[2023-03-18 03:45:10,277] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference
[2023-03-18 03:45:12,148] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,148] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,148] [INFO] Running command: cat /var/lib/cwl/stg557b7e32-cf0b-43cd-a2af-19810b87f9e5/OceanDNA-b37665.fa | prodigal -d OceanDNA-b37665/cds.fna -a OceanDNA-b37665/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:36,241] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:36,242] [INFO] Task started: HMMsearch
[2023-03-18 03:45:36,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b37665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/reference_markers.hmm OceanDNA-b37665/protein.faa > /dev/null
[2023-03-18 03:45:36,467] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:36,467] [INFO] Found 6/6 markers.
[2023-03-18 03:45:36,492] [INFO] Query marker FASTA was written to OceanDNA-b37665/markers.fasta
[2023-03-18 03:45:36,493] [INFO] Task started: Blastn
[2023-03-18 03:45:36,493] [INFO] Running command: blastn -query OceanDNA-b37665/markers.fasta -db /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/reference_markers.fasta -out OceanDNA-b37665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:37,110] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:37,111] [INFO] Selected 26 target genomes.
[2023-03-18 03:45:37,111] [INFO] Target genome list was writen to OceanDNA-b37665/target_genomes.txt
[2023-03-18 03:45:37,121] [INFO] Task started: fastANI
[2023-03-18 03:45:37,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg557b7e32-cf0b-43cd-a2af-19810b87f9e5/OceanDNA-b37665.fa --refList OceanDNA-b37665/target_genomes.txt --output OceanDNA-b37665/fastani_result.tsv --threads 1
[2023-03-18 03:45:53,536] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:53,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:53,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:53,542] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:53,542] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:53,542] [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
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.4725	83	1320	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.4405	92	1320	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.3651	76	1320	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.2443	68	1320	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.221	79	1320	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.0	72	1320	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:53,542] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37665/tc_result.tsv
[2023-03-18 03:45:53,542] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:53,543] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:53,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/checkm_data
[2023-03-18 03:45:53,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:53,652] [INFO] Task started: CheckM
[2023-03-18 03:45:53,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37665/checkm_input OceanDNA-b37665/checkm_result
[2023-03-18 03:46:52,839] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:52,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:52,842] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:52,842] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:52,842] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37665/markers.fasta)
[2023-03-18 03:46:52,843] [INFO] Task started: Blastn
[2023-03-18 03:46:52,843] [INFO] Running command: blastn -query OceanDNA-b37665/markers.fasta -db /var/lib/cwl/stg1a7d07da-dd13-4c9b-8ab1-c153d81f3233/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:53,875] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:53,876] [INFO] Selected 23 target genomes.
[2023-03-18 03:46:53,876] [INFO] Target genome list was writen to OceanDNA-b37665/target_genomes_gtdb.txt
[2023-03-18 03:46:53,915] [INFO] Task started: fastANI
[2023-03-18 03:46:53,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg557b7e32-cf0b-43cd-a2af-19810b87f9e5/OceanDNA-b37665.fa --refList OceanDNA-b37665/target_genomes_gtdb.txt --output OceanDNA-b37665/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:08,286] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:08,295] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:47:08,295] [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_002862985.1	s__Halioglobus sp002862985	95.3647	969	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016704305.1	s__Halioglobus sp016704305	76.7217	193	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.6536	178	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	76.5884	106	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.4725	83	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.4405	92	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.4027	92	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.3864	106	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_014652275.1	s__Halioglobus_A pacificus	76.3622	59	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus_A	95.0	98.67	98.67	0.96	0.96	2	-
GCA_002692965.1	s__NZNC01 sp002692965	76.245	62	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.2394	81	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.1487	68	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.0892	82	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	76.0202	60	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCA_002414665.1	s__Haliea sp002414665	76.0202	68	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_010669285.1	s__Kineobactrum salinum	76.0	72	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:08,296] [INFO] GTDB search result was written to OceanDNA-b37665/result_gtdb.tsv
[2023-03-18 03:47:08,296] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:08,297] [INFO] DFAST_QC result json was written to OceanDNA-b37665/dqc_result.json
[2023-03-18 03:47:08,297] [INFO] DFAST_QC completed!
[2023-03-18 03:47:08,298] [INFO] Total running time: 0h1m58s