[2023-03-15 10:52:57,299] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,299] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference
[2023-03-15 10:52:58,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,866] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,866] [INFO] Running command: cat /var/lib/cwl/stge70a0ac4-b99a-47d2-926f-9a6f1ca54250/OceanDNA-b44488.fa | prodigal -d OceanDNA-b44488/cds.fna -a OceanDNA-b44488/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:06,222] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:06,223] [INFO] Task started: HMMsearch
[2023-03-15 10:53:06,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b44488/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/reference_markers.hmm OceanDNA-b44488/protein.faa > /dev/null
[2023-03-15 10:53:06,388] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:06,389] [INFO] Found 6/6 markers.
[2023-03-15 10:53:06,399] [INFO] Query marker FASTA was written to OceanDNA-b44488/markers.fasta
[2023-03-15 10:53:06,401] [INFO] Task started: Blastn
[2023-03-15 10:53:06,401] [INFO] Running command: blastn -query OceanDNA-b44488/markers.fasta -db /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/reference_markers.fasta -out OceanDNA-b44488/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:06,919] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:06,920] [INFO] Selected 25 target genomes.
[2023-03-15 10:53:06,920] [INFO] Target genome list was writen to OceanDNA-b44488/target_genomes.txt
[2023-03-15 10:53:06,938] [INFO] Task started: fastANI
[2023-03-15 10:53:06,939] [INFO] Running command: fastANI --query /var/lib/cwl/stge70a0ac4-b99a-47d2-926f-9a6f1ca54250/OceanDNA-b44488.fa --refList OceanDNA-b44488/target_genomes.txt --output OceanDNA-b44488/fastani_result.tsv --threads 1
[2023-03-15 10:53:20,907] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:20,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:20,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:20,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:20,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:20,907] [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 10:53:20,908] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44488/tc_result.tsv
[2023-03-15 10:53:20,908] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:20,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:20,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/checkm_data
[2023-03-15 10:53:20,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:20,990] [INFO] Task started: CheckM
[2023-03-15 10:53:20,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44488/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44488/checkm_input OceanDNA-b44488/checkm_result
[2023-03-15 10:53:44,901] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:44,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:44,904] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:44,904] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:44,904] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44488/markers.fasta)
[2023-03-15 10:53:44,904] [INFO] Task started: Blastn
[2023-03-15 10:53:44,904] [INFO] Running command: blastn -query OceanDNA-b44488/markers.fasta -db /var/lib/cwl/stgcf620d36-c13c-4221-aeef-aa8eb3056e86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44488/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:45,663] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:45,664] [INFO] Selected 26 target genomes.
[2023-03-15 10:53:45,664] [INFO] Target genome list was writen to OceanDNA-b44488/target_genomes_gtdb.txt
[2023-03-15 10:53:45,740] [INFO] Task started: fastANI
[2023-03-15 10:53:45,740] [INFO] Running command: fastANI --query /var/lib/cwl/stge70a0ac4-b99a-47d2-926f-9a6f1ca54250/OceanDNA-b44488.fa --refList OceanDNA-b44488/target_genomes_gtdb.txt --output OceanDNA-b44488/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:53,474] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:53,477] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 10:53:53,477] [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_902510755.1	s__SP4260 sp902510755	98.7783	270	467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902512585.1	s__SP4260 sp902512585	98.5548	241	467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_905182415.1	s__SP4260 sp905182415	77.2948	122	467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:53,478] [INFO] GTDB search result was written to OceanDNA-b44488/result_gtdb.tsv
[2023-03-15 10:53:53,478] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:53,478] [INFO] DFAST_QC result json was written to OceanDNA-b44488/dqc_result.json
[2023-03-15 10:53:53,478] [INFO] DFAST_QC completed!
[2023-03-15 10:53:53,478] [INFO] Total running time: 0h0m56s