[2023-03-16 18:45:23,015] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:45:23,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:45:23,016] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference
[2023-03-16 18:45:24,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:45:24,144] [INFO] Task started: Prodigal
[2023-03-16 18:45:24,144] [INFO] Running command: cat /var/lib/cwl/stg481f7690-b499-4dec-9174-90bcc235a82d/OceanDNA-b22287.fa | prodigal -d OceanDNA-b22287/cds.fna -a OceanDNA-b22287/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:45:38,079] [INFO] Task succeeded: Prodigal
[2023-03-16 18:45:38,079] [INFO] Task started: HMMsearch
[2023-03-16 18:45:38,079] [INFO] Running command: hmmsearch --tblout OceanDNA-b22287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/reference_markers.hmm OceanDNA-b22287/protein.faa > /dev/null
[2023-03-16 18:45:38,247] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:45:38,248] [INFO] Found 6/6 markers.
[2023-03-16 18:45:38,265] [INFO] Query marker FASTA was written to OceanDNA-b22287/markers.fasta
[2023-03-16 18:45:38,265] [INFO] Task started: Blastn
[2023-03-16 18:45:38,266] [INFO] Running command: blastn -query OceanDNA-b22287/markers.fasta -db /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/reference_markers.fasta -out OceanDNA-b22287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:45:38,766] [INFO] Task succeeded: Blastn
[2023-03-16 18:45:38,769] [INFO] Selected 12 target genomes.
[2023-03-16 18:45:38,770] [INFO] Target genome list was writen to OceanDNA-b22287/target_genomes.txt
[2023-03-16 18:45:38,776] [INFO] Task started: fastANI
[2023-03-16 18:45:38,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg481f7690-b499-4dec-9174-90bcc235a82d/OceanDNA-b22287.fa --refList OceanDNA-b22287/target_genomes.txt --output OceanDNA-b22287/fastani_result.tsv --threads 1
[2023-03-16 18:45:48,245] [INFO] Task succeeded: fastANI
[2023-03-16 18:45:48,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:45:48,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:45:48,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:45:48,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:45:48,246] [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 18:45:48,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22287/tc_result.tsv
[2023-03-16 18:45:48,249] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:45:48,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:45:48,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/checkm_data
[2023-03-16 18:45:48,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:45:48,259] [INFO] Task started: CheckM
[2023-03-16 18:45:48,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22287/checkm_input OceanDNA-b22287/checkm_result
[2023-03-16 18:46:54,507] [INFO] Task succeeded: CheckM
[2023-03-16 18:46:54,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:46:54,537] [INFO] ===== Completeness check finished =====
[2023-03-16 18:46:54,538] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:46:54,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22287/markers.fasta)
[2023-03-16 18:46:54,539] [INFO] Task started: Blastn
[2023-03-16 18:46:54,539] [INFO] Running command: blastn -query OceanDNA-b22287/markers.fasta -db /var/lib/cwl/stgfb5e5488-baf7-4b49-ad3b-af86840eea50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:46:55,307] [INFO] Task succeeded: Blastn
[2023-03-16 18:46:55,311] [INFO] Selected 8 target genomes.
[2023-03-16 18:46:55,312] [INFO] Target genome list was writen to OceanDNA-b22287/target_genomes_gtdb.txt
[2023-03-16 18:46:55,321] [INFO] Task started: fastANI
[2023-03-16 18:46:55,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg481f7690-b499-4dec-9174-90bcc235a82d/OceanDNA-b22287.fa --refList OceanDNA-b22287/target_genomes_gtdb.txt --output OceanDNA-b22287/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:46:59,478] [INFO] Task succeeded: fastANI
[2023-03-16 18:46:59,482] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:46:59,482] [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_004213555.1	s__UBA8653 sp002862275	99.815	596	630	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	98.78	97.23	0.90	0.87	4	conclusive
GCA_002168105.2	s__UBA8653 sp002168105	85.7361	542	630	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	99.39	99.39	0.92	0.92	2	-
GCA_002705085.1	s__UBA8653 sp002705085	82.9794	446	630	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700845.1	s__UBA8653 sp002700845	78.3884	205	630	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:46:59,483] [INFO] GTDB search result was written to OceanDNA-b22287/result_gtdb.tsv
[2023-03-16 18:46:59,484] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:46:59,487] [INFO] DFAST_QC result json was written to OceanDNA-b22287/dqc_result.json
[2023-03-16 18:46:59,487] [INFO] DFAST_QC completed!
[2023-03-16 18:46:59,487] [INFO] Total running time: 0h1m36s