:30,937] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:30,940] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:56:30,940] [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_902558495.1	s__BACL14 sp902558495	79.3544	150	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384685.1	s__BACL14 sp002384685	77.3712	82	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.54	99.37	0.90	0.88	8	-
GCA_000168995.1	s__BACL14 sp000168995	77.3025	93	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	98.71	98.43	0.97	0.92	10	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:30,941] [INFO] GTDB search result was written to OceanDNA-b33661/result_gtdb.tsv
[2023-03-18 08:56:30,941] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:30,941] [INFO] DFAST_QC result json was written to OceanDNA-b33661/dqc_result.json
[2023-03-18 08:56:30,941] [INFO] DFAST_QC completed!
[2023-03-18 08:56:30,941] [INFO] Total running time: 0h0m40s