[2023-03-18 05:35:37,309] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference
[2023-03-18 05:35:38,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,971] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,971] [INFO] Running command: cat /var/lib/cwl/stg5d9225dc-b546-4c4c-a576-4d78d2309dba/OceanDNA-b36703.fa | prodigal -d OceanDNA-b36703/cds.fna -a OceanDNA-b36703/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:54,873] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:54,873] [INFO] Task started: HMMsearch
[2023-03-18 05:35:54,874] [INFO] Running command: hmmsearch --tblout OceanDNA-b36703/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/reference_markers.hmm OceanDNA-b36703/protein.faa > /dev/null
[2023-03-18 05:35:55,097] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:55,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d9225dc-b546-4c4c-a576-4d78d2309dba/OceanDNA-b36703.fa]
[2023-03-18 05:35:55,131] [INFO] Query marker FASTA was written to OceanDNA-b36703/markers.fasta
[2023-03-18 05:35:55,132] [INFO] Task started: Blastn
[2023-03-18 05:35:55,132] [INFO] Running command: blastn -query OceanDNA-b36703/markers.fasta -db /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/reference_markers.fasta -out OceanDNA-b36703/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:55,704] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:55,706] [INFO] Selected 26 target genomes.
[2023-03-18 05:35:55,706] [INFO] Target genome list was writen to OceanDNA-b36703/target_genomes.txt
[2023-03-18 05:35:55,725] [INFO] Task started: fastANI
[2023-03-18 05:35:55,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9225dc-b546-4c4c-a576-4d78d2309dba/OceanDNA-b36703.fa --refList OceanDNA-b36703/target_genomes.txt --output OceanDNA-b36703/fastani_result.tsv --threads 1
[2023-03-18 05:36:13,467] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:13,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:13,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:13,473] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:13,473] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:13,473] [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
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.105	124	904	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	77.0591	86	904	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000373945.1	305900	305900	type	True	77.0009	106	904	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000710775.1	305900	305900	type	True	76.9765	107	904	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	76.8995	106	904	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	76.7878	109	904	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	76.6033	110	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:13,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36703/tc_result.tsv
[2023-03-18 05:36:13,474] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:13,474] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:13,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/checkm_data
[2023-03-18 05:36:13,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:13,481] [INFO] Task started: CheckM
[2023-03-18 05:36:13,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36703/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36703/checkm_input OceanDNA-b36703/checkm_result
[2023-03-18 05:36:56,338] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:56,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.02%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:56,347] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:56,348] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:56,348] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36703/markers.fasta)
[2023-03-18 05:36:56,349] [INFO] Task started: Blastn
[2023-03-18 05:36:56,349] [INFO] Running command: blastn -query OceanDNA-b36703/markers.fasta -db /var/lib/cwl/stg2e95f806-ce57-4a4c-a66e-5842b84d9b18/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36703/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:57,110] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:57,111] [INFO] Selected 28 target genomes.
[2023-03-18 05:36:57,111] [INFO] Target genome list was writen to OceanDNA-b36703/target_genomes_gtdb.txt
[2023-03-18 05:36:57,230] [INFO] Task started: fastANI
[2023-03-18 05:36:57,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9225dc-b546-4c4c-a576-4d78d2309dba/OceanDNA-b36703.fa --refList OceanDNA-b36703/target_genomes_gtdb.txt --output OceanDNA-b36703/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:37:15,496] [INFO] Task succeeded: fastANI
[2023-03-18 05:37:15,501] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:37:15,501] [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
GCF_001647025.1	s__Endozoicomonas atrinae	77.0833	125	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562015.1	s__Endozoicomonas arenosclerae	77.0587	87	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710775.1	s__Endozoicomonas elysicola	76.9797	106	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009653635.1	s__Endozoicomonas sp009653635	76.9702	74	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646945.1	s__Endozoicomonas ascidiicola	76.9225	105	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCA_900299555.1	s__Endozoicomonas sp900299555	76.9058	112	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583435.1	s__Endozoicomonas montiporae	76.5684	111	904	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 05:37:15,503] [INFO] GTDB search result was written to OceanDNA-b36703/result_gtdb.tsv
[2023-03-18 05:37:15,503] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:37:15,504] [INFO] DFAST_QC result json was written to OceanDNA-b36703/dqc_result.json
[2023-03-18 05:37:15,504] [INFO] DFAST_QC completed!
[2023-03-18 05:37:15,504] [INFO] Total running time: 0h1m38s