[2023-03-15 08:09:45,434] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,434] [INFO] DQC Reference Directory: /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference
[2023-03-15 08:09:46,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,719] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,720] [INFO] Running command: cat /var/lib/cwl/stgc36cdded-7e24-499c-8488-5cf427bed1da/OceanDNA-b44097.fa | prodigal -d OceanDNA-b44097/cds.fna -a OceanDNA-b44097/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:52,915] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:52,915] [INFO] Task started: HMMsearch
[2023-03-15 08:09:52,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b44097/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/reference_markers.hmm OceanDNA-b44097/protein.faa > /dev/null
[2023-03-15 08:09:53,159] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:53,159] [INFO] Found 6/6 markers.
[2023-03-15 08:09:53,169] [INFO] Query marker FASTA was written to OceanDNA-b44097/markers.fasta
[2023-03-15 08:09:53,169] [INFO] Task started: Blastn
[2023-03-15 08:09:53,169] [INFO] Running command: blastn -query OceanDNA-b44097/markers.fasta -db /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/reference_markers.fasta -out OceanDNA-b44097/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:53,883] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:53,883] [INFO] Selected 24 target genomes.
[2023-03-15 08:09:53,884] [INFO] Target genome list was writen to OceanDNA-b44097/target_genomes.txt
[2023-03-15 08:09:53,899] [INFO] Task started: fastANI
[2023-03-15 08:09:53,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36cdded-7e24-499c-8488-5cf427bed1da/OceanDNA-b44097.fa --refList OceanDNA-b44097/target_genomes.txt --output OceanDNA-b44097/fastani_result.tsv --threads 1
[2023-03-15 08:10:06,207] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:06,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:06,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:06,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:06,208] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:06,208] [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 08:10:06,208] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44097/tc_result.tsv
[2023-03-15 08:10:06,208] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:06,208] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:06,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/checkm_data
[2023-03-15 08:10:06,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:06,219] [INFO] Task started: CheckM
[2023-03-15 08:10:06,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44097/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44097/checkm_input OceanDNA-b44097/checkm_result
[2023-03-15 08:10:29,784] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:29,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:29,790] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:29,790] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:29,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44097/markers.fasta)
[2023-03-15 08:10:29,791] [INFO] Task started: Blastn
[2023-03-15 08:10:29,791] [INFO] Running command: blastn -query OceanDNA-b44097/markers.fasta -db /var/lib/cwl/stge8bc8663-6a39-4db3-9a06-0d2a243b5558/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44097/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:30,677] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:30,680] [INFO] Selected 23 target genomes.
[2023-03-15 08:10:30,680] [INFO] Target genome list was writen to OceanDNA-b44097/target_genomes_gtdb.txt
[2023-03-15 08:10:30,700] [INFO] Task started: fastANI
[2023-03-15 08:10:30,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36cdded-7e24-499c-8488-5cf427bed1da/OceanDNA-b44097.fa --refList OceanDNA-b44097/target_genomes_gtdb.txt --output OceanDNA-b44097/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:38,877] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:38,880] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:10:38,880] [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_002692205.1	s__UBA11869 sp002692205	99.2295	317	400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002698845.1	s__UBA11869 sp002698845	79.6038	223	400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239225.1	s__UBA11869 sp014239225	77.8	85	400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721165.1	s__UBA11869 sp002721165	77.693	152	400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:38,880] [INFO] GTDB search result was written to OceanDNA-b44097/result_gtdb.tsv
[2023-03-15 08:10:38,881] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:38,881] [INFO] DFAST_QC result json was written to OceanDNA-b44097/dqc_result.json
[2023-03-15 08:10:38,881] [INFO] DFAST_QC completed!
[2023-03-15 08:10:38,881] [INFO] Total running time: 0h0m53s