[2023-03-17 06:30:51,161] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:51,161] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:51,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference
[2023-03-17 06:30:52,295] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:52,295] [INFO] Task started: Prodigal
[2023-03-17 06:30:52,295] [INFO] Running command: cat /var/lib/cwl/stg084e38de-5375-41ae-a6b0-8ecf3764ccb0/OceanDNA-b44160.fa | prodigal -d OceanDNA-b44160/cds.fna -a OceanDNA-b44160/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:07,408] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:07,408] [INFO] Task started: HMMsearch
[2023-03-17 06:31:07,408] [INFO] Running command: hmmsearch --tblout OceanDNA-b44160/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/reference_markers.hmm OceanDNA-b44160/protein.faa > /dev/null
[2023-03-17 06:31:07,623] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:07,623] [INFO] Found 6/6 markers.
[2023-03-17 06:31:07,640] [INFO] Query marker FASTA was written to OceanDNA-b44160/markers.fasta
[2023-03-17 06:31:07,641] [INFO] Task started: Blastn
[2023-03-17 06:31:07,641] [INFO] Running command: blastn -query OceanDNA-b44160/markers.fasta -db /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/reference_markers.fasta -out OceanDNA-b44160/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:08,212] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:08,213] [INFO] Selected 23 target genomes.
[2023-03-17 06:31:08,213] [INFO] Target genome list was writen to OceanDNA-b44160/target_genomes.txt
[2023-03-17 06:31:08,225] [INFO] Task started: fastANI
[2023-03-17 06:31:08,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg084e38de-5375-41ae-a6b0-8ecf3764ccb0/OceanDNA-b44160.fa --refList OceanDNA-b44160/target_genomes.txt --output OceanDNA-b44160/fastani_result.tsv --threads 1
[2023-03-17 06:31:20,906] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:20,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:20,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:20,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:20,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:20,907] [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
--------------------------------------------------------------------------------
[2023-03-17 06:31:20,907] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44160/tc_result.tsv
[2023-03-17 06:31:20,908] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:20,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:20,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/checkm_data
[2023-03-17 06:31:20,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:20,916] [INFO] Task started: CheckM
[2023-03-17 06:31:20,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44160/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44160/checkm_input OceanDNA-b44160/checkm_result
[2023-03-17 06:32:01,404] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:01,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:01,407] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:01,407] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:01,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44160/markers.fasta)
[2023-03-17 06:32:01,407] [INFO] Task started: Blastn
[2023-03-17 06:32:01,407] [INFO] Running command: blastn -query OceanDNA-b44160/markers.fasta -db /var/lib/cwl/stg8636614b-6e3c-434d-95ec-77a02a1c513f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44160/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:02,340] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:02,342] [INFO] Selected 20 target genomes.
[2023-03-17 06:32:02,342] [INFO] Target genome list was writen to OceanDNA-b44160/target_genomes_gtdb.txt
[2023-03-17 06:32:02,719] [INFO] Task started: fastANI
[2023-03-17 06:32:02,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg084e38de-5375-41ae-a6b0-8ecf3764ccb0/OceanDNA-b44160.fa --refList OceanDNA-b44160/target_genomes_gtdb.txt --output OceanDNA-b44160/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:12,860] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:12,865] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:12,865] [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_002292815.1	s__UBA7359 sp002292815	82.391	561	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002470825.1	s__UBA7359 sp002470825	78.9925	289	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.91	99.91	0.91	0.91	2	-
GCA_905182825.1	s__UBA7359 sp905182825	78.9087	271	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112535.1	s__UBA7359 sp013112535	77.4813	173	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012960105.1	s__UBA7359 sp012960105	77.2899	166	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.96	99.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:12,865] [INFO] GTDB search result was written to OceanDNA-b44160/result_gtdb.tsv
[2023-03-17 06:32:12,865] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:12,866] [INFO] DFAST_QC result json was written to OceanDNA-b44160/dqc_result.json
[2023-03-17 06:32:12,866] [INFO] DFAST_QC completed!
[2023-03-17 06:32:12,866] [INFO] Total running time: 0h1m22s