[2023-03-14 13:27:15,138] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:27:15,138] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:27:15,138] [INFO] DQC Reference Directory: /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference
[2023-03-14 13:27:16,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:27:16,346] [INFO] Task started: Prodigal
[2023-03-14 13:27:16,346] [INFO] Running command: cat /var/lib/cwl/stgd5200b9e-d781-4195-903c-f587c3898be4/OceanDNA-b9151.fa | prodigal -d OceanDNA-b9151/cds.fna -a OceanDNA-b9151/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:27:25,028] [INFO] Task succeeded: Prodigal
[2023-03-14 13:27:25,029] [INFO] Task started: HMMsearch
[2023-03-14 13:27:25,029] [INFO] Running command: hmmsearch --tblout OceanDNA-b9151/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/reference_markers.hmm OceanDNA-b9151/protein.faa > /dev/null
[2023-03-14 13:27:25,276] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:27:25,277] [INFO] Found 6/6 markers.
[2023-03-14 13:27:25,307] [INFO] Query marker FASTA was written to OceanDNA-b9151/markers.fasta
[2023-03-14 13:27:25,309] [INFO] Task started: Blastn
[2023-03-14 13:27:25,309] [INFO] Running command: blastn -query OceanDNA-b9151/markers.fasta -db /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/reference_markers.fasta -out OceanDNA-b9151/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:27:26,308] [INFO] Task succeeded: Blastn
[2023-03-14 13:27:26,309] [INFO] Selected 36 target genomes.
[2023-03-14 13:27:26,309] [INFO] Target genome list was writen to OceanDNA-b9151/target_genomes.txt
[2023-03-14 13:27:26,382] [INFO] Task started: fastANI
[2023-03-14 13:27:26,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5200b9e-d781-4195-903c-f587c3898be4/OceanDNA-b9151.fa --refList OceanDNA-b9151/target_genomes.txt --output OceanDNA-b9151/fastani_result.tsv --threads 1
[2023-03-14 13:27:59,915] [INFO] Task succeeded: fastANI
[2023-03-14 13:27:59,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:27:59,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:27:59,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:27:59,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:27:59,916] [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
--------------------------------------------------------------------------------
[2023-03-14 13:27:59,916] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9151/tc_result.tsv
[2023-03-14 13:27:59,917] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:27:59,917] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:27:59,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/checkm_data
[2023-03-14 13:27:59,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:27:59,923] [INFO] Task started: CheckM
[2023-03-14 13:27:59,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9151/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9151/checkm_input OceanDNA-b9151/checkm_result
[2023-03-14 13:28:25,621] [INFO] Task succeeded: CheckM
[2023-03-14 13:28:25,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.29%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:28:25,624] [INFO] ===== Completeness check finished =====
[2023-03-14 13:28:25,624] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:28:25,624] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9151/markers.fasta)
[2023-03-14 13:28:25,625] [INFO] Task started: Blastn
[2023-03-14 13:28:25,625] [INFO] Running command: blastn -query OceanDNA-b9151/markers.fasta -db /var/lib/cwl/stge0a2bdcb-b43b-4661-b080-4cca957ed21f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9151/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:28:26,612] [INFO] Task succeeded: Blastn
[2023-03-14 13:28:26,614] [INFO] Selected 32 target genomes.
[2023-03-14 13:28:26,614] [INFO] Target genome list was writen to OceanDNA-b9151/target_genomes_gtdb.txt
[2023-03-14 13:28:26,641] [INFO] Task started: fastANI
[2023-03-14 13:28:26,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5200b9e-d781-4195-903c-f587c3898be4/OceanDNA-b9151.fa --refList OceanDNA-b9151/target_genomes_gtdb.txt --output OceanDNA-b9151/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:28:38,282] [INFO] Task succeeded: fastANI
[2023-03-14 13:28:38,293] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:28:38,293] [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_902512755.1	s__MS024-2A sp902512755	82.9781	228	431	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_902517245.1	s__MS024-2A sp902517245	80.3249	232	431	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_002169865.1	s__MS024-2A sp002169865	79.5038	124	431	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_902606525.1	s__MS024-2A sp902606525	79.3761	170	431	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_002705385.1	s__MS024-2A sp002705385	77.2581	67	431	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_009886625.1	s__MS024-2A sp009886625	76.904	104	431	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_905182305.1	s__MS024-2A sp905182305	76.7944	115	431	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_000173095.1	s__MS024-2A sp000173095	76.7394	77	431	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_902618245.1	s__MS024-2A sp902618245	76.7352	79	431	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_017852075.1	s__MS024-2A sp017852075	76.6687	96	431	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_905480425.1	s__MS024-2A sp905480425	76.6189	125	431	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_902616905.1	s__MS024-2A sp902616905	76.612	79	431	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_002714815.1	s__MS024-2A sp002714815	76.5863	134	431	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_003130815.1	s__MS024-2A sp003130815	76.4243	85	431	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_902561795.1	s__MS024-2A sp902561795	76.3665	76	431	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_902613595.1	s__MS024-2A sp902613595	76.1042	88	431	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_011525195.1	s__MS024-2A sp011525195	76.0633	59	431	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_017858055.1	s__MS024-2A sp002384715	75.9521	68	431	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:28:38,293] [INFO] GTDB search result was written to OceanDNA-b9151/result_gtdb.tsv
[2023-03-14 13:28:38,293] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:28:38,295] [INFO] DFAST_QC result json was written to OceanDNA-b9151/dqc_result.json
[2023-03-14 13:28:38,295] [INFO] DFAST_QC completed!
[2023-03-14 13:28:38,295] [INFO] Total running time: 0h1m23s