[2023-03-15 03:14:16,367] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,367] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference
[2023-03-15 03:14:17,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,552] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,552] [INFO] Running command: cat /var/lib/cwl/stg4752f242-fe3a-44e6-bbff-dc6fc5ab0725/OceanDNA-b24481.fa | prodigal -d OceanDNA-b24481/cds.fna -a OceanDNA-b24481/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:22,074] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:22,075] [INFO] Task started: HMMsearch
[2023-03-15 03:14:22,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b24481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/reference_markers.hmm OceanDNA-b24481/protein.faa > /dev/null
[2023-03-15 03:14:22,231] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:22,231] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4752f242-fe3a-44e6-bbff-dc6fc5ab0725/OceanDNA-b24481.fa]
[2023-03-15 03:14:22,239] [INFO] Query marker FASTA was written to OceanDNA-b24481/markers.fasta
[2023-03-15 03:14:22,239] [INFO] Task started: Blastn
[2023-03-15 03:14:22,239] [INFO] Running command: blastn -query OceanDNA-b24481/markers.fasta -db /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/reference_markers.fasta -out OceanDNA-b24481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:22,692] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:22,693] [INFO] Selected 10 target genomes.
[2023-03-15 03:14:22,693] [INFO] Target genome list was writen to OceanDNA-b24481/target_genomes.txt
[2023-03-15 03:14:22,700] [INFO] Task started: fastANI
[2023-03-15 03:14:22,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg4752f242-fe3a-44e6-bbff-dc6fc5ab0725/OceanDNA-b24481.fa --refList OceanDNA-b24481/target_genomes.txt --output OceanDNA-b24481/fastani_result.tsv --threads 1
[2023-03-15 03:14:26,181] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:26,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:26,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:26,182] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:26,182] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:26,182] [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 03:14:26,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24481/tc_result.tsv
[2023-03-15 03:14:26,182] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:26,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:26,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/checkm_data
[2023-03-15 03:14:26,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:26,188] [INFO] Task started: CheckM
[2023-03-15 03:14:26,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24481/checkm_input OceanDNA-b24481/checkm_result
[2023-03-15 03:14:44,137] [INFO] Task succeeded: CheckM
[2023-03-15 03:14:44,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.99%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:14:44,139] [INFO] ===== Completeness check finished =====
[2023-03-15 03:14:44,139] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:14:44,139] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24481/markers.fasta)
[2023-03-15 03:14:44,140] [INFO] Task started: Blastn
[2023-03-15 03:14:44,140] [INFO] Running command: blastn -query OceanDNA-b24481/markers.fasta -db /var/lib/cwl/stg46f07c0c-ee19-471c-9eda-4860c8cf55ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:44,594] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:44,595] [INFO] Selected 13 target genomes.
[2023-03-15 03:14:44,595] [INFO] Target genome list was writen to OceanDNA-b24481/target_genomes_gtdb.txt
[2023-03-15 03:14:44,606] [INFO] Task started: fastANI
[2023-03-15 03:14:44,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg4752f242-fe3a-44e6-bbff-dc6fc5ab0725/OceanDNA-b24481.fa --refList OceanDNA-b24481/target_genomes_gtdb.txt --output OceanDNA-b24481/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:14:47,175] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:47,185] [INFO] Found 13 fastANI hits (11 hits with ANI > circumscription radius)
[2023-03-15 03:14:47,185] [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_902546975.1	s__HIMB59 sp902546975	96.8459	196	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	inconclusive
GCA_902538085.1	s__HIMB59 sp902538085	96.5037	206	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.32	95.03	0.79	0.77	3	inconclusive
GCA_902574995.1	s__HIMB59 sp902574995	96.2304	193	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902518505.1	s__HIMB59 sp902518505	96.224	193	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.57	95.11	0.80	0.80	4	inconclusive
GCA_902542505.1	s__HIMB59 sp902542505	96.1928	96	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.42	95.42	0.57	0.57	2	inconclusive
GCA_902613185.1	s__HIMB59 sp902613185	96.1677	208	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.58	0.93	0.92	5	inconclusive
GCA_902521485.1	s__HIMB59 sp902521485	95.931	187	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	98.22	98.22	0.76	0.76	2	inconclusive
GCA_902530745.1	s__HIMB59 sp902530745	95.8979	199	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.01	95.70	0.83	0.77	8	inconclusive
GCA_902591315.1	s__HIMB59 sp902591315	95.8906	161	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	inconclusive
GCA_902621205.1	s__HIMB59 sp902621205	95.7668	197	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	inconclusive
GCA_902617465.1	s__HIMB59 sp902617465	95.7641	127	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	98.39	95.06	0.61	0.58	5	inconclusive
GCA_902543855.1	s__HIMB59 sp902543855	94.8777	105	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.86	99.86	0.80	0.80	2	-
GCA_902595525.1	s__HIMB59 sp902595525	94.7061	123	228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:14:47,185] [INFO] GTDB search result was written to OceanDNA-b24481/result_gtdb.tsv
[2023-03-15 03:14:47,185] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:14:47,187] [INFO] DFAST_QC result json was written to OceanDNA-b24481/dqc_result.json
[2023-03-15 03:14:47,187] [INFO] DFAST_QC completed!
[2023-03-15 03:14:47,187] [INFO] Total running time: 0h0m31s