[2023-03-18 10:24:55,196] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:24:55,196] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:24:55,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference
[2023-03-18 10:24:56,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:24:56,333] [INFO] Task started: Prodigal
[2023-03-18 10:24:56,333] [INFO] Running command: cat /var/lib/cwl/stg1658220c-8da4-412c-b125-86e8439ffbd7/OceanDNA-b31171.fa | prodigal -d OceanDNA-b31171/cds.fna -a OceanDNA-b31171/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:25:06,932] [INFO] Task succeeded: Prodigal
[2023-03-18 10:25:06,933] [INFO] Task started: HMMsearch
[2023-03-18 10:25:06,933] [INFO] Running command: hmmsearch --tblout OceanDNA-b31171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/reference_markers.hmm OceanDNA-b31171/protein.faa > /dev/null
[2023-03-18 10:25:07,099] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:25:07,100] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1658220c-8da4-412c-b125-86e8439ffbd7/OceanDNA-b31171.fa]
[2023-03-18 10:25:07,117] [INFO] Query marker FASTA was written to OceanDNA-b31171/markers.fasta
[2023-03-18 10:25:07,118] [INFO] Task started: Blastn
[2023-03-18 10:25:07,118] [INFO] Running command: blastn -query OceanDNA-b31171/markers.fasta -db /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/reference_markers.fasta -out OceanDNA-b31171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:25:07,631] [INFO] Task succeeded: Blastn
[2023-03-18 10:25:07,632] [INFO] Selected 15 target genomes.
[2023-03-18 10:25:07,632] [INFO] Target genome list was writen to OceanDNA-b31171/target_genomes.txt
[2023-03-18 10:25:07,666] [INFO] Task started: fastANI
[2023-03-18 10:25:07,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg1658220c-8da4-412c-b125-86e8439ffbd7/OceanDNA-b31171.fa --refList OceanDNA-b31171/target_genomes.txt --output OceanDNA-b31171/fastani_result.tsv --threads 1
[2023-03-18 10:25:17,735] [INFO] Task succeeded: fastANI
[2023-03-18 10:25:17,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:25:17,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:25:17,736] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:25:17,736] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:25:17,736] [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
--------------------------------------------------------------------------------
[2023-03-18 10:25:17,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31171/tc_result.tsv
[2023-03-18 10:25:17,736] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:25:17,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:25:17,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/checkm_data
[2023-03-18 10:25:17,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:25:17,941] [INFO] Task started: CheckM
[2023-03-18 10:25:17,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31171/checkm_input OceanDNA-b31171/checkm_result
[2023-03-18 10:25:49,535] [INFO] Task succeeded: CheckM
[2023-03-18 10:25:49,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:25:49,543] [INFO] ===== Completeness check finished =====
[2023-03-18 10:25:49,543] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:25:49,543] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31171/markers.fasta)
[2023-03-18 10:25:49,544] [INFO] Task started: Blastn
[2023-03-18 10:25:49,544] [INFO] Running command: blastn -query OceanDNA-b31171/markers.fasta -db /var/lib/cwl/stg437056f6-82de-464a-bbb3-02d8e1d6c851/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:25:50,281] [INFO] Task succeeded: Blastn
[2023-03-18 10:25:50,283] [INFO] Selected 17 target genomes.
[2023-03-18 10:25:50,283] [INFO] Target genome list was writen to OceanDNA-b31171/target_genomes_gtdb.txt
[2023-03-18 10:25:50,329] [INFO] Task started: fastANI
[2023-03-18 10:25:50,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg1658220c-8da4-412c-b125-86e8439ffbd7/OceanDNA-b31171.fa --refList OceanDNA-b31171/target_genomes_gtdb.txt --output OceanDNA-b31171/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:25:58,981] [INFO] Task succeeded: fastANI
[2023-03-18 10:25:58,984] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:25:58,984] [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_002327565.1	s__UBA2165 sp002327565	78.4769	232	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018649725.1	s__TMED23 sp018649725	78.0161	214	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	99.78	99.75	0.87	0.87	3	-
GCA_018649245.1	s__UBA2165 sp018649245	77.9435	153	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	99.23	99.23	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 10:25:58,984] [INFO] GTDB search result was written to OceanDNA-b31171/result_gtdb.tsv
[2023-03-18 10:25:58,984] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:25:58,985] [INFO] DFAST_QC result json was written to OceanDNA-b31171/dqc_result.json
[2023-03-18 10:25:58,985] [INFO] DFAST_QC completed!
[2023-03-18 10:25:58,985] [INFO] Total running time: 0h1m4s