[2023-03-16 05:52:41,082] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,082] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference
[2023-03-16 05:52:42,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,219] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,219] [INFO] Running command: cat /var/lib/cwl/stg22a81eef-86cc-4dfe-a888-20475634199d/OceanDNA-b20196.fa | prodigal -d OceanDNA-b20196/cds.fna -a OceanDNA-b20196/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:52,993] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:52,993] [INFO] Task started: HMMsearch
[2023-03-16 05:52:52,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b20196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/reference_markers.hmm OceanDNA-b20196/protein.faa > /dev/null
[2023-03-16 05:52:53,155] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:53,156] [INFO] Found 6/6 markers.
[2023-03-16 05:52:53,172] [INFO] Query marker FASTA was written to OceanDNA-b20196/markers.fasta
[2023-03-16 05:52:53,173] [INFO] Task started: Blastn
[2023-03-16 05:52:53,173] [INFO] Running command: blastn -query OceanDNA-b20196/markers.fasta -db /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/reference_markers.fasta -out OceanDNA-b20196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:53,714] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:53,716] [INFO] Selected 14 target genomes.
[2023-03-16 05:52:53,717] [INFO] Target genome list was writen to OceanDNA-b20196/target_genomes.txt
[2023-03-16 05:52:53,728] [INFO] Task started: fastANI
[2023-03-16 05:52:53,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a81eef-86cc-4dfe-a888-20475634199d/OceanDNA-b20196.fa --refList OceanDNA-b20196/target_genomes.txt --output OceanDNA-b20196/fastani_result.tsv --threads 1
[2023-03-16 05:53:01,403] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:01,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:01,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:01,404] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:01,404] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:53:01,404] [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 05:53:01,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20196/tc_result.tsv
[2023-03-16 05:53:01,406] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:01,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:01,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/checkm_data
[2023-03-16 05:53:01,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:01,413] [INFO] Task started: CheckM
[2023-03-16 05:53:01,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20196/checkm_input OceanDNA-b20196/checkm_result
[2023-03-16 05:53:29,090] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:29,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:29,093] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:29,093] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:29,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20196/markers.fasta)
[2023-03-16 05:53:29,094] [INFO] Task started: Blastn
[2023-03-16 05:53:29,094] [INFO] Running command: blastn -query OceanDNA-b20196/markers.fasta -db /var/lib/cwl/stg36e16985-8fac-4c11-ba5f-3e8510e9cd2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:29,869] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:29,871] [INFO] Selected 18 target genomes.
[2023-03-16 05:53:29,871] [INFO] Target genome list was writen to OceanDNA-b20196/target_genomes_gtdb.txt
[2023-03-16 05:53:29,908] [INFO] Task started: fastANI
[2023-03-16 05:53:29,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a81eef-86cc-4dfe-a888-20475634199d/OceanDNA-b20196.fa --refList OceanDNA-b20196/target_genomes_gtdb.txt --output OceanDNA-b20196/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:35,896] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:35,899] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:53:35,899] [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_002321855.1	s__UBA1611 sp002321855	93.6282	223	340	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA1611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964275.1	s__UBA1611 sp012964275	79.0326	179	340	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA1611	95.0	98.90	98.90	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:35,900] [INFO] GTDB search result was written to OceanDNA-b20196/result_gtdb.tsv
[2023-03-16 05:53:35,901] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:35,902] [INFO] DFAST_QC result json was written to OceanDNA-b20196/dqc_result.json
[2023-03-16 05:53:35,902] [INFO] DFAST_QC completed!
[2023-03-16 05:53:35,902] [INFO] Total running time: 0h0m55s