[2023-03-19 00:44:19,972] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference
[2023-03-19 00:44:21,048] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,048] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,048] [INFO] Running command: cat /var/lib/cwl/stgc4c02878-7eaa-4123-8eb0-7e689361a6c1/OceanDNA-b36158.fa | prodigal -d OceanDNA-b36158/cds.fna -a OceanDNA-b36158/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:29,316] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:29,316] [INFO] Task started: HMMsearch
[2023-03-19 00:44:29,316] [INFO] Running command: hmmsearch --tblout OceanDNA-b36158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/reference_markers.hmm OceanDNA-b36158/protein.faa > /dev/null
[2023-03-19 00:44:29,475] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:29,476] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc4c02878-7eaa-4123-8eb0-7e689361a6c1/OceanDNA-b36158.fa]
[2023-03-19 00:44:29,493] [INFO] Query marker FASTA was written to OceanDNA-b36158/markers.fasta
[2023-03-19 00:44:29,493] [INFO] Task started: Blastn
[2023-03-19 00:44:29,494] [INFO] Running command: blastn -query OceanDNA-b36158/markers.fasta -db /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/reference_markers.fasta -out OceanDNA-b36158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:30,083] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:30,084] [INFO] Selected 20 target genomes.
[2023-03-19 00:44:30,084] [INFO] Target genome list was writen to OceanDNA-b36158/target_genomes.txt
[2023-03-19 00:44:30,096] [INFO] Task started: fastANI
[2023-03-19 00:44:30,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4c02878-7eaa-4123-8eb0-7e689361a6c1/OceanDNA-b36158.fa --refList OceanDNA-b36158/target_genomes.txt --output OceanDNA-b36158/fastani_result.tsv --threads 1
[2023-03-19 00:44:42,226] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:42,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:42,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:42,231] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:44:42,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:44:42,231] [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
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	92.8234	234	264	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	78.8129	84	264	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	78.1148	80	264	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	77.9696	72	264	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:44:42,232] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36158/tc_result.tsv
[2023-03-19 00:44:42,232] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:42,232] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:42,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/checkm_data
[2023-03-19 00:44:42,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:42,236] [INFO] Task started: CheckM
[2023-03-19 00:44:42,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36158/checkm_input OceanDNA-b36158/checkm_result
[2023-03-19 00:45:08,184] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:08,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 5.59%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:08,186] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:08,186] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:08,187] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36158/markers.fasta)
[2023-03-19 00:45:08,188] [INFO] Task started: Blastn
[2023-03-19 00:45:08,188] [INFO] Running command: blastn -query OceanDNA-b36158/markers.fasta -db /var/lib/cwl/stg62b3a75c-9cf7-4589-b6d4-4ee3f8a7e4a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:09,074] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:09,075] [INFO] Selected 10 target genomes.
[2023-03-19 00:45:09,075] [INFO] Target genome list was writen to OceanDNA-b36158/target_genomes_gtdb.txt
[2023-03-19 00:45:09,087] [INFO] Task started: fastANI
[2023-03-19 00:45:09,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4c02878-7eaa-4123-8eb0-7e689361a6c1/OceanDNA-b36158.fa --refList OceanDNA-b36158/target_genomes_gtdb.txt --output OceanDNA-b36158/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:45:14,466] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:14,472] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:45:14,472] [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_003788585.1	s__Salinisphaera japonica	92.8234	234	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715985.1	s__Salinisphaera sp002715985	91.4291	189	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	-
GCA_002320455.1	s__Salinisphaera sp002320455	81.9885	186	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	79.6434	124	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602005.1	s__Salinisphaera sp003602005	79.327	129	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	78.8129	84	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	78.7529	104	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002729955.1	s__Salinisphaera sp002729955	78.1925	95	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	78.1172	80	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:45:14,473] [INFO] GTDB search result was written to OceanDNA-b36158/result_gtdb.tsv
[2023-03-19 00:45:14,473] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:45:14,474] [INFO] DFAST_QC result json was written to OceanDNA-b36158/dqc_result.json
[2023-03-19 00:45:14,474] [INFO] DFAST_QC completed!
[2023-03-19 00:45:14,475] [INFO] Total running time: 0h0m55s