[2023-03-16 10:20:34,583] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,583] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference
[2023-03-16 10:20:35,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,805] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,805] [INFO] Running command: cat /var/lib/cwl/stg753a0115-9e1a-4e8c-bb0f-b0ee2908f752/OceanDNA-b11170.fa | prodigal -d OceanDNA-b11170/cds.fna -a OceanDNA-b11170/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:50,095] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:50,095] [INFO] Task started: HMMsearch
[2023-03-16 10:20:50,095] [INFO] Running command: hmmsearch --tblout OceanDNA-b11170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/reference_markers.hmm OceanDNA-b11170/protein.faa > /dev/null
[2023-03-16 10:20:50,447] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:50,448] [INFO] Found 6/6 markers.
[2023-03-16 10:20:50,461] [INFO] Query marker FASTA was written to OceanDNA-b11170/markers.fasta
[2023-03-16 10:20:50,463] [INFO] Task started: Blastn
[2023-03-16 10:20:50,463] [INFO] Running command: blastn -query OceanDNA-b11170/markers.fasta -db /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/reference_markers.fasta -out OceanDNA-b11170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:51,032] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:51,033] [INFO] Selected 34 target genomes.
[2023-03-16 10:20:51,033] [INFO] Target genome list was writen to OceanDNA-b11170/target_genomes.txt
[2023-03-16 10:20:51,057] [INFO] Task started: fastANI
[2023-03-16 10:20:51,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg753a0115-9e1a-4e8c-bb0f-b0ee2908f752/OceanDNA-b11170.fa --refList OceanDNA-b11170/target_genomes.txt --output OceanDNA-b11170/fastani_result.tsv --threads 1
[2023-03-16 10:21:10,935] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:10,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:10,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:10,936] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:10,936] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:21:10,936] [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
--------------------------------------------------------------------------------
[2023-03-16 10:21:10,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11170/tc_result.tsv
[2023-03-16 10:21:10,937] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:10,937] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:10,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/checkm_data
[2023-03-16 10:21:10,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:10,944] [INFO] Task started: CheckM
[2023-03-16 10:21:10,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11170/checkm_input OceanDNA-b11170/checkm_result
[2023-03-16 10:21:51,614] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:51,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:51,617] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:51,617] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:51,617] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11170/markers.fasta)
[2023-03-16 10:21:51,619] [INFO] Task started: Blastn
[2023-03-16 10:21:51,619] [INFO] Running command: blastn -query OceanDNA-b11170/markers.fasta -db /var/lib/cwl/stgeb05167f-68e7-4177-8e9f-8d47b243a45c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:52,362] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:52,363] [INFO] Selected 20 target genomes.
[2023-03-16 10:21:52,363] [INFO] Target genome list was writen to OceanDNA-b11170/target_genomes_gtdb.txt
[2023-03-16 10:21:52,425] [INFO] Task started: fastANI
[2023-03-16 10:21:52,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg753a0115-9e1a-4e8c-bb0f-b0ee2908f752/OceanDNA-b11170.fa --refList OceanDNA-b11170/target_genomes_gtdb.txt --output OceanDNA-b11170/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:59,078] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:59,087] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:59,087] [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_002390455.1	s__UBA8316 sp002390455	79.0326	271	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_009936675.1	s__UBA8316 sp009936675	78.8444	225	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_018623955.1	s__UBA8316 sp018623955	78.7083	146	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364535.1	s__UBA8316 sp002364535	78.6905	257	584	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	78.0763	213	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687665.1	s__UBA8316 sp002687665	77.5962	118	584	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	77.5553	155	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_002336305.1	s__UBA8316 sp002336305	77.491	150	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	77.2697	131	584	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	76.5918	96	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858055.1	s__MS024-2A sp002384715	76.2989	53	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_018699935.1	s__MS024-2A sp018699935	76.0968	58	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_902590705.1	s__UBA8316 sp902590705	76.0176	59	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.92	99.92	0.88	0.88	2	-
GCA_017857815.1	s__UBA8316 sp017857815	75.9829	67	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:59,087] [INFO] GTDB search result was written to OceanDNA-b11170/result_gtdb.tsv
[2023-03-16 10:21:59,088] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:59,089] [INFO] DFAST_QC result json was written to OceanDNA-b11170/dqc_result.json
[2023-03-16 10:21:59,089] [INFO] DFAST_QC completed!
[2023-03-16 10:21:59,089] [INFO] Total running time: 0h1m25s