[2023-03-18 08:31:58,249] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:58,249] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:58,250] [INFO] DQC Reference Directory: /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference
[2023-03-18 08:31:59,371] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:59,372] [INFO] Task started: Prodigal
[2023-03-18 08:31:59,372] [INFO] Running command: cat /var/lib/cwl/stgb8481d84-31fe-4bea-9ecd-97286c3a1310/OceanDNA-b35278.fa | prodigal -d OceanDNA-b35278/cds.fna -a OceanDNA-b35278/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:24,122] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:24,123] [INFO] Task started: HMMsearch
[2023-03-18 08:32:24,123] [INFO] Running command: hmmsearch --tblout OceanDNA-b35278/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/reference_markers.hmm OceanDNA-b35278/protein.faa > /dev/null
[2023-03-18 08:32:24,353] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:24,353] [INFO] Found 6/6 markers.
[2023-03-18 08:32:24,378] [INFO] Query marker FASTA was written to OceanDNA-b35278/markers.fasta
[2023-03-18 08:32:24,378] [INFO] Task started: Blastn
[2023-03-18 08:32:24,378] [INFO] Running command: blastn -query OceanDNA-b35278/markers.fasta -db /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/reference_markers.fasta -out OceanDNA-b35278/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:25,061] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:25,061] [INFO] Selected 8 target genomes.
[2023-03-18 08:32:25,062] [INFO] Target genome list was writen to OceanDNA-b35278/target_genomes.txt
[2023-03-18 08:32:25,065] [INFO] Task started: fastANI
[2023-03-18 08:32:25,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8481d84-31fe-4bea-9ecd-97286c3a1310/OceanDNA-b35278.fa --refList OceanDNA-b35278/target_genomes.txt --output OceanDNA-b35278/fastani_result.tsv --threads 1
[2023-03-18 08:32:33,547] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:33,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:33,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:33,553] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 08:32:33,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 08:32:33,553] [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
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	98.5009	1400	1504	95	conclusive
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	98.4732	1405	1504	95	conclusive
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	85.4805	1195	1504	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	84.4728	1113	1504	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	84.4195	1143	1504	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	83.5127	1072	1504	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	81.1924	881	1504	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	81.1687	837	1504	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:33,554] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35278/tc_result.tsv
[2023-03-18 08:32:33,554] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:33,554] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:33,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/checkm_data
[2023-03-18 08:32:33,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:33,580] [INFO] Task started: CheckM
[2023-03-18 08:32:33,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35278/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35278/checkm_input OceanDNA-b35278/checkm_result
[2023-03-18 08:33:34,484] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:34,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:34,487] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:34,488] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:34,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35278/markers.fasta)
[2023-03-18 08:33:34,488] [INFO] Task started: Blastn
[2023-03-18 08:33:34,488] [INFO] Running command: blastn -query OceanDNA-b35278/markers.fasta -db /var/lib/cwl/stgda910125-d199-4dc2-bc06-06b460abfc33/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35278/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:35,515] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:35,516] [INFO] Selected 7 target genomes.
[2023-03-18 08:33:35,516] [INFO] Target genome list was writen to OceanDNA-b35278/target_genomes_gtdb.txt
[2023-03-18 08:33:35,574] [INFO] Task started: fastANI
[2023-03-18 08:33:35,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8481d84-31fe-4bea-9ecd-97286c3a1310/OceanDNA-b35278.fa --refList OceanDNA-b35278/target_genomes_gtdb.txt --output OceanDNA-b35278/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:43,336] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:43,341] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:33:43,341] [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
GCF_003797885.1	s__Shewanella vesiculosa	98.5009	1400	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	conclusive
GCF_010092445.1	s__Shewanella sp002836315	85.736	1231	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_003797125.1	s__Shewanella frigidimarina	85.6199	1205	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003855395.1	s__Shewanella livingstonensis	85.4839	1194	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164505.1	s__Shewanella sp014164505	85.4533	959	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855155.1	s__Shewanella sp002836275	84.4064	1144	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_006385555.1	s__Shewanella polaris	83.5044	1073	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:43,341] [INFO] GTDB search result was written to OceanDNA-b35278/result_gtdb.tsv
[2023-03-18 08:33:43,341] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:43,342] [INFO] DFAST_QC result json was written to OceanDNA-b35278/dqc_result.json
[2023-03-18 08:33:43,342] [INFO] DFAST_QC completed!
[2023-03-18 08:33:43,342] [INFO] Total running time: 0h1m45s