[2023-03-19 01:38:53,942] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,942] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference
[2023-03-19 01:38:55,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:55,032] [INFO] Task started: Prodigal
[2023-03-19 01:38:55,033] [INFO] Running command: cat /var/lib/cwl/stg3791366c-4524-4af7-9db4-9587d6305b85/OceanDNA-b12089.fa | prodigal -d OceanDNA-b12089/cds.fna -a OceanDNA-b12089/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:05,990] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:05,990] [INFO] Task started: HMMsearch
[2023-03-19 01:39:05,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b12089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/reference_markers.hmm OceanDNA-b12089/protein.faa > /dev/null
[2023-03-19 01:39:06,152] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:06,153] [INFO] Found 6/6 markers.
[2023-03-19 01:39:06,174] [INFO] Query marker FASTA was written to OceanDNA-b12089/markers.fasta
[2023-03-19 01:39:06,174] [INFO] Task started: Blastn
[2023-03-19 01:39:06,174] [INFO] Running command: blastn -query OceanDNA-b12089/markers.fasta -db /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/reference_markers.fasta -out OceanDNA-b12089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:06,692] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:06,694] [INFO] Selected 25 target genomes.
[2023-03-19 01:39:06,694] [INFO] Target genome list was writen to OceanDNA-b12089/target_genomes.txt
[2023-03-19 01:39:06,710] [INFO] Task started: fastANI
[2023-03-19 01:39:06,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg3791366c-4524-4af7-9db4-9587d6305b85/OceanDNA-b12089.fa --refList OceanDNA-b12089/target_genomes.txt --output OceanDNA-b12089/fastani_result.tsv --threads 1
[2023-03-19 01:39:20,727] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:20,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:20,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:20,728] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:20,728] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:20,728] [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
--------------------------------------------------------------------------------
[2023-03-19 01:39:20,729] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12089/tc_result.tsv
[2023-03-19 01:39:20,731] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:20,731] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:20,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/checkm_data
[2023-03-19 01:39:20,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:20,738] [INFO] Task started: CheckM
[2023-03-19 01:39:20,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12089/checkm_input OceanDNA-b12089/checkm_result
[2023-03-19 01:39:52,724] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:52,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.64%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:52,798] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:52,798] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:52,798] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12089/markers.fasta)
[2023-03-19 01:39:52,799] [INFO] Task started: Blastn
[2023-03-19 01:39:52,800] [INFO] Running command: blastn -query OceanDNA-b12089/markers.fasta -db /var/lib/cwl/stg4e9666aa-8f64-4068-be00-209084881842/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:53,480] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:53,509] [INFO] Selected 22 target genomes.
[2023-03-19 01:39:53,509] [INFO] Target genome list was writen to OceanDNA-b12089/target_genomes_gtdb.txt
[2023-03-19 01:39:53,651] [INFO] Task started: fastANI
[2023-03-19 01:39:53,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg3791366c-4524-4af7-9db4-9587d6305b85/OceanDNA-b12089.fa --refList OceanDNA-b12089/target_genomes_gtdb.txt --output OceanDNA-b12089/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:40:05,836] [INFO] Task succeeded: fastANI
[2023-03-19 01:40:05,840] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:40:05,840] [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_002693775.1	s__UBA974 sp002693775	99.7901	501	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902578505.1	s__UBA974 sp902578505	78.5206	87	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	98.75	98.75	0.58	0.58	2	-
GCA_002722795.1	s__UBA974 sp002722795	78.2884	183	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723115.1	s__UBA974 sp002723115	78.2564	174	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746975.1	s__UBA974 sp002746975	76.5536	63	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:40:05,841] [INFO] GTDB search result was written to OceanDNA-b12089/result_gtdb.tsv
[2023-03-19 01:40:05,844] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:40:05,846] [INFO] DFAST_QC result json was written to OceanDNA-b12089/dqc_result.json
[2023-03-19 01:40:05,846] [INFO] DFAST_QC completed!
[2023-03-19 01:40:05,847] [INFO] Total running time: 0h1m12s