[2023-03-15 08:09:45,405] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,405] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,405] [INFO] DQC Reference Directory: /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference
[2023-03-15 08:09:46,662] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,662] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,662] [INFO] Running command: cat /var/lib/cwl/stg312dd1f2-9f54-476b-98d8-3ca304a59209/OceanDNA-b41407.fa | prodigal -d OceanDNA-b41407/cds.fna -a OceanDNA-b41407/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:03,339] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:03,340] [INFO] Task started: HMMsearch
[2023-03-15 08:10:03,340] [INFO] Running command: hmmsearch --tblout OceanDNA-b41407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/reference_markers.hmm OceanDNA-b41407/protein.faa > /dev/null
[2023-03-15 08:10:03,621] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:03,622] [INFO] Found 6/6 markers.
[2023-03-15 08:10:03,653] [INFO] Query marker FASTA was written to OceanDNA-b41407/markers.fasta
[2023-03-15 08:10:03,654] [INFO] Task started: Blastn
[2023-03-15 08:10:03,654] [INFO] Running command: blastn -query OceanDNA-b41407/markers.fasta -db /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/reference_markers.fasta -out OceanDNA-b41407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:04,445] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:04,446] [INFO] Selected 28 target genomes.
[2023-03-15 08:10:04,446] [INFO] Target genome list was writen to OceanDNA-b41407/target_genomes.txt
[2023-03-15 08:10:04,463] [INFO] Task started: fastANI
[2023-03-15 08:10:04,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg312dd1f2-9f54-476b-98d8-3ca304a59209/OceanDNA-b41407.fa --refList OceanDNA-b41407/target_genomes.txt --output OceanDNA-b41407/fastani_result.tsv --threads 1
[2023-03-15 08:10:24,828] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:24,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:24,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:24,835] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 08:10:24,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 08:10:24,835] [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
Reinekea forsetii	strain=Hel1_31_D35	GCA_002795845.1	1336806	1336806	type	True	99.5673	921	925	95	conclusive
Reinekea thalattae	strain=SSH23	GCA_008041945.1	2593301	2593301	type	True	77.5889	54	925	95	below_threshold
Reinekea marinisedimentorum	strain=DSM 15388	GCA_004341165.1	230495	230495	type	True	76.9633	79	925	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	76.5811	85	925	95	below_threshold
Saccharospirillum impatiens	strain=DSM 12546	GCA_000423605.1	169438	169438	type	True	76.1231	54	925	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	76.1032	52	925	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	75.9656	53	925	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:24,940] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41407/tc_result.tsv
[2023-03-15 08:10:24,941] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:24,941] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:24,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/checkm_data
[2023-03-15 08:10:24,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:24,985] [INFO] Task started: CheckM
[2023-03-15 08:10:24,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41407/checkm_input OceanDNA-b41407/checkm_result
[2023-03-15 08:11:08,577] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:08,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:08,580] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:08,580] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:08,580] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41407/markers.fasta)
[2023-03-15 08:11:08,581] [INFO] Task started: Blastn
[2023-03-15 08:11:08,581] [INFO] Running command: blastn -query OceanDNA-b41407/markers.fasta -db /var/lib/cwl/stgfebdd96f-c31c-4223-b97b-4f70d000b841/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:09,645] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:09,646] [INFO] Selected 25 target genomes.
[2023-03-15 08:11:09,646] [INFO] Target genome list was writen to OceanDNA-b41407/target_genomes_gtdb.txt
[2023-03-15 08:11:09,669] [INFO] Task started: fastANI
[2023-03-15 08:11:09,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg312dd1f2-9f54-476b-98d8-3ca304a59209/OceanDNA-b41407.fa --refList OceanDNA-b41407/target_genomes_gtdb.txt --output OceanDNA-b41407/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:26,011] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:26,016] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:11:26,016] [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_002795845.1	s__Reinekea forsetii	99.5673	921	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	99.43	98.93	0.96	0.91	7	conclusive
GCF_008041945.1	s__Reinekea thalattae	77.5889	54	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015687175.1	s__Reinekea sp015687175	77.3713	84	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341165.1	s__Reinekea marinisedimentorum	76.9633	79	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153185.1	s__Reinekea blandensis	76.5811	85	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367315.1	s__Saccharospirillum mangrovi	76.1343	51	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423605.1	s__Saccharospirillum impatiens	76.1231	54	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:26,016] [INFO] GTDB search result was written to OceanDNA-b41407/result_gtdb.tsv
[2023-03-15 08:11:26,016] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:26,017] [INFO] DFAST_QC result json was written to OceanDNA-b41407/dqc_result.json
[2023-03-15 08:11:26,017] [INFO] DFAST_QC completed!
[2023-03-15 08:11:26,018] [INFO] Total running time: 0h1m41s