[2023-03-16 05:52:41,095] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,096] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference
[2023-03-16 05:52:42,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,199] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,199] [INFO] Running command: cat /var/lib/cwl/stgc601f10b-0f70-4a7a-bf13-d28b37cdef9d/OceanDNA-a1206.fa | prodigal -d OceanDNA-a1206/cds.fna -a OceanDNA-a1206/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:44,873] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:44,873] [INFO] Task started: HMMsearch
[2023-03-16 05:52:44,873] [INFO] Running command: hmmsearch --tblout OceanDNA-a1206/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/reference_markers.hmm OceanDNA-a1206/protein.faa > /dev/null
[2023-03-16 05:52:45,001] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:45,001] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc601f10b-0f70-4a7a-bf13-d28b37cdef9d/OceanDNA-a1206.fa]
[2023-03-16 05:52:45,009] [INFO] Query marker FASTA was written to OceanDNA-a1206/markers.fasta
[2023-03-16 05:52:45,009] [INFO] Task started: Blastn
[2023-03-16 05:52:45,009] [INFO] Running command: blastn -query OceanDNA-a1206/markers.fasta -db /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/reference_markers.fasta -out OceanDNA-a1206/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:45,485] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:45,486] [INFO] Selected 5 target genomes.
[2023-03-16 05:52:45,487] [INFO] Target genome list was writen to OceanDNA-a1206/target_genomes.txt
[2023-03-16 05:52:45,489] [INFO] Task started: fastANI
[2023-03-16 05:52:45,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgc601f10b-0f70-4a7a-bf13-d28b37cdef9d/OceanDNA-a1206.fa --refList OceanDNA-a1206/target_genomes.txt --output OceanDNA-a1206/fastani_result.tsv --threads 1
[2023-03-16 05:52:46,883] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:46,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:52:46,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:52:46,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:52:46,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:52:46,884] [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 05:52:46,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1206/tc_result.tsv
[2023-03-16 05:52:46,885] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:52:46,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:52:46,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/checkm_data
[2023-03-16 05:52:46,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:52:46,891] [INFO] Task started: CheckM
[2023-03-16 05:52:46,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1206/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1206/checkm_input OceanDNA-a1206/checkm_result
[2023-03-16 05:53:00,230] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:00,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:00,233] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:00,233] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:00,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1206/markers.fasta)
[2023-03-16 05:53:00,234] [INFO] Task started: Blastn
[2023-03-16 05:53:00,234] [INFO] Running command: blastn -query OceanDNA-a1206/markers.fasta -db /var/lib/cwl/stg8f31fa62-e29d-4b71-aa37-e5d6aec89e0c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1206/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:00,822] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:00,824] [INFO] Selected 8 target genomes.
[2023-03-16 05:53:00,824] [INFO] Target genome list was writen to OceanDNA-a1206/target_genomes_gtdb.txt
[2023-03-16 05:53:00,834] [INFO] Task started: fastANI
[2023-03-16 05:53:00,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgc601f10b-0f70-4a7a-bf13-d28b37cdef9d/OceanDNA-a1206.fa --refList OceanDNA-a1206/target_genomes_gtdb.txt --output OceanDNA-a1206/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:02,681] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:02,684] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:53:02,684] [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_018655015.1	s__JABIKK01 sp018655015	99.894	153	163	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__UBA489;g__JABIKK01	95.0	99.94	99.94	0.97	0.97	2	conclusive
GCA_018658265.1	s__JABIKK01 sp018658265	80.3265	88	163	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__UBA489;g__JABIKK01	95.0	99.59	99.59	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:02,684] [INFO] GTDB search result was written to OceanDNA-a1206/result_gtdb.tsv
[2023-03-16 05:53:02,685] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:02,686] [INFO] DFAST_QC result json was written to OceanDNA-a1206/dqc_result.json
[2023-03-16 05:53:02,686] [INFO] DFAST_QC completed!
[2023-03-16 05:53:02,686] [INFO] Total running time: 0h0m22s