[2023-03-17 02:31:12,850] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,850] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,378] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,378] [INFO] Running command: cat /var/lib/cwl/stg7ea2cc49-c77d-4860-823f-bb0318b44d27/OceanDNA-b43405.fa | prodigal -d OceanDNA-b43405/cds.fna -a OceanDNA-b43405/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:18,466] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:18,466] [INFO] Task started: HMMsearch
[2023-03-17 02:31:18,466] [INFO] Running command: hmmsearch --tblout OceanDNA-b43405/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/reference_markers.hmm OceanDNA-b43405/protein.faa > /dev/null
[2023-03-17 02:31:18,627] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:18,628] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ea2cc49-c77d-4860-823f-bb0318b44d27/OceanDNA-b43405.fa]
[2023-03-17 02:31:18,635] [INFO] Query marker FASTA was written to OceanDNA-b43405/markers.fasta
[2023-03-17 02:31:18,635] [INFO] Task started: Blastn
[2023-03-17 02:31:18,635] [INFO] Running command: blastn -query OceanDNA-b43405/markers.fasta -db /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/reference_markers.fasta -out OceanDNA-b43405/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:19,175] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:19,175] [INFO] Selected 28 target genomes.
[2023-03-17 02:31:19,176] [INFO] Target genome list was writen to OceanDNA-b43405/target_genomes.txt
[2023-03-17 02:31:19,190] [INFO] Task started: fastANI
[2023-03-17 02:31:19,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea2cc49-c77d-4860-823f-bb0318b44d27/OceanDNA-b43405.fa --refList OceanDNA-b43405/target_genomes.txt --output OceanDNA-b43405/fastani_result.tsv --threads 1
[2023-03-17 02:31:34,797] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:34,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:34,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:34,801] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:34,801] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:34,801] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	78.9805	104	236	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:34,801] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43405/tc_result.tsv
[2023-03-17 02:31:34,801] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:34,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:34,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/checkm_data
[2023-03-17 02:31:34,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:34,806] [INFO] Task started: CheckM
[2023-03-17 02:31:34,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43405/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43405/checkm_input OceanDNA-b43405/checkm_result
[2023-03-17 02:31:51,367] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:51,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.06%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 02:31:51,369] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:51,369] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:51,369] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43405/markers.fasta)
[2023-03-17 02:31:51,369] [INFO] Task started: Blastn
[2023-03-17 02:31:51,369] [INFO] Running command: blastn -query OceanDNA-b43405/markers.fasta -db /var/lib/cwl/stg34c8b3b5-3528-409b-9f1e-6969fa18f677/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43405/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:52,203] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:52,204] [INFO] Selected 13 target genomes.
[2023-03-17 02:31:52,204] [INFO] Target genome list was writen to OceanDNA-b43405/target_genomes_gtdb.txt
[2023-03-17 02:31:52,603] [INFO] Task started: fastANI
[2023-03-17 02:31:52,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea2cc49-c77d-4860-823f-bb0318b44d27/OceanDNA-b43405.fa --refList OceanDNA-b43405/target_genomes_gtdb.txt --output OceanDNA-b43405/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:31:55,899] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:55,906] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:31:55,907] [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_018648985.1	s__UBA2013 sp018648985	99.1566	192	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003489145.1	s__UBA2013 sp003489145	84.0832	159	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_003978285.1	s__UBA2013 sp003978285	83.2899	129	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	82.5536	176	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_016845205.1	s__UBA2013 sp016845205	82.388	180	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910595805.1	s__UBA2013 sp910595805	82.3509	136	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978185.1	s__UBA2013 sp003978185	81.8974	90	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658965.1	s__UBA2013 sp015658965	80.2541	141	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293165.1	s__Thioglobus autotrophicus	78.9805	104	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963565.1	s__DTVJ01 sp012963565	78.7437	117	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384345.1	s__Thioglobus pontius	78.2816	108	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCF_001298715.1	s__Thiodubiliella sp001298715	77.5675	74	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.96	97.97	0.90	0.82	38	-
--------------------------------------------------------------------------------
[2023-03-17 02:31:55,907] [INFO] GTDB search result was written to OceanDNA-b43405/result_gtdb.tsv
[2023-03-17 02:31:55,907] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:31:55,908] [INFO] DFAST_QC result json was written to OceanDNA-b43405/dqc_result.json
[2023-03-17 02:31:55,908] [INFO] DFAST_QC completed!
[2023-03-17 02:31:55,908] [INFO] Total running time: 0h0m43s