[2023-03-18 08:42:34,542] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,544] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,544] [INFO] DQC Reference Directory: /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference
[2023-03-18 08:42:35,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,647] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,647] [INFO] Running command: cat /var/lib/cwl/stgf047b9d2-332c-4e14-9aed-66a0aabe3f1b/OceanDNA-b42079.fa | prodigal -d OceanDNA-b42079/cds.fna -a OceanDNA-b42079/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:39,999] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:39,999] [INFO] Task started: HMMsearch
[2023-03-18 08:42:39,999] [INFO] Running command: hmmsearch --tblout OceanDNA-b42079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/reference_markers.hmm OceanDNA-b42079/protein.faa > /dev/null
[2023-03-18 08:42:40,147] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:40,148] [INFO] Found 6/6 markers.
[2023-03-18 08:42:40,168] [INFO] Query marker FASTA was written to OceanDNA-b42079/markers.fasta
[2023-03-18 08:42:40,168] [INFO] Task started: Blastn
[2023-03-18 08:42:40,168] [INFO] Running command: blastn -query OceanDNA-b42079/markers.fasta -db /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/reference_markers.fasta -out OceanDNA-b42079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:40,670] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:40,672] [INFO] Selected 15 target genomes.
[2023-03-18 08:42:40,672] [INFO] Target genome list was writen to OceanDNA-b42079/target_genomes.txt
[2023-03-18 08:42:40,679] [INFO] Task started: fastANI
[2023-03-18 08:42:40,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgf047b9d2-332c-4e14-9aed-66a0aabe3f1b/OceanDNA-b42079.fa --refList OceanDNA-b42079/target_genomes.txt --output OceanDNA-b42079/fastani_result.tsv --threads 1
[2023-03-18 08:42:47,694] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:47,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:47,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:47,695] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:47,695] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:47,695] [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
--------------------------------------------------------------------------------
[2023-03-18 08:42:47,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42079/tc_result.tsv
[2023-03-18 08:42:47,700] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:47,700] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:47,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/checkm_data
[2023-03-18 08:42:47,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:47,708] [INFO] Task started: CheckM
[2023-03-18 08:42:47,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42079/checkm_input OceanDNA-b42079/checkm_result
[2023-03-18 08:43:04,983] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:04,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:04,988] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:04,988] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:04,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42079/markers.fasta)
[2023-03-18 08:43:04,989] [INFO] Task started: Blastn
[2023-03-18 08:43:04,989] [INFO] Running command: blastn -query OceanDNA-b42079/markers.fasta -db /var/lib/cwl/stga561f070-9094-47ac-8532-3c9eeba41697/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:05,686] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:05,688] [INFO] Selected 24 target genomes.
[2023-03-18 08:43:05,688] [INFO] Target genome list was writen to OceanDNA-b42079/target_genomes_gtdb.txt
[2023-03-18 08:43:05,712] [INFO] Task started: fastANI
[2023-03-18 08:43:05,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgf047b9d2-332c-4e14-9aed-66a0aabe3f1b/OceanDNA-b42079.fa --refList OceanDNA-b42079/target_genomes_gtdb.txt --output OceanDNA-b42079/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:10,865] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:10,875] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:43:10,875] [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_905181595.1	s__D2472 sp905181595	93.802	253	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469975.1	s__D2472 sp002469975	80.1295	108	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	-
GCA_002358345.1	s__D2472 sp002358345	79.6557	129	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
GCA_905181645.1	s__MED-G78 sp905181645	78.86	75	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	78.5769	95	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902511575.1	s__D2472 sp902511575	78.4932	90	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307935.1	s__D2472 sp000307935	78.3131	96	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	77.8574	86	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	77.8469	91	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902593675.1	s__D2472 sp902593675	77.6937	87	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608115.1	s__D2472 sp902608115	77.6478	71	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513515.1	s__D2472 sp902513515	77.5496	66	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	77.5043	71	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902599315.1	s__D2472 sp902599315	77.4267	72	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	97.18	96.37	0.89	0.86	3	-
GCA_902515775.1	s__D2472 sp902515775	77.2432	73	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528215.1	s__D2472 sp902528215	76.9618	60	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:10,877] [INFO] GTDB search result was written to OceanDNA-b42079/result_gtdb.tsv
[2023-03-18 08:43:10,877] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:10,881] [INFO] DFAST_QC result json was written to OceanDNA-b42079/dqc_result.json
[2023-03-18 08:43:10,881] [INFO] DFAST_QC completed!
[2023-03-18 08:43:10,881] [INFO] Total running time: 0h0m36s