[2023-03-16 04:24:46,331] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference
[2023-03-16 04:24:48,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,113] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,114] [INFO] Running command: cat /var/lib/cwl/stg45b607da-93f1-4034-a508-f1e6d2f7f1ca/OceanDNA-b24825.fa | prodigal -d OceanDNA-b24825/cds.fna -a OceanDNA-b24825/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:24:58,646] [INFO] Task succeeded: Prodigal
[2023-03-16 04:24:58,647] [INFO] Task started: HMMsearch
[2023-03-16 04:24:58,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b24825/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/reference_markers.hmm OceanDNA-b24825/protein.faa > /dev/null
[2023-03-16 04:24:58,884] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:24:58,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45b607da-93f1-4034-a508-f1e6d2f7f1ca/OceanDNA-b24825.fa]
[2023-03-16 04:24:58,903] [INFO] Query marker FASTA was written to OceanDNA-b24825/markers.fasta
[2023-03-16 04:24:58,904] [INFO] Task started: Blastn
[2023-03-16 04:24:58,904] [INFO] Running command: blastn -query OceanDNA-b24825/markers.fasta -db /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/reference_markers.fasta -out OceanDNA-b24825/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:24:59,471] [INFO] Task succeeded: Blastn
[2023-03-16 04:24:59,471] [INFO] Selected 16 target genomes.
[2023-03-16 04:24:59,472] [INFO] Target genome list was writen to OceanDNA-b24825/target_genomes.txt
[2023-03-16 04:24:59,480] [INFO] Task started: fastANI
[2023-03-16 04:24:59,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b607da-93f1-4034-a508-f1e6d2f7f1ca/OceanDNA-b24825.fa --refList OceanDNA-b24825/target_genomes.txt --output OceanDNA-b24825/fastani_result.tsv --threads 1
[2023-03-16 04:25:07,273] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:07,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:07,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:07,274] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:07,274] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:25:07,274] [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 04:25:07,275] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24825/tc_result.tsv
[2023-03-16 04:25:07,275] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:07,275] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:07,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/checkm_data
[2023-03-16 04:25:07,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:07,283] [INFO] Task started: CheckM
[2023-03-16 04:25:07,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24825/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24825/checkm_input OceanDNA-b24825/checkm_result
[2023-03-16 04:25:38,166] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:38,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:38,170] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:38,170] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:38,171] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24825/markers.fasta)
[2023-03-16 04:25:38,171] [INFO] Task started: Blastn
[2023-03-16 04:25:38,171] [INFO] Running command: blastn -query OceanDNA-b24825/markers.fasta -db /var/lib/cwl/stgd0ad87e9-c1aa-48cc-bb1a-4b8be0f8a324/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24825/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:38,953] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:38,954] [INFO] Selected 17 target genomes.
[2023-03-16 04:25:38,954] [INFO] Target genome list was writen to OceanDNA-b24825/target_genomes_gtdb.txt
[2023-03-16 04:25:39,005] [INFO] Task started: fastANI
[2023-03-16 04:25:39,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b607da-93f1-4034-a508-f1e6d2f7f1ca/OceanDNA-b24825.fa --refList OceanDNA-b24825/target_genomes_gtdb.txt --output OceanDNA-b24825/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:25:45,422] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:45,426] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:25:45,426] [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_003212315.1	s__UBA7326 sp003212315	96.9734	474	635	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	97.47	96.36	0.77	0.69	6	conclusive
GCA_003284265.1	s__UBA7326 sp003284265	91.6606	460	635	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002709155.1	s__UBA7326 sp002709155	91.5531	349	635	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708305.1	s__UBA7326 sp002708305	77.2362	147	635	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	98.40	98.02	0.79	0.75	5	-
--------------------------------------------------------------------------------
[2023-03-16 04:25:45,426] [INFO] GTDB search result was written to OceanDNA-b24825/result_gtdb.tsv
[2023-03-16 04:25:45,426] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:25:45,427] [INFO] DFAST_QC result json was written to OceanDNA-b24825/dqc_result.json
[2023-03-16 04:25:45,427] [INFO] DFAST_QC completed!
[2023-03-16 04:25:45,427] [INFO] Total running time: 0h0m59s