[2023-03-15 15:51:29,970] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,975] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg368b2af1-0876-4f89-9887-05db13112d68/OceanDNA-b26663.fa | prodigal -d OceanDNA-b26663/cds.fna -a OceanDNA-b26663/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:42,213] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:42,213] [INFO] Task started: HMMsearch
[2023-03-15 15:51:42,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b26663/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/reference_markers.hmm OceanDNA-b26663/protein.faa > /dev/null
[2023-03-15 15:51:42,400] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:42,400] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg368b2af1-0876-4f89-9887-05db13112d68/OceanDNA-b26663.fa]
[2023-03-15 15:51:42,752] [INFO] Query marker FASTA was written to OceanDNA-b26663/markers.fasta
[2023-03-15 15:51:42,752] [INFO] Task started: Blastn
[2023-03-15 15:51:42,752] [INFO] Running command: blastn -query OceanDNA-b26663/markers.fasta -db /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/reference_markers.fasta -out OceanDNA-b26663/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:43,300] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:43,301] [INFO] Selected 20 target genomes.
[2023-03-15 15:51:43,301] [INFO] Target genome list was writen to OceanDNA-b26663/target_genomes.txt
[2023-03-15 15:51:43,313] [INFO] Task started: fastANI
[2023-03-15 15:51:43,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg368b2af1-0876-4f89-9887-05db13112d68/OceanDNA-b26663.fa --refList OceanDNA-b26663/target_genomes.txt --output OceanDNA-b26663/fastani_result.tsv --threads 1
[2023-03-15 15:51:58,325] [INFO] Task succeeded: fastANI
[2023-03-15 15:51:58,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:51:58,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:51:58,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:51:58,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:51:58,326] [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 15:51:58,326] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26663/tc_result.tsv
[2023-03-15 15:51:58,326] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:51:58,326] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:51:58,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/checkm_data
[2023-03-15 15:51:58,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:51:58,334] [INFO] Task started: CheckM
[2023-03-15 15:51:58,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26663/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26663/checkm_input OceanDNA-b26663/checkm_result
[2023-03-15 15:52:30,483] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:30,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.88%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:30,486] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:30,486] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:30,486] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26663/markers.fasta)
[2023-03-15 15:52:30,487] [INFO] Task started: Blastn
[2023-03-15 15:52:30,487] [INFO] Running command: blastn -query OceanDNA-b26663/markers.fasta -db /var/lib/cwl/stgae253d6e-47ab-494c-8411-b9fdd754869b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26663/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:31,203] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:31,204] [INFO] Selected 16 target genomes.
[2023-03-15 15:52:31,204] [INFO] Target genome list was writen to OceanDNA-b26663/target_genomes_gtdb.txt
[2023-03-15 15:52:31,222] [INFO] Task started: fastANI
[2023-03-15 15:52:31,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg368b2af1-0876-4f89-9887-05db13112d68/OceanDNA-b26663.fa --refList OceanDNA-b26663/target_genomes_gtdb.txt --output OceanDNA-b26663/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:43,930] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:43,933] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:52:43,933] [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_900149695.1	s__Anderseniella sp900149695	82.1861	192	245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Anderseniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041995.1	s__Anderseniella sp013041995	81.9473	149	245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Anderseniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:52:43,933] [INFO] GTDB search result was written to OceanDNA-b26663/result_gtdb.tsv
[2023-03-15 15:52:43,933] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:43,934] [INFO] DFAST_QC result json was written to OceanDNA-b26663/dqc_result.json
[2023-03-15 15:52:43,934] [INFO] DFAST_QC completed!
[2023-03-15 15:52:43,934] [INFO] Total running time: 0h1m14s