[2023-03-15 17:05:43,620] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:05:43,621] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:05:43,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference
[2023-03-15 17:05:45,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:05:45,976] [INFO] Task started: Prodigal
[2023-03-15 17:05:45,976] [INFO] Running command: cat /var/lib/cwl/stg971efd36-7a40-4d0f-88bb-2be397640060/OceanDNA-b11244.fa | prodigal -d OceanDNA-b11244/cds.fna -a OceanDNA-b11244/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:05:58,223] [INFO] Task succeeded: Prodigal
[2023-03-15 17:05:58,223] [INFO] Task started: HMMsearch
[2023-03-15 17:05:58,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b11244/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/reference_markers.hmm OceanDNA-b11244/protein.faa > /dev/null
[2023-03-15 17:05:58,420] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:05:58,420] [INFO] Found 6/6 markers.
[2023-03-15 17:05:58,432] [INFO] Query marker FASTA was written to OceanDNA-b11244/markers.fasta
[2023-03-15 17:05:58,434] [INFO] Task started: Blastn
[2023-03-15 17:05:58,434] [INFO] Running command: blastn -query OceanDNA-b11244/markers.fasta -db /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/reference_markers.fasta -out OceanDNA-b11244/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:05:59,022] [INFO] Task succeeded: Blastn
[2023-03-15 17:05:59,023] [INFO] Selected 28 target genomes.
[2023-03-15 17:05:59,024] [INFO] Target genome list was writen to OceanDNA-b11244/target_genomes.txt
[2023-03-15 17:05:59,068] [INFO] Task started: fastANI
[2023-03-15 17:05:59,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg971efd36-7a40-4d0f-88bb-2be397640060/OceanDNA-b11244.fa --refList OceanDNA-b11244/target_genomes.txt --output OceanDNA-b11244/fastani_result.tsv --threads 1
[2023-03-15 17:06:14,447] [INFO] Task succeeded: fastANI
[2023-03-15 17:06:14,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:06:14,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:06:14,448] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:06:14,448] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:06:14,448] [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 17:06:14,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11244/tc_result.tsv
[2023-03-15 17:06:14,448] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:06:14,448] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:06:14,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/checkm_data
[2023-03-15 17:06:14,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:06:14,459] [INFO] Task started: CheckM
[2023-03-15 17:06:14,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11244/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11244/checkm_input OceanDNA-b11244/checkm_result
[2023-03-15 17:06:50,220] [INFO] Task succeeded: CheckM
[2023-03-15 17:06:50,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:06:50,258] [INFO] ===== Completeness check finished =====
[2023-03-15 17:06:50,258] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:06:50,258] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11244/markers.fasta)
[2023-03-15 17:06:50,259] [INFO] Task started: Blastn
[2023-03-15 17:06:50,260] [INFO] Running command: blastn -query OceanDNA-b11244/markers.fasta -db /var/lib/cwl/stgcac8d62e-793f-48b5-b622-10115b655fe5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11244/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:06:51,116] [INFO] Task succeeded: Blastn
[2023-03-15 17:06:51,119] [INFO] Selected 29 target genomes.
[2023-03-15 17:06:51,119] [INFO] Target genome list was writen to OceanDNA-b11244/target_genomes_gtdb.txt
[2023-03-15 17:06:51,226] [INFO] Task started: fastANI
[2023-03-15 17:06:51,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg971efd36-7a40-4d0f-88bb-2be397640060/OceanDNA-b11244.fa --refList OceanDNA-b11244/target_genomes_gtdb.txt --output OceanDNA-b11244/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:07:01,458] [INFO] Task succeeded: fastANI
[2023-03-15 17:07:01,468] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:07:01,469] [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_902584445.1	s__UBA8316 sp902584445	78.4329	229	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171295.2	s__UBA8316 sp002171295	78.4039	184	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590705.1	s__UBA8316 sp902590705	78.0882	242	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.92	99.92	0.88	0.88	2	-
GCA_902515395.1	s__UBA8316 sp902515395	78.042	210	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	96.55	96.55	0.73	0.73	2	-
GCA_002695445.1	s__UBA8316 sp002695445	77.2587	150	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	97.71	97.71	0.68	0.68	2	-
GCA_003538555.1	s__UBA8316 sp003538555	77.1868	58	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
GCA_002390455.1	s__UBA8316 sp002390455	77.1617	120	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_018623955.1	s__UBA8316 sp018623955	77.0067	58	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711215.1	s__UBA8316 sp002711215	76.9366	85	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_002364535.1	s__UBA8316 sp002364535	76.9139	119	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018647605.1	s__UBA8316 sp018647605	76.8695	130	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	76.78	108	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_902619315.1	s__UBA8316 sp902619315	76.7388	80	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716845.1	s__UBA8316 sp002716845	76.2323	73	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857815.1	s__UBA8316 sp017857815	76.1691	79	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	75.9208	52	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182575.1	s__UBA8316 sp905182575	75.8579	81	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:07:01,470] [INFO] GTDB search result was written to OceanDNA-b11244/result_gtdb.tsv
[2023-03-15 17:07:01,471] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:07:01,473] [INFO] DFAST_QC result json was written to OceanDNA-b11244/dqc_result.json
[2023-03-15 17:07:01,473] [INFO] DFAST_QC completed!
[2023-03-15 17:07:01,473] [INFO] Total running time: 0h1m18s