[2023-03-15 18:12:37,905] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,905] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference
[2023-03-15 18:12:39,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,781] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,781] [INFO] Running command: cat /var/lib/cwl/stgf8da39a0-490a-48e4-b031-ff9e972557c7/OceanDNA-b33379.fa | prodigal -d OceanDNA-b33379/cds.fna -a OceanDNA-b33379/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:12:48,913] [INFO] Task succeeded: Prodigal
[2023-03-15 18:12:48,913] [INFO] Task started: HMMsearch
[2023-03-15 18:12:48,913] [INFO] Running command: hmmsearch --tblout OceanDNA-b33379/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/reference_markers.hmm OceanDNA-b33379/protein.faa > /dev/null
[2023-03-15 18:12:49,056] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:12:49,056] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf8da39a0-490a-48e4-b031-ff9e972557c7/OceanDNA-b33379.fa]
[2023-03-15 18:12:49,068] [INFO] Query marker FASTA was written to OceanDNA-b33379/markers.fasta
[2023-03-15 18:12:49,070] [INFO] Task started: Blastn
[2023-03-15 18:12:49,070] [INFO] Running command: blastn -query OceanDNA-b33379/markers.fasta -db /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/reference_markers.fasta -out OceanDNA-b33379/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:12:49,550] [INFO] Task succeeded: Blastn
[2023-03-15 18:12:49,551] [INFO] Selected 19 target genomes.
[2023-03-15 18:12:49,551] [INFO] Target genome list was writen to OceanDNA-b33379/target_genomes.txt
[2023-03-15 18:12:49,651] [INFO] Task started: fastANI
[2023-03-15 18:12:49,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8da39a0-490a-48e4-b031-ff9e972557c7/OceanDNA-b33379.fa --refList OceanDNA-b33379/target_genomes.txt --output OceanDNA-b33379/fastani_result.tsv --threads 1
[2023-03-15 18:13:00,803] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:00,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:13:00,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:13:00,809] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:13:00,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:13:00,810] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.0496	88	415	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.5922	55	415	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.5179	57	415	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.5015	62	415	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.4958	61	415	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.1642	54	415	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:13:00,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33379/tc_result.tsv
[2023-03-15 18:13:00,810] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:13:00,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:13:00,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/checkm_data
[2023-03-15 18:13:00,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:13:00,815] [INFO] Task started: CheckM
[2023-03-15 18:13:00,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33379/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33379/checkm_input OceanDNA-b33379/checkm_result
[2023-03-15 18:13:29,256] [INFO] Task succeeded: CheckM
[2023-03-15 18:13:29,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:13:29,258] [INFO] ===== Completeness check finished =====
[2023-03-15 18:13:29,258] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:13:29,258] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33379/markers.fasta)
[2023-03-15 18:13:29,260] [INFO] Task started: Blastn
[2023-03-15 18:13:29,260] [INFO] Running command: blastn -query OceanDNA-b33379/markers.fasta -db /var/lib/cwl/stg00ca3a0e-a5d5-4f03-8d32-ce27be3d9568/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33379/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:29,803] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:29,804] [INFO] Selected 15 target genomes.
[2023-03-15 18:13:29,804] [INFO] Target genome list was writen to OceanDNA-b33379/target_genomes_gtdb.txt
[2023-03-15 18:13:29,968] [INFO] Task started: fastANI
[2023-03-15 18:13:29,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8da39a0-490a-48e4-b031-ff9e972557c7/OceanDNA-b33379.fa --refList OceanDNA-b33379/target_genomes_gtdb.txt --output OceanDNA-b33379/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:13:38,008] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:38,016] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:13:38,016] [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_005789825.1	s__Limnohabitans sp005789825	91.6758	308	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	96.68	96.68	0.84	0.84	2	-
GCA_009925585.1	s__Limnohabitans sp009925585	82.8952	313	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.01	99.01	0.84	0.84	2	-
GCA_903887325.1	s__Limnohabitans sp903887325	80.2246	241	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.65	99.44	0.91	0.87	5	-
GCA_018969975.1	s__Limnohabitans sp018969975	78.5792	75	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	78.5571	184	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832625.1	s__Limnohabitans sp903832625	77.3565	104	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_002778315.1	s__Limnohabitans sp002778315	77.1387	100	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.08	98.08	0.92	0.92	2	-
GCA_009921465.1	s__Limnohabitans sp009921465	77.0601	63	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925445.1	s__Limnohabitans sp903925445	76.9605	81	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	76.6784	54	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413605.1	s__JAAFIP01 sp018413605	76.147	50	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948265.1	s__Rhodoferax sp017948265	75.9373	50	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:13:38,072] [INFO] GTDB search result was written to OceanDNA-b33379/result_gtdb.tsv
[2023-03-15 18:13:38,072] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:13:38,076] [INFO] DFAST_QC result json was written to OceanDNA-b33379/dqc_result.json
[2023-03-15 18:13:38,076] [INFO] DFAST_QC completed!
[2023-03-15 18:13:38,076] [INFO] Total running time: 0h1m0s