[2023-03-15 09:48:18,537] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,537] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference
[2023-03-15 09:48:19,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,639] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,639] [INFO] Running command: cat /var/lib/cwl/stg35349c7c-b42f-4018-80f8-83e5cff94be3/OceanDNA-b22112.fa | prodigal -d OceanDNA-b22112/cds.fna -a OceanDNA-b22112/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:29,053] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:29,053] [INFO] Task started: HMMsearch
[2023-03-15 09:48:29,053] [INFO] Running command: hmmsearch --tblout OceanDNA-b22112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/reference_markers.hmm OceanDNA-b22112/protein.faa > /dev/null
[2023-03-15 09:48:29,225] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:29,225] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg35349c7c-b42f-4018-80f8-83e5cff94be3/OceanDNA-b22112.fa]
[2023-03-15 09:48:29,244] [INFO] Query marker FASTA was written to OceanDNA-b22112/markers.fasta
[2023-03-15 09:48:29,244] [INFO] Task started: Blastn
[2023-03-15 09:48:29,244] [INFO] Running command: blastn -query OceanDNA-b22112/markers.fasta -db /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/reference_markers.fasta -out OceanDNA-b22112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:29,687] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:29,688] [INFO] Selected 15 target genomes.
[2023-03-15 09:48:29,688] [INFO] Target genome list was writen to OceanDNA-b22112/target_genomes.txt
[2023-03-15 09:48:29,696] [INFO] Task started: fastANI
[2023-03-15 09:48:29,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg35349c7c-b42f-4018-80f8-83e5cff94be3/OceanDNA-b22112.fa --refList OceanDNA-b22112/target_genomes.txt --output OceanDNA-b22112/fastani_result.tsv --threads 1
[2023-03-15 09:48:40,951] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:40,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:40,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:40,951] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:40,951] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:40,951] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:40,952] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22112/tc_result.tsv
[2023-03-15 09:48:40,952] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:40,952] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:40,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/checkm_data
[2023-03-15 09:48:40,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:40,958] [INFO] Task started: CheckM
[2023-03-15 09:48:40,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22112/checkm_input OceanDNA-b22112/checkm_result
[2023-03-15 09:49:17,772] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:17,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:17,774] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:17,775] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:17,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22112/markers.fasta)
[2023-03-15 09:49:17,775] [INFO] Task started: Blastn
[2023-03-15 09:49:17,775] [INFO] Running command: blastn -query OceanDNA-b22112/markers.fasta -db /var/lib/cwl/stg37884035-5bea-4efb-aab4-6f4d2688f991/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:18,227] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:18,227] [INFO] Selected 19 target genomes.
[2023-03-15 09:49:18,227] [INFO] Target genome list was writen to OceanDNA-b22112/target_genomes_gtdb.txt
[2023-03-15 09:49:18,640] [INFO] Task started: fastANI
[2023-03-15 09:49:18,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg35349c7c-b42f-4018-80f8-83e5cff94be3/OceanDNA-b22112.fa --refList OceanDNA-b22112/target_genomes_gtdb.txt --output OceanDNA-b22112/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:30,059] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:30,063] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:30,063] [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_002862305.1	s__UBA8087 sp002862305	77.522	98	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709755.1	s__UBA8087 sp002709755	77.0024	59	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	98.89	98.89	0.90	0.90	2	-
GCA_002171655.1	s__UBA8087 sp002171655	76.5392	53	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	100.00	100.00	0.94	0.94	2	-
GCA_002709295.1	s__GCA-002862325 sp002709295	76.216	56	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:30,063] [INFO] GTDB search result was written to OceanDNA-b22112/result_gtdb.tsv
[2023-03-15 09:49:30,063] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:30,064] [INFO] DFAST_QC result json was written to OceanDNA-b22112/dqc_result.json
[2023-03-15 09:49:30,064] [INFO] DFAST_QC completed!
[2023-03-15 09:49:30,064] [INFO] Total running time: 0h1m12s