[2023-03-15 11:36:00,596] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:36:00,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:36:00,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference
[2023-03-15 11:36:02,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:36:02,577] [INFO] Task started: Prodigal
[2023-03-15 11:36:02,577] [INFO] Running command: cat /var/lib/cwl/stg9b5c6cb0-03a7-40bf-845f-fa8aa0ec91ed/OceanDNA-b26167.fa | prodigal -d OceanDNA-b26167/cds.fna -a OceanDNA-b26167/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:36:11,587] [INFO] Task succeeded: Prodigal
[2023-03-15 11:36:11,588] [INFO] Task started: HMMsearch
[2023-03-15 11:36:11,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b26167/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/reference_markers.hmm OceanDNA-b26167/protein.faa > /dev/null
[2023-03-15 11:36:11,766] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:36:11,766] [INFO] Found 6/6 markers.
[2023-03-15 11:36:11,840] [INFO] Query marker FASTA was written to OceanDNA-b26167/markers.fasta
[2023-03-15 11:36:11,841] [INFO] Task started: Blastn
[2023-03-15 11:36:11,842] [INFO] Running command: blastn -query OceanDNA-b26167/markers.fasta -db /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/reference_markers.fasta -out OceanDNA-b26167/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:14,715] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:14,732] [INFO] Selected 30 target genomes.
[2023-03-15 11:36:14,732] [INFO] Target genome list was writen to OceanDNA-b26167/target_genomes.txt
[2023-03-15 11:36:14,748] [INFO] Task started: fastANI
[2023-03-15 11:36:14,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5c6cb0-03a7-40bf-845f-fa8aa0ec91ed/OceanDNA-b26167.fa --refList OceanDNA-b26167/target_genomes.txt --output OceanDNA-b26167/fastani_result.tsv --threads 1
[2023-03-15 11:36:33,841] [INFO] Task succeeded: fastANI
[2023-03-15 11:36:33,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:36:33,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:36:33,842] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:36:33,842] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:36:33,842] [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 11:36:33,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26167/tc_result.tsv
[2023-03-15 11:36:33,868] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:36:33,868] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:36:33,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/checkm_data
[2023-03-15 11:36:33,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:36:33,892] [INFO] Task started: CheckM
[2023-03-15 11:36:33,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26167/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26167/checkm_input OceanDNA-b26167/checkm_result
[2023-03-15 11:37:01,641] [INFO] Task succeeded: CheckM
[2023-03-15 11:37:01,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:37:01,696] [INFO] ===== Completeness check finished =====
[2023-03-15 11:37:01,696] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:37:01,697] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26167/markers.fasta)
[2023-03-15 11:37:01,697] [INFO] Task started: Blastn
[2023-03-15 11:37:01,697] [INFO] Running command: blastn -query OceanDNA-b26167/markers.fasta -db /var/lib/cwl/stg5f5f80e4-f276-48e6-8eca-3050de915e99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26167/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:37:02,753] [INFO] Task succeeded: Blastn
[2023-03-15 11:37:02,773] [INFO] Selected 22 target genomes.
[2023-03-15 11:37:02,773] [INFO] Target genome list was writen to OceanDNA-b26167/target_genomes_gtdb.txt
[2023-03-15 11:37:02,813] [INFO] Task started: fastANI
[2023-03-15 11:37:02,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5c6cb0-03a7-40bf-845f-fa8aa0ec91ed/OceanDNA-b26167.fa --refList OceanDNA-b26167/target_genomes_gtdb.txt --output OceanDNA-b26167/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:37:10,384] [INFO] Task succeeded: fastANI
[2023-03-15 11:37:10,391] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:37:10,391] [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_002722385.1	s__HIMB100 sp002722385	98.5856	230	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	98.88	98.88	0.69	0.69	2	conclusive
GCA_000238815.2	s__HIMB100 sp000238815	83.7822	428	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520575.1	s__HIMB100 sp902520575	78.0013	69	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348585.1	s__HIMB100 sp002348585	77.8793	113	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700485.1	s__HIMB100 sp002700485	77.7378	124	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	98.09	96.19	0.88	0.78	3	-
GCA_902518965.1	s__HIMB100 sp902518965	77.5922	120	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524805.1	s__WTJO01 sp011524805	76.7719	81	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__WTJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780775.1	s__JADHLI01 sp016780775	76.7031	80	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLI01	95.0	99.93	99.93	0.97	0.97	2	-
GCA_016780695.1	s__JADHLK01 sp016780695	76.688	55	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387605.1	s__UBA4588 sp002387605	76.5631	55	476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA4588	95.0	99.40	98.72	0.91	0.85	18	-
--------------------------------------------------------------------------------
[2023-03-15 11:37:10,397] [INFO] GTDB search result was written to OceanDNA-b26167/result_gtdb.tsv
[2023-03-15 11:37:10,407] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:37:10,414] [INFO] DFAST_QC result json was written to OceanDNA-b26167/dqc_result.json
[2023-03-15 11:37:10,414] [INFO] DFAST_QC completed!
[2023-03-15 11:37:10,414] [INFO] Total running time: 0h1m10s