[2023-03-15 09:48:16,409] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,409] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,409] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference
[2023-03-15 09:48:18,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stg8474fc24-d504-4507-a286-08991adad610/OceanDNA-b32571.fa | prodigal -d OceanDNA-b32571/cds.fna -a OceanDNA-b32571/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:22,279] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:22,280] [INFO] Task started: HMMsearch
[2023-03-15 09:48:22,280] [INFO] Running command: hmmsearch --tblout OceanDNA-b32571/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/reference_markers.hmm OceanDNA-b32571/protein.faa > /dev/null
[2023-03-15 09:48:22,461] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:22,461] [INFO] Found 6/6 markers.
[2023-03-15 09:48:22,470] [INFO] Query marker FASTA was written to OceanDNA-b32571/markers.fasta
[2023-03-15 09:48:22,472] [INFO] Task started: Blastn
[2023-03-15 09:48:22,472] [INFO] Running command: blastn -query OceanDNA-b32571/markers.fasta -db /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/reference_markers.fasta -out OceanDNA-b32571/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:25,021] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:25,021] [INFO] Selected 16 target genomes.
[2023-03-15 09:48:25,022] [INFO] Target genome list was writen to OceanDNA-b32571/target_genomes.txt
[2023-03-15 09:48:25,054] [INFO] Task started: fastANI
[2023-03-15 09:48:25,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg8474fc24-d504-4507-a286-08991adad610/OceanDNA-b32571.fa --refList OceanDNA-b32571/target_genomes.txt --output OceanDNA-b32571/fastani_result.tsv --threads 1
[2023-03-15 09:48:33,367] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:33,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:33,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:33,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:33,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:33,368] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:33,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32571/tc_result.tsv
[2023-03-15 09:48:33,368] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:33,369] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:33,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/checkm_data
[2023-03-15 09:48:33,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:33,374] [INFO] Task started: CheckM
[2023-03-15 09:48:33,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32571/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32571/checkm_input OceanDNA-b32571/checkm_result
[2023-03-15 09:48:50,555] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:50,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:48:50,557] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:50,557] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:50,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32571/markers.fasta)
[2023-03-15 09:48:50,557] [INFO] Task started: Blastn
[2023-03-15 09:48:50,557] [INFO] Running command: blastn -query OceanDNA-b32571/markers.fasta -db /var/lib/cwl/stgf0f2f6cf-029c-4ce7-b2c2-673aa72a34d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32571/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:51,999] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:52,000] [INFO] Selected 16 target genomes.
[2023-03-15 09:48:52,000] [INFO] Target genome list was writen to OceanDNA-b32571/target_genomes_gtdb.txt
[2023-03-15 09:48:52,516] [INFO] Task started: fastANI
[2023-03-15 09:48:52,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg8474fc24-d504-4507-a286-08991adad610/OceanDNA-b32571.fa --refList OceanDNA-b32571/target_genomes_gtdb.txt --output OceanDNA-b32571/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:48:55,900] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:55,904] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:48:55,904] [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_902595755.1	s__TMED13 sp902595755	99.7417	233	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167825.1	s__TMED13 sp002167825	84.6107	223	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902547955.1	s__MED-G10 sp902547955	76.6153	54	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_002167215.1	s__GCA-2691245 sp002167215	75.9724	54	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	97.98	96.11	0.71	0.71	3	-
GCA_002712255.1	s__MED-G10 sp002712255	75.8274	52	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:48:55,904] [INFO] GTDB search result was written to OceanDNA-b32571/result_gtdb.tsv
[2023-03-15 09:48:55,904] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:48:55,905] [INFO] DFAST_QC result json was written to OceanDNA-b32571/dqc_result.json
[2023-03-15 09:48:55,905] [INFO] DFAST_QC completed!
[2023-03-15 09:48:55,905] [INFO] Total running time: 0h0m39s