[2023-03-19 01:13:44,309] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,310] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference
[2023-03-19 01:13:45,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,414] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,414] [INFO] Running command: cat /var/lib/cwl/stga26695bd-4226-4c49-bdca-7c41ed970b45/OceanDNA-b3596.fa | prodigal -d OceanDNA-b3596/cds.fna -a OceanDNA-b3596/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:51,967] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:51,967] [INFO] Task started: HMMsearch
[2023-03-19 01:13:51,967] [INFO] Running command: hmmsearch --tblout OceanDNA-b3596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/reference_markers.hmm OceanDNA-b3596/protein.faa > /dev/null
[2023-03-19 01:13:52,137] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:52,137] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga26695bd-4226-4c49-bdca-7c41ed970b45/OceanDNA-b3596.fa]
[2023-03-19 01:13:52,145] [INFO] Query marker FASTA was written to OceanDNA-b3596/markers.fasta
[2023-03-19 01:13:52,147] [INFO] Task started: Blastn
[2023-03-19 01:13:52,147] [INFO] Running command: blastn -query OceanDNA-b3596/markers.fasta -db /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/reference_markers.fasta -out OceanDNA-b3596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:52,666] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:52,667] [INFO] Selected 18 target genomes.
[2023-03-19 01:13:52,667] [INFO] Target genome list was writen to OceanDNA-b3596/target_genomes.txt
[2023-03-19 01:13:52,677] [INFO] Task started: fastANI
[2023-03-19 01:13:52,677] [INFO] Running command: fastANI --query /var/lib/cwl/stga26695bd-4226-4c49-bdca-7c41ed970b45/OceanDNA-b3596.fa --refList OceanDNA-b3596/target_genomes.txt --output OceanDNA-b3596/fastani_result.tsv --threads 1
[2023-03-19 01:14:07,582] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:07,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:07,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:07,582] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:07,582] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:07,582] [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 01:14:07,583] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3596/tc_result.tsv
[2023-03-19 01:14:07,583] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:07,583] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:07,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/checkm_data
[2023-03-19 01:14:07,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:07,843] [INFO] Task started: CheckM
[2023-03-19 01:14:07,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3596/checkm_input OceanDNA-b3596/checkm_result
[2023-03-19 01:14:30,015] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:30,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:30,017] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:30,017] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:30,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3596/markers.fasta)
[2023-03-19 01:14:30,019] [INFO] Task started: Blastn
[2023-03-19 01:14:30,019] [INFO] Running command: blastn -query OceanDNA-b3596/markers.fasta -db /var/lib/cwl/stgd1dde97c-7289-46bb-bbdf-e5f4ecde3089/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:30,690] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:30,691] [INFO] Selected 16 target genomes.
[2023-03-19 01:14:30,691] [INFO] Target genome list was writen to OceanDNA-b3596/target_genomes_gtdb.txt
[2023-03-19 01:14:30,707] [INFO] Task started: fastANI
[2023-03-19 01:14:30,707] [INFO] Running command: fastANI --query /var/lib/cwl/stga26695bd-4226-4c49-bdca-7c41ed970b45/OceanDNA-b3596.fa --refList OceanDNA-b3596/target_genomes_gtdb.txt --output OceanDNA-b3596/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:40,562] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:40,565] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:40,565] [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_003489485.1	s__JJ008 sp003489485	83.3092	174	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.38	96.92	0.79	0.76	3	-
GCA_016872155.1	s__JJ008 sp016872155	78.5623	154	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872195.1	s__JJ008 sp016872195	77.7006	118	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:40,565] [INFO] GTDB search result was written to OceanDNA-b3596/result_gtdb.tsv
[2023-03-19 01:14:40,565] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:40,566] [INFO] DFAST_QC result json was written to OceanDNA-b3596/dqc_result.json
[2023-03-19 01:14:40,566] [INFO] DFAST_QC completed!
[2023-03-19 01:14:40,566] [INFO] Total running time: 0h0m56s