[2023-03-15 05:37:29,653] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:29,653] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:29,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference
[2023-03-15 05:37:30,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:30,734] [INFO] Task started: Prodigal
[2023-03-15 05:37:30,735] [INFO] Running command: cat /var/lib/cwl/stgdf13883c-e35f-4f49-880b-6a7aba381d92/OceanDNA-b22190.fa | prodigal -d OceanDNA-b22190/cds.fna -a OceanDNA-b22190/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:40,445] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:40,446] [INFO] Task started: HMMsearch
[2023-03-15 05:37:40,446] [INFO] Running command: hmmsearch --tblout OceanDNA-b22190/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/reference_markers.hmm OceanDNA-b22190/protein.faa > /dev/null
[2023-03-15 05:37:40,619] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:40,619] [INFO] Found 6/6 markers.
[2023-03-15 05:37:40,636] [INFO] Query marker FASTA was written to OceanDNA-b22190/markers.fasta
[2023-03-15 05:37:40,636] [INFO] Task started: Blastn
[2023-03-15 05:37:40,636] [INFO] Running command: blastn -query OceanDNA-b22190/markers.fasta -db /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/reference_markers.fasta -out OceanDNA-b22190/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:41,203] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:41,204] [INFO] Selected 34 target genomes.
[2023-03-15 05:37:41,204] [INFO] Target genome list was writen to OceanDNA-b22190/target_genomes.txt
[2023-03-15 05:37:41,219] [INFO] Task started: fastANI
[2023-03-15 05:37:41,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf13883c-e35f-4f49-880b-6a7aba381d92/OceanDNA-b22190.fa --refList OceanDNA-b22190/target_genomes.txt --output OceanDNA-b22190/fastani_result.tsv --threads 1
[2023-03-15 05:38:06,048] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:06,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:38:06,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:38:06,049] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:38:06,049] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:38:06,049] [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 05:38:06,050] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22190/tc_result.tsv
[2023-03-15 05:38:06,050] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:38:06,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:38:06,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/checkm_data
[2023-03-15 05:38:06,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:38:06,057] [INFO] Task started: CheckM
[2023-03-15 05:38:06,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22190/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22190/checkm_input OceanDNA-b22190/checkm_result
[2023-03-15 05:38:35,123] [INFO] Task succeeded: CheckM
[2023-03-15 05:38:35,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 6.11%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-15 05:38:35,125] [INFO] ===== Completeness check finished =====
[2023-03-15 05:38:35,126] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:38:35,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22190/markers.fasta)
[2023-03-15 05:38:35,127] [INFO] Task started: Blastn
[2023-03-15 05:38:35,127] [INFO] Running command: blastn -query OceanDNA-b22190/markers.fasta -db /var/lib/cwl/stg00de1cb1-3408-4cdc-9f7f-3184926366f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22190/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:38:36,060] [INFO] Task succeeded: Blastn
[2023-03-15 05:38:36,061] [INFO] Selected 19 target genomes.
[2023-03-15 05:38:36,061] [INFO] Target genome list was writen to OceanDNA-b22190/target_genomes_gtdb.txt
[2023-03-15 05:38:36,084] [INFO] Task started: fastANI
[2023-03-15 05:38:36,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf13883c-e35f-4f49-880b-6a7aba381d92/OceanDNA-b22190.fa --refList OceanDNA-b22190/target_genomes_gtdb.txt --output OceanDNA-b22190/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:38:47,857] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:47,867] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:38:47,868] [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_003712165.1	s__GCA-2732755 sp003712165	79.5509	240	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827205.1	s__GCA-2732755 sp009827205	78.9517	183	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480345.1	s__UBA1926 sp002480345	77.9352	77	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	77.513	74	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_011053195.1	s__GCA-2732755 sp011053195	77.4425	136	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	77.4136	86	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706885.1	s__GCA-2706885 sp002706885	77.3773	64	429	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	76.9314	81	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360695.1	s__JABWBC01 sp013360695	76.818	55	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.7649	59	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.7113	72	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	76.7074	69	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360675.1	s__JABWBB01 sp013360675	76.5212	57	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBB01	95.0	95.57	95.57	0.94	0.94	2	-
GCA_008363215.1	s__J022 sp008363215	76.5	52	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
GCA_900696545.1	s__CAADGN01 sp900696545	76.4137	63	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	99.87	99.83	0.94	0.92	3	-
GCA_016793195.1	s__JABWBC01 sp016793195	76.248	65	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015200025.1	s__UBA2396 sp015200025	76.1998	58	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242645.1	s__JAFEBO01 sp018242645	75.867	50	429	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:38:47,868] [INFO] GTDB search result was written to OceanDNA-b22190/result_gtdb.tsv
[2023-03-15 05:38:47,868] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:38:47,870] [INFO] DFAST_QC result json was written to OceanDNA-b22190/dqc_result.json
[2023-03-15 05:38:47,870] [INFO] DFAST_QC completed!
[2023-03-15 05:38:47,870] [INFO] Total running time: 0h1m18s