[2023-03-16 07:49:29,129] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:29,129] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:29,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference
[2023-03-16 07:49:30,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:30,899] [INFO] Task started: Prodigal
[2023-03-16 07:49:30,899] [INFO] Running command: cat /var/lib/cwl/stgedd66e0e-c7ee-4b92-8e45-d3667a8e2821/OceanDNA-b41972.fa | prodigal -d OceanDNA-b41972/cds.fna -a OceanDNA-b41972/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:34,969] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:34,970] [INFO] Task started: HMMsearch
[2023-03-16 07:49:34,970] [INFO] Running command: hmmsearch --tblout OceanDNA-b41972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/reference_markers.hmm OceanDNA-b41972/protein.faa > /dev/null
[2023-03-16 07:49:35,127] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:35,128] [INFO] Found 6/6 markers.
[2023-03-16 07:49:35,135] [INFO] Query marker FASTA was written to OceanDNA-b41972/markers.fasta
[2023-03-16 07:49:35,136] [INFO] Task started: Blastn
[2023-03-16 07:49:35,136] [INFO] Running command: blastn -query OceanDNA-b41972/markers.fasta -db /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/reference_markers.fasta -out OceanDNA-b41972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:37,701] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:37,702] [INFO] Selected 22 target genomes.
[2023-03-16 07:49:37,702] [INFO] Target genome list was writen to OceanDNA-b41972/target_genomes.txt
[2023-03-16 07:49:37,717] [INFO] Task started: fastANI
[2023-03-16 07:49:37,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd66e0e-c7ee-4b92-8e45-d3667a8e2821/OceanDNA-b41972.fa --refList OceanDNA-b41972/target_genomes.txt --output OceanDNA-b41972/fastani_result.tsv --threads 1
[2023-03-16 07:49:46,876] [INFO] Task succeeded: fastANI
[2023-03-16 07:49:46,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:49:46,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:49:46,877] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:49:46,877] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:49:46,877] [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 07:49:46,878] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41972/tc_result.tsv
[2023-03-16 07:49:46,878] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:49:46,878] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:49:46,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/checkm_data
[2023-03-16 07:49:46,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:49:47,128] [INFO] Task started: CheckM
[2023-03-16 07:49:47,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41972/checkm_input OceanDNA-b41972/checkm_result
[2023-03-16 07:50:09,014] [INFO] Task succeeded: CheckM
[2023-03-16 07:50:09,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.82%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:50:09,016] [INFO] ===== Completeness check finished =====
[2023-03-16 07:50:09,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:50:09,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41972/markers.fasta)
[2023-03-16 07:50:09,018] [INFO] Task started: Blastn
[2023-03-16 07:50:09,018] [INFO] Running command: blastn -query OceanDNA-b41972/markers.fasta -db /var/lib/cwl/stg08e9bb6a-a054-4dc2-af7a-c226e5b258bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:50:11,022] [INFO] Task succeeded: Blastn
[2023-03-16 07:50:11,023] [INFO] Selected 6 target genomes.
[2023-03-16 07:50:11,023] [INFO] Target genome list was writen to OceanDNA-b41972/target_genomes_gtdb.txt
[2023-03-16 07:50:11,034] [INFO] Task started: fastANI
[2023-03-16 07:50:11,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd66e0e-c7ee-4b92-8e45-d3667a8e2821/OceanDNA-b41972.fa --refList OceanDNA-b41972/target_genomes_gtdb.txt --output OceanDNA-b41972/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:50:12,455] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:12,459] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:50:12,459] [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_003331565.1	s__MED-G82 sp003331565	94.0802	156	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594515.1	s__MED-G82 sp902594515	93.7826	238	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.37	95.15	0.90	0.90	3	-
GCA_902601475.1	s__MED-G82 sp902601475	93.2409	228	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.97	95.73	0.86	0.83	4	-
GCA_002172535.2	s__MED-G82 sp002172535	93.0257	214	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628925.1	s__MED-G82 sp902628925	92.7285	235	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623535.1	s__MED-G82 sp902623535	91.6543	208	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:50:12,460] [INFO] GTDB search result was written to OceanDNA-b41972/result_gtdb.tsv
[2023-03-16 07:50:12,460] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:50:12,460] [INFO] DFAST_QC result json was written to OceanDNA-b41972/dqc_result.json
[2023-03-16 07:50:12,461] [INFO] DFAST_QC completed!
[2023-03-16 07:50:12,461] [INFO] Total running time: 0h0m43s