[2023-03-16 16:55:43,742] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:55:43,742] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:55:43,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference
[2023-03-16 16:55:47,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:55:47,135] [INFO] Task started: Prodigal
[2023-03-16 16:55:47,135] [INFO] Running command: cat /var/lib/cwl/stgaf66c53e-9b9c-47b6-941c-8ec28feb8ba0/OceanDNA-b27495.fa | prodigal -d OceanDNA-b27495/cds.fna -a OceanDNA-b27495/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:56:00,620] [INFO] Task succeeded: Prodigal
[2023-03-16 16:56:00,621] [INFO] Task started: HMMsearch
[2023-03-16 16:56:00,621] [INFO] Running command: hmmsearch --tblout OceanDNA-b27495/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/reference_markers.hmm OceanDNA-b27495/protein.faa > /dev/null
[2023-03-16 16:56:00,805] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:56:00,806] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaf66c53e-9b9c-47b6-941c-8ec28feb8ba0/OceanDNA-b27495.fa]
[2023-03-16 16:56:00,834] [INFO] Query marker FASTA was written to OceanDNA-b27495/markers.fasta
[2023-03-16 16:56:00,835] [INFO] Task started: Blastn
[2023-03-16 16:56:00,835] [INFO] Running command: blastn -query OceanDNA-b27495/markers.fasta -db /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/reference_markers.fasta -out OceanDNA-b27495/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:56:01,437] [INFO] Task succeeded: Blastn
[2023-03-16 16:56:01,438] [INFO] Selected 10 target genomes.
[2023-03-16 16:56:01,438] [INFO] Target genome list was writen to OceanDNA-b27495/target_genomes.txt
[2023-03-16 16:56:01,468] [INFO] Task started: fastANI
[2023-03-16 16:56:01,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf66c53e-9b9c-47b6-941c-8ec28feb8ba0/OceanDNA-b27495.fa --refList OceanDNA-b27495/target_genomes.txt --output OceanDNA-b27495/fastani_result.tsv --threads 1
[2023-03-16 16:56:15,276] [INFO] Task succeeded: fastANI
[2023-03-16 16:56:15,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:56:15,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:56:15,291] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:56:15,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:56:15,291] [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
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	89.2863	268	350	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	84.8903	239	350	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	84.2059	234	350	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	83.8692	222	350	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	78.6908	134	350	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	78.5512	142	350	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	78.547	138	350	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	78.4283	143	350	95	below_threshold
Bradyrhizobium guangdongense	strain=CGMCC 1.15034	GCA_014640515.1	1325090	1325090	type	True	78.3439	125	350	95	below_threshold
Nitrobacter hamburgensis	strain=X14	GCA_000013885.1	912	912	type	True	78.1938	80	350	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:56:15,292] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27495/tc_result.tsv
[2023-03-16 16:56:15,293] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:56:15,293] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:56:15,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/checkm_data
[2023-03-16 16:56:15,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:56:15,299] [INFO] Task started: CheckM
[2023-03-16 16:56:15,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27495/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27495/checkm_input OceanDNA-b27495/checkm_result
[2023-03-16 16:56:55,447] [INFO] Task succeeded: CheckM
[2023-03-16 16:56:55,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:56:55,451] [INFO] ===== Completeness check finished =====
[2023-03-16 16:56:55,451] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:56:55,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27495/markers.fasta)
[2023-03-16 16:56:55,452] [INFO] Task started: Blastn
[2023-03-16 16:56:55,452] [INFO] Running command: blastn -query OceanDNA-b27495/markers.fasta -db /var/lib/cwl/stgcb5746bd-f4cb-4c80-b54f-66888e0e1f40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27495/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:56:56,317] [INFO] Task succeeded: Blastn
[2023-03-16 16:56:56,319] [INFO] Selected 9 target genomes.
[2023-03-16 16:56:56,319] [INFO] Target genome list was writen to OceanDNA-b27495/target_genomes_gtdb.txt
[2023-03-16 16:56:56,333] [INFO] Task started: fastANI
[2023-03-16 16:56:56,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf66c53e-9b9c-47b6-941c-8ec28feb8ba0/OceanDNA-b27495.fa --refList OceanDNA-b27495/target_genomes_gtdb.txt --output OceanDNA-b27495/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:57:02,991] [INFO] Task succeeded: fastANI
[2023-03-16 16:57:02,997] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:57:02,998] [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_000497575.1	s__Afipia sp000497575	97.3109	282	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	conclusive
GCF_000314675.2	s__Afipia broomeae	89.2863	268	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCA_017474385.1	s__Afipia sp017474385	87.229	230	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203115.1	s__Afipia massiliensis	84.8903	239	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006325.2	s__Afipia massiliensis_A	84.8141	227	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308295.2	s__Afipia birgiae	84.1641	235	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	-
GCF_000336555.1	s__Afipia clevelandensis	83.9114	221	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.84	97.84	0.91	0.91	2	-
GCA_017308595.1	s__Afipia sp017308595	83.2518	220	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308495.1	s__Afipia sp017308495	80.8701	163	350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:57:02,998] [INFO] GTDB search result was written to OceanDNA-b27495/result_gtdb.tsv
[2023-03-16 16:57:02,998] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:57:03,001] [INFO] DFAST_QC result json was written to OceanDNA-b27495/dqc_result.json
[2023-03-16 16:57:03,001] [INFO] DFAST_QC completed!
[2023-03-16 16:57:03,001] [INFO] Total running time: 0h1m19s