[2023-03-15 22:48:49,172] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:48:49,172] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:48:49,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference
[2023-03-15 22:48:50,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:48:50,295] [INFO] Task started: Prodigal
[2023-03-15 22:48:50,295] [INFO] Running command: cat /var/lib/cwl/stgdc3610c4-9c3f-4255-b98f-cc9d6e991aea/OceanDNA-b4866.fa | prodigal -d OceanDNA-b4866/cds.fna -a OceanDNA-b4866/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:48:56,643] [INFO] Task succeeded: Prodigal
[2023-03-15 22:48:56,643] [INFO] Task started: HMMsearch
[2023-03-15 22:48:56,643] [INFO] Running command: hmmsearch --tblout OceanDNA-b4866/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/reference_markers.hmm OceanDNA-b4866/protein.faa > /dev/null
[2023-03-15 22:48:56,796] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:48:56,796] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdc3610c4-9c3f-4255-b98f-cc9d6e991aea/OceanDNA-b4866.fa]
[2023-03-15 22:48:56,807] [INFO] Query marker FASTA was written to OceanDNA-b4866/markers.fasta
[2023-03-15 22:48:56,807] [INFO] Task started: Blastn
[2023-03-15 22:48:56,807] [INFO] Running command: blastn -query OceanDNA-b4866/markers.fasta -db /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/reference_markers.fasta -out OceanDNA-b4866/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:48:57,305] [INFO] Task succeeded: Blastn
[2023-03-15 22:48:57,306] [INFO] Selected 21 target genomes.
[2023-03-15 22:48:57,307] [INFO] Target genome list was writen to OceanDNA-b4866/target_genomes.txt
[2023-03-15 22:48:57,411] [INFO] Task started: fastANI
[2023-03-15 22:48:57,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3610c4-9c3f-4255-b98f-cc9d6e991aea/OceanDNA-b4866.fa --refList OceanDNA-b4866/target_genomes.txt --output OceanDNA-b4866/fastani_result.tsv --threads 1
[2023-03-15 22:49:07,752] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:07,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:49:07,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:49:07,753] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:49:07,753] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:49:07,753] [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 22:49:07,753] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4866/tc_result.tsv
[2023-03-15 22:49:07,754] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:49:07,754] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:49:07,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/checkm_data
[2023-03-15 22:49:07,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:49:07,762] [INFO] Task started: CheckM
[2023-03-15 22:49:07,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4866/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4866/checkm_input OceanDNA-b4866/checkm_result
[2023-03-15 22:49:28,983] [INFO] Task succeeded: CheckM
[2023-03-15 22:49:28,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:49:28,985] [INFO] ===== Completeness check finished =====
[2023-03-15 22:49:28,985] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:49:28,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4866/markers.fasta)
[2023-03-15 22:49:28,986] [INFO] Task started: Blastn
[2023-03-15 22:49:28,986] [INFO] Running command: blastn -query OceanDNA-b4866/markers.fasta -db /var/lib/cwl/stg4ddb8901-3f76-497b-bafd-82d58bb5d2d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4866/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:29,663] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:29,664] [INFO] Selected 17 target genomes.
[2023-03-15 22:49:29,664] [INFO] Target genome list was writen to OceanDNA-b4866/target_genomes_gtdb.txt
[2023-03-15 22:49:30,032] [INFO] Task started: fastANI
[2023-03-15 22:49:30,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3610c4-9c3f-4255-b98f-cc9d6e991aea/OceanDNA-b4866.fa --refList OceanDNA-b4866/target_genomes_gtdb.txt --output OceanDNA-b4866/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:49:34,379] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:34,388] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:49:34,388] [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_002730985.1	s__BACL11 sp002730985	77.9097	129	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	77.7671	119	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002705205.1	s__GCA-2705205 sp002705205	77.3464	87	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627575.1	s__GCA-2711125 sp902627575	77.2935	80	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	77.2689	126	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_018652335.1	s__GCA-2683775 sp018652335	77.1689	103	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	77.1292	130	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182255.1	s__UWMA-0277 sp905182255	77.039	59	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.999	106	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	76.9479	52	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.9047	88	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.7943	127	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.7024	93	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683775.1	s__GCA-2683775 sp002683775	76.6947	80	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	76.6058	73	348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:49:34,388] [INFO] GTDB search result was written to OceanDNA-b4866/result_gtdb.tsv
[2023-03-15 22:49:34,388] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:49:34,390] [INFO] DFAST_QC result json was written to OceanDNA-b4866/dqc_result.json
[2023-03-15 22:49:34,390] [INFO] DFAST_QC completed!
[2023-03-15 22:49:34,390] [INFO] Total running time: 0h0m45s