[2023-03-16 09:13:21,070] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:13:21,070] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:13:21,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference
[2023-03-16 09:13:22,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:13:22,474] [INFO] Task started: Prodigal
[2023-03-16 09:13:22,474] [INFO] Running command: cat /var/lib/cwl/stg1bc933ab-b71c-4539-8a23-3f4a15f41153/OceanDNA-b13174.fa | prodigal -d OceanDNA-b13174/cds.fna -a OceanDNA-b13174/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:13:35,005] [INFO] Task succeeded: Prodigal
[2023-03-16 09:13:35,005] [INFO] Task started: HMMsearch
[2023-03-16 09:13:35,005] [INFO] Running command: hmmsearch --tblout OceanDNA-b13174/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/reference_markers.hmm OceanDNA-b13174/protein.faa > /dev/null
[2023-03-16 09:13:35,192] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:13:35,192] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bc933ab-b71c-4539-8a23-3f4a15f41153/OceanDNA-b13174.fa]
[2023-03-16 09:13:35,213] [INFO] Query marker FASTA was written to OceanDNA-b13174/markers.fasta
[2023-03-16 09:13:35,214] [INFO] Task started: Blastn
[2023-03-16 09:13:35,214] [INFO] Running command: blastn -query OceanDNA-b13174/markers.fasta -db /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/reference_markers.fasta -out OceanDNA-b13174/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:13:35,707] [INFO] Task succeeded: Blastn
[2023-03-16 09:13:35,715] [INFO] Selected 17 target genomes.
[2023-03-16 09:13:35,715] [INFO] Target genome list was writen to OceanDNA-b13174/target_genomes.txt
[2023-03-16 09:13:35,739] [INFO] Task started: fastANI
[2023-03-16 09:13:35,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc933ab-b71c-4539-8a23-3f4a15f41153/OceanDNA-b13174.fa --refList OceanDNA-b13174/target_genomes.txt --output OceanDNA-b13174/fastani_result.tsv --threads 1
[2023-03-16 09:13:44,392] [INFO] Task succeeded: fastANI
[2023-03-16 09:13:44,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:13:44,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:13:44,393] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:13:44,393] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:13:44,393] [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
--------------------------------------------------------------------------------
[2023-03-16 09:13:44,393] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13174/tc_result.tsv
[2023-03-16 09:13:44,394] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:13:44,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:13:44,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/checkm_data
[2023-03-16 09:13:44,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:13:44,433] [INFO] Task started: CheckM
[2023-03-16 09:13:44,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13174/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13174/checkm_input OceanDNA-b13174/checkm_result
[2023-03-16 09:14:19,327] [INFO] Task succeeded: CheckM
[2023-03-16 09:14:19,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:14:19,380] [INFO] ===== Completeness check finished =====
[2023-03-16 09:14:19,380] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:14:19,381] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13174/markers.fasta)
[2023-03-16 09:14:19,382] [INFO] Task started: Blastn
[2023-03-16 09:14:19,382] [INFO] Running command: blastn -query OceanDNA-b13174/markers.fasta -db /var/lib/cwl/stg0220eecc-3945-4a10-9157-4585c1099f80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13174/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:14:20,025] [INFO] Task succeeded: Blastn
[2023-03-16 09:14:20,025] [INFO] Selected 19 target genomes.
[2023-03-16 09:14:20,026] [INFO] Target genome list was writen to OceanDNA-b13174/target_genomes_gtdb.txt
[2023-03-16 09:14:20,071] [INFO] Task started: fastANI
[2023-03-16 09:14:20,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc933ab-b71c-4539-8a23-3f4a15f41153/OceanDNA-b13174.fa --refList OceanDNA-b13174/target_genomes_gtdb.txt --output OceanDNA-b13174/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:14:29,503] [INFO] Task succeeded: fastANI
[2023-03-16 09:14:29,505] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:14:29,505] [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_002787775.1	s__UBA4207 sp002787775	81.0294	472	804	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA4207	95.0	99.91	99.91	0.96	0.96	3	-
GCA_002716825.1	s__UBA4207 sp002716825	78.2969	189	804	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA4207	95.0	99.84	99.84	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:14:29,506] [INFO] GTDB search result was written to OceanDNA-b13174/result_gtdb.tsv
[2023-03-16 09:14:29,506] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:14:29,506] [INFO] DFAST_QC result json was written to OceanDNA-b13174/dqc_result.json
[2023-03-16 09:14:29,506] [INFO] DFAST_QC completed!
[2023-03-16 09:14:29,506] [INFO] Total running time: 0h1m8s