[2023-03-15 10:34:47,982] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stg1329983d-3df9-46f4-bd9c-d6a2a3e854dc/OceanDNA-b41773.fa | prodigal -d OceanDNA-b41773/cds.fna -a OceanDNA-b41773/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:54,361] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:54,361] [INFO] Task started: HMMsearch
[2023-03-15 10:34:54,361] [INFO] Running command: hmmsearch --tblout OceanDNA-b41773/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/reference_markers.hmm OceanDNA-b41773/protein.faa > /dev/null
[2023-03-15 10:34:54,516] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:54,516] [INFO] Found 6/6 markers.
[2023-03-15 10:34:54,528] [INFO] Query marker FASTA was written to OceanDNA-b41773/markers.fasta
[2023-03-15 10:34:54,529] [INFO] Task started: Blastn
[2023-03-15 10:34:54,529] [INFO] Running command: blastn -query OceanDNA-b41773/markers.fasta -db /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/reference_markers.fasta -out OceanDNA-b41773/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:55,083] [INFO] Task succeeded: Blastn
[2023-03-15 10:34:55,087] [INFO] Selected 20 target genomes.
[2023-03-15 10:34:55,087] [INFO] Target genome list was writen to OceanDNA-b41773/target_genomes.txt
[2023-03-15 10:34:55,096] [INFO] Task started: fastANI
[2023-03-15 10:34:55,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg1329983d-3df9-46f4-bd9c-d6a2a3e854dc/OceanDNA-b41773.fa --refList OceanDNA-b41773/target_genomes.txt --output OceanDNA-b41773/fastani_result.tsv --threads 1
[2023-03-15 10:35:03,018] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:03,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:03,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:03,019] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:03,019] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:35:03,019] [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 10:35:03,023] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41773/tc_result.tsv
[2023-03-15 10:35:03,023] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:03,023] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:03,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/checkm_data
[2023-03-15 10:35:03,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:03,055] [INFO] Task started: CheckM
[2023-03-15 10:35:03,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41773/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41773/checkm_input OceanDNA-b41773/checkm_result
[2023-03-15 10:35:21,463] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:21,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:21,709] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:21,710] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:21,710] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41773/markers.fasta)
[2023-03-15 10:35:21,711] [INFO] Task started: Blastn
[2023-03-15 10:35:21,711] [INFO] Running command: blastn -query OceanDNA-b41773/markers.fasta -db /var/lib/cwl/stg4c7bc87e-3dce-4705-8c29-29d7e0523edd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41773/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:22,641] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:22,646] [INFO] Selected 22 target genomes.
[2023-03-15 10:35:22,646] [INFO] Target genome list was writen to OceanDNA-b41773/target_genomes_gtdb.txt
[2023-03-15 10:35:23,413] [INFO] Task started: fastANI
[2023-03-15 10:35:23,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg1329983d-3df9-46f4-bd9c-d6a2a3e854dc/OceanDNA-b41773.fa --refList OceanDNA-b41773/target_genomes_gtdb.txt --output OceanDNA-b41773/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:28,525] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:28,530] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:35:28,530] [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_902522825.1	s__AG-339-G14 sp902522825	77.5194	106	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523885.1	s__AG-339-G14 sp902523885	76.9196	94	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614235.1	s__AG-339-G14 sp902614235	76.8818	99	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.30	98.01	0.83	0.80	7	-
GCA_902635045.1	s__AG-339-G14 sp902635045	76.7934	97	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.24	96.50	0.87	0.84	4	-
GCA_902524805.1	s__AG-339-G14 sp902524805	76.6851	88	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525735.1	s__AG-339-G14 sp902525735	76.524	111	325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.66	98.66	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:35:28,532] [INFO] GTDB search result was written to OceanDNA-b41773/result_gtdb.tsv
[2023-03-15 10:35:28,532] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:28,535] [INFO] DFAST_QC result json was written to OceanDNA-b41773/dqc_result.json
[2023-03-15 10:35:28,535] [INFO] DFAST_QC completed!
[2023-03-15 10:35:28,535] [INFO] Total running time: 0h0m41s