[2023-03-19 02:05:13,379] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference
[2023-03-19 02:05:14,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,691] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,692] [INFO] Running command: cat /var/lib/cwl/stg092068b1-91c4-4610-bff8-c414c0a520f9/OceanDNA-b44091.fa | prodigal -d OceanDNA-b44091/cds.fna -a OceanDNA-b44091/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:18,490] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:18,491] [INFO] Task started: HMMsearch
[2023-03-19 02:05:18,491] [INFO] Running command: hmmsearch --tblout OceanDNA-b44091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/reference_markers.hmm OceanDNA-b44091/protein.faa > /dev/null
[2023-03-19 02:05:18,652] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:18,652] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg092068b1-91c4-4610-bff8-c414c0a520f9/OceanDNA-b44091.fa]
[2023-03-19 02:05:18,659] [INFO] Query marker FASTA was written to OceanDNA-b44091/markers.fasta
[2023-03-19 02:05:18,659] [INFO] Task started: Blastn
[2023-03-19 02:05:18,659] [INFO] Running command: blastn -query OceanDNA-b44091/markers.fasta -db /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/reference_markers.fasta -out OceanDNA-b44091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:19,134] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:19,135] [INFO] Selected 11 target genomes.
[2023-03-19 02:05:19,135] [INFO] Target genome list was writen to OceanDNA-b44091/target_genomes.txt
[2023-03-19 02:05:19,142] [INFO] Task started: fastANI
[2023-03-19 02:05:19,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg092068b1-91c4-4610-bff8-c414c0a520f9/OceanDNA-b44091.fa --refList OceanDNA-b44091/target_genomes.txt --output OceanDNA-b44091/fastani_result.tsv --threads 1
[2023-03-19 02:05:24,873] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:24,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:24,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:24,873] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:24,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:24,873] [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 02:05:24,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44091/tc_result.tsv
[2023-03-19 02:05:24,874] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:24,874] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:24,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/checkm_data
[2023-03-19 02:05:24,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:24,879] [INFO] Task started: CheckM
[2023-03-19 02:05:24,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44091/checkm_input OceanDNA-b44091/checkm_result
[2023-03-19 02:05:40,768] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:40,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.20%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:40,770] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:40,771] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:40,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44091/markers.fasta)
[2023-03-19 02:05:40,772] [INFO] Task started: Blastn
[2023-03-19 02:05:40,772] [INFO] Running command: blastn -query OceanDNA-b44091/markers.fasta -db /var/lib/cwl/stg17c5f723-2e1c-4c39-b827-d9557789c1c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:41,245] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:41,245] [INFO] Selected 16 target genomes.
[2023-03-19 02:05:41,245] [INFO] Target genome list was writen to OceanDNA-b44091/target_genomes_gtdb.txt
[2023-03-19 02:05:41,523] [INFO] Task started: fastANI
[2023-03-19 02:05:41,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg092068b1-91c4-4610-bff8-c414c0a520f9/OceanDNA-b44091.fa --refList OceanDNA-b44091/target_genomes_gtdb.txt --output OceanDNA-b44091/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:05:46,716] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:46,718] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:05:46,719] [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_002721165.1	s__UBA11869 sp002721165	79.8295	165	248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239225.1	s__UBA11869 sp014239225	78.6628	99	248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692205.1	s__UBA11869 sp002692205	77.2172	78	248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:05:46,719] [INFO] GTDB search result was written to OceanDNA-b44091/result_gtdb.tsv
[2023-03-19 02:05:46,719] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:05:46,719] [INFO] DFAST_QC result json was written to OceanDNA-b44091/dqc_result.json
[2023-03-19 02:05:46,720] [INFO] DFAST_QC completed!
[2023-03-19 02:05:46,720] [INFO] Total running time: 0h0m33s