[2023-03-16 16:26:08,063] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:26:08,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:26:08,064] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference
[2023-03-16 16:26:09,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:26:09,235] [INFO] Task started: Prodigal
[2023-03-16 16:26:09,236] [INFO] Running command: cat /var/lib/cwl/stgb2b3af4a-fef1-4f29-a75c-6282dae3d212/OceanDNA-b31677.fa | prodigal -d OceanDNA-b31677/cds.fna -a OceanDNA-b31677/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:26:21,365] [INFO] Task succeeded: Prodigal
[2023-03-16 16:26:21,365] [INFO] Task started: HMMsearch
[2023-03-16 16:26:21,365] [INFO] Running command: hmmsearch --tblout OceanDNA-b31677/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/reference_markers.hmm OceanDNA-b31677/protein.faa > /dev/null
[2023-03-16 16:26:21,568] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:26:21,569] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb2b3af4a-fef1-4f29-a75c-6282dae3d212/OceanDNA-b31677.fa]
[2023-03-16 16:26:21,585] [INFO] Query marker FASTA was written to OceanDNA-b31677/markers.fasta
[2023-03-16 16:26:21,587] [INFO] Task started: Blastn
[2023-03-16 16:26:21,587] [INFO] Running command: blastn -query OceanDNA-b31677/markers.fasta -db /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/reference_markers.fasta -out OceanDNA-b31677/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:22,223] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:22,224] [INFO] Selected 15 target genomes.
[2023-03-16 16:26:22,224] [INFO] Target genome list was writen to OceanDNA-b31677/target_genomes.txt
[2023-03-16 16:26:22,238] [INFO] Task started: fastANI
[2023-03-16 16:26:22,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2b3af4a-fef1-4f29-a75c-6282dae3d212/OceanDNA-b31677.fa --refList OceanDNA-b31677/target_genomes.txt --output OceanDNA-b31677/fastani_result.tsv --threads 1
[2023-03-16 16:26:29,638] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:29,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:26:29,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:26:29,736] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:26:29,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:26:29,736] [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
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.84	57	197	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.7031	62	197	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.6895	63	197	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.6252	56	197	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	77.5609	71	197	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.3073	61	197	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.264	62	197	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.0714	75	197	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	76.9162	54	197	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:26:29,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31677/tc_result.tsv
[2023-03-16 16:26:29,737] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:26:29,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:26:29,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/checkm_data
[2023-03-16 16:26:29,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:26:29,767] [INFO] Task started: CheckM
[2023-03-16 16:26:29,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31677/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31677/checkm_input OceanDNA-b31677/checkm_result
[2023-03-16 16:26:57,356] [INFO] Task succeeded: CheckM
[2023-03-16 16:26:57,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:26:57,358] [INFO] ===== Completeness check finished =====
[2023-03-16 16:26:57,359] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:26:57,359] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31677/markers.fasta)
[2023-03-16 16:26:57,360] [INFO] Task started: Blastn
[2023-03-16 16:26:57,360] [INFO] Running command: blastn -query OceanDNA-b31677/markers.fasta -db /var/lib/cwl/stgdd1343f5-9810-4289-b366-a96c089c2a43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31677/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:58,220] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:58,221] [INFO] Selected 17 target genomes.
[2023-03-16 16:26:58,221] [INFO] Target genome list was writen to OceanDNA-b31677/target_genomes_gtdb.txt
[2023-03-16 16:26:58,411] [INFO] Task started: fastANI
[2023-03-16 16:26:58,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2b3af4a-fef1-4f29-a75c-6282dae3d212/OceanDNA-b31677.fa --refList OceanDNA-b31677/target_genomes_gtdb.txt --output OceanDNA-b31677/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:27:10,367] [INFO] Task succeeded: fastANI
[2023-03-16 16:27:10,374] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:27:10,375] [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_000152865.1	s__Erythrobacter sp000152865	78.5447	76	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264115.1	s__Erythrobacter sp003264115	78.0484	82	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	78.0269	62	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011765465.1	s__Erythrobacter sp011765465	77.9903	75	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	77.9427	80	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	77.84	57	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	77.6903	67	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	77.5609	71	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.5236	78	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009363635.1	s__Erythrobacter sp009363635	77.3776	69	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	77.3073	61	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:27:10,375] [INFO] GTDB search result was written to OceanDNA-b31677/result_gtdb.tsv
[2023-03-16 16:27:10,375] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:27:10,376] [INFO] DFAST_QC result json was written to OceanDNA-b31677/dqc_result.json
[2023-03-16 16:27:10,376] [INFO] DFAST_QC completed!
[2023-03-16 16:27:10,376] [INFO] Total running time: 0h1m2s