[2023-03-16 17:05:30,906] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:05:30,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:05:30,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference
[2023-03-16 17:05:32,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:05:32,726] [INFO] Task started: Prodigal
[2023-03-16 17:05:32,727] [INFO] Running command: cat /var/lib/cwl/stgec800069-9148-42a1-8841-af21c90754a9/OceanDNA-b27295.fa | prodigal -d OceanDNA-b27295/cds.fna -a OceanDNA-b27295/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:05:42,931] [INFO] Task succeeded: Prodigal
[2023-03-16 17:05:42,932] [INFO] Task started: HMMsearch
[2023-03-16 17:05:42,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b27295/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/reference_markers.hmm OceanDNA-b27295/protein.faa > /dev/null
[2023-03-16 17:05:43,294] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:05:43,295] [INFO] Found 6/6 markers.
[2023-03-16 17:05:43,305] [INFO] Query marker FASTA was written to OceanDNA-b27295/markers.fasta
[2023-03-16 17:05:43,313] [INFO] Task started: Blastn
[2023-03-16 17:05:43,313] [INFO] Running command: blastn -query OceanDNA-b27295/markers.fasta -db /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/reference_markers.fasta -out OceanDNA-b27295/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:05:44,060] [INFO] Task succeeded: Blastn
[2023-03-16 17:05:44,061] [INFO] Selected 14 target genomes.
[2023-03-16 17:05:44,061] [INFO] Target genome list was writen to OceanDNA-b27295/target_genomes.txt
[2023-03-16 17:05:44,122] [INFO] Task started: fastANI
[2023-03-16 17:05:44,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgec800069-9148-42a1-8841-af21c90754a9/OceanDNA-b27295.fa --refList OceanDNA-b27295/target_genomes.txt --output OceanDNA-b27295/fastani_result.tsv --threads 1
[2023-03-16 17:05:51,054] [INFO] Task succeeded: fastANI
[2023-03-16 17:05:51,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:05:51,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:05:51,055] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:05:51,055] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:05:51,055] [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 17:05:51,055] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27295/tc_result.tsv
[2023-03-16 17:05:51,055] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:05:51,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:05:51,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/checkm_data
[2023-03-16 17:05:51,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:05:51,102] [INFO] Task started: CheckM
[2023-03-16 17:05:51,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27295/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27295/checkm_input OceanDNA-b27295/checkm_result
[2023-03-16 17:06:11,126] [INFO] Task succeeded: CheckM
[2023-03-16 17:06:11,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:06:11,128] [INFO] ===== Completeness check finished =====
[2023-03-16 17:06:11,128] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:06:11,128] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27295/markers.fasta)
[2023-03-16 17:06:11,130] [INFO] Task started: Blastn
[2023-03-16 17:06:11,130] [INFO] Running command: blastn -query OceanDNA-b27295/markers.fasta -db /var/lib/cwl/stg9b298053-56ca-4aa4-b7e2-a5226205fb54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27295/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:06:12,549] [INFO] Task succeeded: Blastn
[2023-03-16 17:06:12,550] [INFO] Selected 19 target genomes.
[2023-03-16 17:06:12,550] [INFO] Target genome list was writen to OceanDNA-b27295/target_genomes_gtdb.txt
[2023-03-16 17:06:12,598] [INFO] Task started: fastANI
[2023-03-16 17:06:12,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgec800069-9148-42a1-8841-af21c90754a9/OceanDNA-b27295.fa --refList OceanDNA-b27295/target_genomes_gtdb.txt --output OceanDNA-b27295/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:06:16,582] [INFO] Task succeeded: fastANI
[2023-03-16 17:06:16,587] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:06:16,587] [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_905182015.1	s__MED-G09 sp905182015	99.7221	323	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002704345.1	s__MED-G09 sp002704345	79.0833	146	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.20	99.20	0.77	0.77	2	-
GCA_018658685.1	s__MED-G09 sp018658685	78.7562	158	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279705.1	s__MED-G09 sp003279705	76.9329	81	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.31	98.62	0.86	0.72	3	-
GCA_003278145.1	s__MED-G09 sp003278145	76.8235	109	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	-
GCA_002170885.2	s__MED-G09 sp002170885	76.559	56	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:06:16,587] [INFO] GTDB search result was written to OceanDNA-b27295/result_gtdb.tsv
[2023-03-16 17:06:16,587] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:06:16,588] [INFO] DFAST_QC result json was written to OceanDNA-b27295/dqc_result.json
[2023-03-16 17:06:16,589] [INFO] DFAST_QC completed!
[2023-03-16 17:06:16,589] [INFO] Total running time: 0h0m46s