[2023-03-18 23:32:58,551] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:32:58,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:32:58,552] [INFO] DQC Reference Directory: /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference
[2023-03-18 23:32:59,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:32:59,887] [INFO] Task started: Prodigal
[2023-03-18 23:32:59,887] [INFO] Running command: cat /var/lib/cwl/stgfd4fe6a9-9676-485e-84e4-42683a343ed4/OceanDNA-b42603.fa | prodigal -d OceanDNA-b42603/cds.fna -a OceanDNA-b42603/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:33:04,631] [INFO] Task succeeded: Prodigal
[2023-03-18 23:33:04,631] [INFO] Task started: HMMsearch
[2023-03-18 23:33:04,631] [INFO] Running command: hmmsearch --tblout OceanDNA-b42603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/reference_markers.hmm OceanDNA-b42603/protein.faa > /dev/null
[2023-03-18 23:33:04,768] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:33:04,768] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfd4fe6a9-9676-485e-84e4-42683a343ed4/OceanDNA-b42603.fa]
[2023-03-18 23:33:04,775] [INFO] Query marker FASTA was written to OceanDNA-b42603/markers.fasta
[2023-03-18 23:33:05,170] [INFO] Task started: Blastn
[2023-03-18 23:33:05,170] [INFO] Running command: blastn -query OceanDNA-b42603/markers.fasta -db /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/reference_markers.fasta -out OceanDNA-b42603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:33:05,736] [INFO] Task succeeded: Blastn
[2023-03-18 23:33:05,977] [INFO] Selected 8 target genomes.
[2023-03-18 23:33:05,977] [INFO] Target genome list was writen to OceanDNA-b42603/target_genomes.txt
[2023-03-18 23:33:05,982] [INFO] Task started: fastANI
[2023-03-18 23:33:05,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd4fe6a9-9676-485e-84e4-42683a343ed4/OceanDNA-b42603.fa --refList OceanDNA-b42603/target_genomes.txt --output OceanDNA-b42603/fastani_result.tsv --threads 1
[2023-03-18 23:33:08,670] [INFO] Task succeeded: fastANI
[2023-03-18 23:33:08,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:33:08,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:33:08,671] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:33:08,671] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:33:08,671] [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 23:33:08,671] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42603/tc_result.tsv
[2023-03-18 23:33:08,671] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:33:08,672] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:33:08,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/checkm_data
[2023-03-18 23:33:08,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:33:08,685] [INFO] Task started: CheckM
[2023-03-18 23:33:08,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42603/checkm_input OceanDNA-b42603/checkm_result
[2023-03-18 23:33:26,864] [INFO] Task succeeded: CheckM
[2023-03-18 23:33:26,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:33:26,866] [INFO] ===== Completeness check finished =====
[2023-03-18 23:33:26,867] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:33:26,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42603/markers.fasta)
[2023-03-18 23:33:26,868] [INFO] Task started: Blastn
[2023-03-18 23:33:26,868] [INFO] Running command: blastn -query OceanDNA-b42603/markers.fasta -db /var/lib/cwl/stga607171e-f2a4-45d4-b58d-7abaff0da475/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:33:27,436] [INFO] Task succeeded: Blastn
[2023-03-18 23:33:27,437] [INFO] Selected 13 target genomes.
[2023-03-18 23:33:27,437] [INFO] Target genome list was writen to OceanDNA-b42603/target_genomes_gtdb.txt
[2023-03-18 23:33:27,457] [INFO] Task started: fastANI
[2023-03-18 23:33:27,457] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd4fe6a9-9676-485e-84e4-42683a343ed4/OceanDNA-b42603.fa --refList OceanDNA-b42603/target_genomes_gtdb.txt --output OceanDNA-b42603/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:33:30,290] [INFO] Task succeeded: fastANI
[2023-03-18 23:33:30,294] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:33:30,295] [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_902517565.1	s__GCA-2707915 sp902517565	98.3376	234	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004214065.1	s__GCA-2707915 sp004214065	79.3002	150	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
GCA_003212335.1	s__GCA-2707915 sp003212335	78.0488	122	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_902620785.1	s__GCA-2707915 sp902620785	77.2309	106	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_016777005.1	s__GCA-2707915 sp016777005	77.0981	80	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707915.1	s__GCA-2707915 sp002707915	76.7949	71	311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.24	96.30	0.83	0.75	4	-
--------------------------------------------------------------------------------
[2023-03-18 23:33:30,295] [INFO] GTDB search result was written to OceanDNA-b42603/result_gtdb.tsv
[2023-03-18 23:33:30,295] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:33:30,296] [INFO] DFAST_QC result json was written to OceanDNA-b42603/dqc_result.json
[2023-03-18 23:33:30,296] [INFO] DFAST_QC completed!
[2023-03-18 23:33:30,296] [INFO] Total running time: 0h0m32s