[2023-03-15 09:48:18,568] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,568] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference
[2023-03-15 09:48:19,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,838] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,838] [INFO] Running command: cat /var/lib/cwl/stg5813ea48-0cad-4fb4-b88c-977862497d4e/OceanDNA-b4835.fa | prodigal -d OceanDNA-b4835/cds.fna -a OceanDNA-b4835/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:27,433] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:27,433] [INFO] Task started: HMMsearch
[2023-03-15 09:48:27,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b4835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/reference_markers.hmm OceanDNA-b4835/protein.faa > /dev/null
[2023-03-15 09:48:27,622] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:27,623] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5813ea48-0cad-4fb4-b88c-977862497d4e/OceanDNA-b4835.fa]
[2023-03-15 09:48:27,637] [INFO] Query marker FASTA was written to OceanDNA-b4835/markers.fasta
[2023-03-15 09:48:27,637] [INFO] Task started: Blastn
[2023-03-15 09:48:27,637] [INFO] Running command: blastn -query OceanDNA-b4835/markers.fasta -db /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/reference_markers.fasta -out OceanDNA-b4835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:28,234] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:28,235] [INFO] Selected 28 target genomes.
[2023-03-15 09:48:28,235] [INFO] Target genome list was writen to OceanDNA-b4835/target_genomes.txt
[2023-03-15 09:48:28,249] [INFO] Task started: fastANI
[2023-03-15 09:48:28,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg5813ea48-0cad-4fb4-b88c-977862497d4e/OceanDNA-b4835.fa --refList OceanDNA-b4835/target_genomes.txt --output OceanDNA-b4835/fastani_result.tsv --threads 1
[2023-03-15 09:48:43,385] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:43,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:43,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:43,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:43,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:43,386] [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 09:48:43,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4835/tc_result.tsv
[2023-03-15 09:48:43,386] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:43,387] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:43,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/checkm_data
[2023-03-15 09:48:43,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:43,392] [INFO] Task started: CheckM
[2023-03-15 09:48:43,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4835/checkm_input OceanDNA-b4835/checkm_result
[2023-03-15 09:49:07,622] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:07,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:07,624] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:07,624] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:07,624] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4835/markers.fasta)
[2023-03-15 09:49:07,624] [INFO] Task started: Blastn
[2023-03-15 09:49:07,624] [INFO] Running command: blastn -query OceanDNA-b4835/markers.fasta -db /var/lib/cwl/stg95d40e31-818f-4616-9b94-8d3e5b089b52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:08,516] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:08,517] [INFO] Selected 25 target genomes.
[2023-03-15 09:49:08,517] [INFO] Target genome list was writen to OceanDNA-b4835/target_genomes_gtdb.txt
[2023-03-15 09:49:08,914] [INFO] Task started: fastANI
[2023-03-15 09:49:08,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg5813ea48-0cad-4fb4-b88c-977862497d4e/OceanDNA-b4835.fa --refList OceanDNA-b4835/target_genomes_gtdb.txt --output OceanDNA-b4835/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:15,483] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:15,492] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:15,492] [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_018675825.1	s__GCA-002715885 sp018675825	81.8127	229	399	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_014239655.1	s__GCA-002715885 sp014239655	78.1854	185	399	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_002689735.1	s__GCA-002715885 sp002689735	77.6359	102	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_902579065.1	s__GCA-002715885 sp902579065	77.2842	110	399	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_905181585.1	s__CAJIYG01 sp905181585	77.0325	162	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715885.1	s__GCA-002715885 sp002715885	76.6246	81	399	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_002711125.1	s__GCA-2711125 sp002711125	76.2776	64	399	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_002724895.1	s__GCA-2693335 sp002724895	76.2616	69	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_902627575.1	s__GCA-2711125 sp902627575	76.2473	53	399	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_002730985.1	s__BACL11 sp002730985	76.217	51	399	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	76.1744	56	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.0827	56	399	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_018645865.1	s__UWMA-0277 sp018645865	75.9706	55	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_018647945.1	s__GCA-002697625 sp018647945	75.8564	54	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_002728175.1	s__GCA-2697505 sp002728175	75.7982	51	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:15,492] [INFO] GTDB search result was written to OceanDNA-b4835/result_gtdb.tsv
[2023-03-15 09:49:15,492] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:15,493] [INFO] DFAST_QC result json was written to OceanDNA-b4835/dqc_result.json
[2023-03-15 09:49:15,494] [INFO] DFAST_QC completed!
[2023-03-15 09:49:15,494] [INFO] Total running time: 0h0m57s