[2023-03-16 10:08:11,072] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:08:11,072] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:08:11,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference
[2023-03-16 10:08:12,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:08:12,191] [INFO] Task started: Prodigal
[2023-03-16 10:08:12,192] [INFO] Running command: cat /var/lib/cwl/stge5c6ec5a-a0f1-4fa0-9c06-e37471829e69/OceanDNA-b24128.fa | prodigal -d OceanDNA-b24128/cds.fna -a OceanDNA-b24128/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:08:23,810] [INFO] Task succeeded: Prodigal
[2023-03-16 10:08:23,810] [INFO] Task started: HMMsearch
[2023-03-16 10:08:23,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b24128/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/reference_markers.hmm OceanDNA-b24128/protein.faa > /dev/null
[2023-03-16 10:08:24,044] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:08:24,045] [INFO] Found 6/6 markers.
[2023-03-16 10:08:24,068] [INFO] Query marker FASTA was written to OceanDNA-b24128/markers.fasta
[2023-03-16 10:08:24,068] [INFO] Task started: Blastn
[2023-03-16 10:08:24,068] [INFO] Running command: blastn -query OceanDNA-b24128/markers.fasta -db /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/reference_markers.fasta -out OceanDNA-b24128/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:24,701] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:24,702] [INFO] Selected 38 target genomes.
[2023-03-16 10:08:24,702] [INFO] Target genome list was writen to OceanDNA-b24128/target_genomes.txt
[2023-03-16 10:08:24,725] [INFO] Task started: fastANI
[2023-03-16 10:08:24,725] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c6ec5a-a0f1-4fa0-9c06-e37471829e69/OceanDNA-b24128.fa --refList OceanDNA-b24128/target_genomes.txt --output OceanDNA-b24128/fastani_result.tsv --threads 1
[2023-03-16 10:08:54,735] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:54,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:08:54,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:08:54,736] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:08:54,736] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:08:54,736] [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
--------------------------------------------------------------------------------
[2023-03-16 10:08:54,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24128/tc_result.tsv
[2023-03-16 10:08:54,736] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:08:54,736] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:08:54,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/checkm_data
[2023-03-16 10:08:54,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:08:54,744] [INFO] Task started: CheckM
[2023-03-16 10:08:54,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24128/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24128/checkm_input OceanDNA-b24128/checkm_result
[2023-03-16 10:09:28,138] [INFO] Task succeeded: CheckM
[2023-03-16 10:09:28,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 9.38%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 10:09:28,141] [INFO] ===== Completeness check finished =====
[2023-03-16 10:09:28,141] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:09:28,141] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24128/markers.fasta)
[2023-03-16 10:09:28,142] [INFO] Task started: Blastn
[2023-03-16 10:09:28,142] [INFO] Running command: blastn -query OceanDNA-b24128/markers.fasta -db /var/lib/cwl/stg1919bd21-ae53-4ec5-8a94-fa4a43ddea0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24128/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:29,019] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:29,020] [INFO] Selected 25 target genomes.
[2023-03-16 10:09:29,020] [INFO] Target genome list was writen to OceanDNA-b24128/target_genomes_gtdb.txt
[2023-03-16 10:09:29,092] [INFO] Task started: fastANI
[2023-03-16 10:09:29,092] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c6ec5a-a0f1-4fa0-9c06-e37471829e69/OceanDNA-b24128.fa --refList OceanDNA-b24128/target_genomes_gtdb.txt --output OceanDNA-b24128/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:46,611] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:46,614] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:09:46,615] [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_905181725.1	s__UBA830 sp905181725	97.7904	395	474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479125.1	s__UBA830 sp905479125	81.9203	343	474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002689465.1	s__UBA830 sp002689465	79.0337	76	474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471575.1	s__UBA830 sp002471575	77.055	146	474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_009377375.1	s__WHUE01 sp009377375	76.4153	55	474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:09:46,615] [INFO] GTDB search result was written to OceanDNA-b24128/result_gtdb.tsv
[2023-03-16 10:09:46,615] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:46,615] [INFO] DFAST_QC result json was written to OceanDNA-b24128/dqc_result.json
[2023-03-16 10:09:46,616] [INFO] DFAST_QC completed!
[2023-03-16 10:09:46,616] [INFO] Total running time: 0h1m36s