[2023-03-18 10:53:04,366] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:53:04,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:53:04,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference
[2023-03-18 10:53:05,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:53:05,508] [INFO] Task started: Prodigal
[2023-03-18 10:53:05,508] [INFO] Running command: cat /var/lib/cwl/stg35c847a3-4a57-4706-b0ed-357b94e2029b/OceanDNA-b32869.fa | prodigal -d OceanDNA-b32869/cds.fna -a OceanDNA-b32869/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:53:23,432] [INFO] Task succeeded: Prodigal
[2023-03-18 10:53:23,432] [INFO] Task started: HMMsearch
[2023-03-18 10:53:23,432] [INFO] Running command: hmmsearch --tblout OceanDNA-b32869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/reference_markers.hmm OceanDNA-b32869/protein.faa > /dev/null
[2023-03-18 10:53:23,618] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:53:23,618] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg35c847a3-4a57-4706-b0ed-357b94e2029b/OceanDNA-b32869.fa]
[2023-03-18 10:53:23,637] [INFO] Query marker FASTA was written to OceanDNA-b32869/markers.fasta
[2023-03-18 10:53:23,639] [INFO] Task started: Blastn
[2023-03-18 10:53:23,639] [INFO] Running command: blastn -query OceanDNA-b32869/markers.fasta -db /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/reference_markers.fasta -out OceanDNA-b32869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:53:24,261] [INFO] Task succeeded: Blastn
[2023-03-18 10:53:24,263] [INFO] Selected 30 target genomes.
[2023-03-18 10:53:24,264] [INFO] Target genome list was writen to OceanDNA-b32869/target_genomes.txt
[2023-03-18 10:53:24,281] [INFO] Task started: fastANI
[2023-03-18 10:53:24,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c847a3-4a57-4706-b0ed-357b94e2029b/OceanDNA-b32869.fa --refList OceanDNA-b32869/target_genomes.txt --output OceanDNA-b32869/fastani_result.tsv --threads 1
[2023-03-18 10:53:41,357] [INFO] Task succeeded: fastANI
[2023-03-18 10:53:41,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:53:41,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:53:41,357] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:53:41,357] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:53:41,357] [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 10:53:41,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32869/tc_result.tsv
[2023-03-18 10:53:41,361] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:53:41,361] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:53:41,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/checkm_data
[2023-03-18 10:53:41,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:53:41,412] [INFO] Task started: CheckM
[2023-03-18 10:53:41,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32869/checkm_input OceanDNA-b32869/checkm_result
[2023-03-18 10:54:28,106] [INFO] Task succeeded: CheckM
[2023-03-18 10:54:28,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:54:28,120] [INFO] ===== Completeness check finished =====
[2023-03-18 10:54:28,121] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:54:28,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32869/markers.fasta)
[2023-03-18 10:54:28,122] [INFO] Task started: Blastn
[2023-03-18 10:54:28,122] [INFO] Running command: blastn -query OceanDNA-b32869/markers.fasta -db /var/lib/cwl/stg4ca34864-8d6d-4f3e-b0a3-7b5663791849/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:54:29,198] [INFO] Task succeeded: Blastn
[2023-03-18 10:54:29,203] [INFO] Selected 16 target genomes.
[2023-03-18 10:54:29,203] [INFO] Target genome list was writen to OceanDNA-b32869/target_genomes_gtdb.txt
[2023-03-18 10:54:29,215] [INFO] Task started: fastANI
[2023-03-18 10:54:29,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c847a3-4a57-4706-b0ed-357b94e2029b/OceanDNA-b32869.fa --refList OceanDNA-b32869/target_genomes_gtdb.txt --output OceanDNA-b32869/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:54:38,449] [INFO] Task succeeded: fastANI
[2023-03-18 10:54:38,453] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:54:38,453] [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_905479265.1	s__UBA7985 sp905479265	99.6148	846	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002705565.1	s__UBA7985 sp002705565	79.9059	404	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.09	99.09	0.80	0.80	2	-
GCA_002700865.1	s__UBA7985 sp002700865	79.0536	324	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.96	99.96	0.93	0.93	2	-
GCA_002708995.1	s__UBA7985 sp002708995	77.5579	253	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	95.44	95.44	0.84	0.83	3	-
GCA_002711265.1	s__UBA7985 sp002711265	77.3476	204	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.38	98.76	0.89	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-18 10:54:38,456] [INFO] GTDB search result was written to OceanDNA-b32869/result_gtdb.tsv
[2023-03-18 10:54:38,458] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:54:38,462] [INFO] DFAST_QC result json was written to OceanDNA-b32869/dqc_result.json
[2023-03-18 10:54:38,462] [INFO] DFAST_QC completed!
[2023-03-18 10:54:38,462] [INFO] Total running time: 0h1m34s