[2023-03-15 08:09:45,316] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,316] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference
[2023-03-15 08:09:46,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,633] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,633] [INFO] Running command: cat /var/lib/cwl/stgae125156-cda9-48e5-9a0d-6a03e1c98029/OceanDNA-b8549.fa | prodigal -d OceanDNA-b8549/cds.fna -a OceanDNA-b8549/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:51,983] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:51,983] [INFO] Task started: HMMsearch
[2023-03-15 08:09:51,983] [INFO] Running command: hmmsearch --tblout OceanDNA-b8549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/reference_markers.hmm OceanDNA-b8549/protein.faa > /dev/null
[2023-03-15 08:09:52,181] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:52,182] [INFO] Found 6/6 markers.
[2023-03-15 08:09:52,190] [INFO] Query marker FASTA was written to OceanDNA-b8549/markers.fasta
[2023-03-15 08:09:52,190] [INFO] Task started: Blastn
[2023-03-15 08:09:52,190] [INFO] Running command: blastn -query OceanDNA-b8549/markers.fasta -db /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/reference_markers.fasta -out OceanDNA-b8549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:52,861] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:52,862] [INFO] Selected 27 target genomes.
[2023-03-15 08:09:52,862] [INFO] Target genome list was writen to OceanDNA-b8549/target_genomes.txt
[2023-03-15 08:09:52,881] [INFO] Task started: fastANI
[2023-03-15 08:09:52,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgae125156-cda9-48e5-9a0d-6a03e1c98029/OceanDNA-b8549.fa --refList OceanDNA-b8549/target_genomes.txt --output OceanDNA-b8549/fastani_result.tsv --threads 1
[2023-03-15 08:10:08,630] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:08,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:08,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:08,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:08,631] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:08,631] [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
--------------------------------------------------------------------------------
[2023-03-15 08:10:08,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8549/tc_result.tsv
[2023-03-15 08:10:08,632] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:08,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:08,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/checkm_data
[2023-03-15 08:10:08,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:08,647] [INFO] Task started: CheckM
[2023-03-15 08:10:08,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8549/checkm_input OceanDNA-b8549/checkm_result
[2023-03-15 08:10:27,844] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:27,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:27,847] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:27,847] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:27,847] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8549/markers.fasta)
[2023-03-15 08:10:27,848] [INFO] Task started: Blastn
[2023-03-15 08:10:27,848] [INFO] Running command: blastn -query OceanDNA-b8549/markers.fasta -db /var/lib/cwl/stg91da1a69-5326-42f3-a820-373e8e4b70fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:28,763] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:28,764] [INFO] Selected 10 target genomes.
[2023-03-15 08:10:28,764] [INFO] Target genome list was writen to OceanDNA-b8549/target_genomes_gtdb.txt
[2023-03-15 08:10:28,773] [INFO] Task started: fastANI
[2023-03-15 08:10:28,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgae125156-cda9-48e5-9a0d-6a03e1c98029/OceanDNA-b8549.fa --refList OceanDNA-b8549/target_genomes_gtdb.txt --output OceanDNA-b8549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:31,058] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:31,064] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:10:31,065] [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_902629505.1	s__MED-G11 sp902629505	90.9344	151	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523665.1	s__MED-G11 sp902523665	88.0473	215	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622595.1	s__MED-G11 sp902622595	87.9285	265	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_902620455.1	s__MED-G11 sp902620455	87.554	234	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.20	98.53	0.88	0.86	7	-
GCA_902516925.1	s__MED-G11 sp902516925	83.6076	174	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519955.1	s__MED-G11 sp902519955	83.5004	186	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.88	99.84	0.80	0.74	3	-
GCA_902593165.1	s__MED-G11 sp902593165	83.3251	226	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.69	96.69	0.86	0.86	2	-
GCA_905380995.1	s__MED-G11 sp905380995	83.1005	210	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517365.1	s__MED-G11 sp902517365	83.0972	124	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594485.1	s__MED-G11 sp902594485	82.9696	154	291	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.32	97.18	0.70	0.65	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:31,065] [INFO] GTDB search result was written to OceanDNA-b8549/result_gtdb.tsv
[2023-03-15 08:10:31,065] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:31,066] [INFO] DFAST_QC result json was written to OceanDNA-b8549/dqc_result.json
[2023-03-15 08:10:31,066] [INFO] DFAST_QC completed!
[2023-03-15 08:10:31,066] [INFO] Total running time: 0h0m46s