[2023-03-15 11:54:50,854] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference
[2023-03-15 11:54:51,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:51,963] [INFO] Task started: Prodigal
[2023-03-15 11:54:51,963] [INFO] Running command: cat /var/lib/cwl/stg9add7187-4433-4fa3-97bd-256bf78b042a/OceanDNA-b22132.fa | prodigal -d OceanDNA-b22132/cds.fna -a OceanDNA-b22132/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:55:03,904] [INFO] Task succeeded: Prodigal
[2023-03-15 11:55:03,904] [INFO] Task started: HMMsearch
[2023-03-15 11:55:03,904] [INFO] Running command: hmmsearch --tblout OceanDNA-b22132/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/reference_markers.hmm OceanDNA-b22132/protein.faa > /dev/null
[2023-03-15 11:55:04,086] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:55:04,086] [INFO] Found 6/6 markers.
[2023-03-15 11:55:04,104] [INFO] Query marker FASTA was written to OceanDNA-b22132/markers.fasta
[2023-03-15 11:55:04,105] [INFO] Task started: Blastn
[2023-03-15 11:55:04,106] [INFO] Running command: blastn -query OceanDNA-b22132/markers.fasta -db /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/reference_markers.fasta -out OceanDNA-b22132/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:04,645] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:04,647] [INFO] Selected 29 target genomes.
[2023-03-15 11:55:04,647] [INFO] Target genome list was writen to OceanDNA-b22132/target_genomes.txt
[2023-03-15 11:55:04,663] [INFO] Task started: fastANI
[2023-03-15 11:55:04,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg9add7187-4433-4fa3-97bd-256bf78b042a/OceanDNA-b22132.fa --refList OceanDNA-b22132/target_genomes.txt --output OceanDNA-b22132/fastani_result.tsv --threads 1
[2023-03-15 11:55:28,624] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:28,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:55:28,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:55:28,625] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:55:28,625] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:55:28,625] [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 11:55:28,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22132/tc_result.tsv
[2023-03-15 11:55:28,632] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:55:28,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:55:28,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/checkm_data
[2023-03-15 11:55:28,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:55:28,644] [INFO] Task started: CheckM
[2023-03-15 11:55:28,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22132/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22132/checkm_input OceanDNA-b22132/checkm_result
[2023-03-15 11:56:02,537] [INFO] Task succeeded: CheckM
[2023-03-15 11:56:02,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:56:02,586] [INFO] ===== Completeness check finished =====
[2023-03-15 11:56:02,586] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:56:02,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22132/markers.fasta)
[2023-03-15 11:56:02,587] [INFO] Task started: Blastn
[2023-03-15 11:56:02,587] [INFO] Running command: blastn -query OceanDNA-b22132/markers.fasta -db /var/lib/cwl/stg092ea5c1-cecf-47f3-8425-c3178c88ad36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22132/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:56:03,361] [INFO] Task succeeded: Blastn
[2023-03-15 11:56:03,366] [INFO] Selected 17 target genomes.
[2023-03-15 11:56:03,366] [INFO] Target genome list was writen to OceanDNA-b22132/target_genomes_gtdb.txt
[2023-03-15 11:56:03,416] [INFO] Task started: fastANI
[2023-03-15 11:56:03,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg9add7187-4433-4fa3-97bd-256bf78b042a/OceanDNA-b22132.fa --refList OceanDNA-b22132/target_genomes_gtdb.txt --output OceanDNA-b22132/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:56:12,795] [INFO] Task succeeded: fastANI
[2023-03-15 11:56:12,803] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:56:12,803] [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_017642965.1	s__UBA1924 sp017642965	77.6161	155	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827215.1	s__UBA1924 sp009827215	77.5008	121	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640485.1	s__UBA1924 sp017640485	77.4853	152	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337545.1	s__UBA1924 sp002337545	77.3096	136	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_002364005.1	s__UBA1924 sp002364005	77.0089	151	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_002706885.1	s__GCA-2706885 sp002706885	76.812	65	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2706885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.8092	75	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	76.732	127	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337215.1	s__UBA1926 sp002337215	76.69	78	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	76.2368	51	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584315.1	s__CAADGN01 sp014584315	76.2322	73	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	75.5286	51	624	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:56:12,805] [INFO] GTDB search result was written to OceanDNA-b22132/result_gtdb.tsv
[2023-03-15 11:56:12,808] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:56:12,812] [INFO] DFAST_QC result json was written to OceanDNA-b22132/dqc_result.json
[2023-03-15 11:56:12,812] [INFO] DFAST_QC completed!
[2023-03-15 11:56:12,812] [INFO] Total running time: 0h1m22s