[2023-03-18 02:02:52,816] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:02:52,817] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:02:52,817] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference
[2023-03-18 02:02:53,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:02:53,915] [INFO] Task started: Prodigal
[2023-03-18 02:02:53,915] [INFO] Running command: cat /var/lib/cwl/stg935eaa0a-632a-4479-ba35-4baeedf91cc8/OceanDNA-b27494.fa | prodigal -d OceanDNA-b27494/cds.fna -a OceanDNA-b27494/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:03:16,068] [INFO] Task succeeded: Prodigal
[2023-03-18 02:03:16,069] [INFO] Task started: HMMsearch
[2023-03-18 02:03:16,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b27494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/reference_markers.hmm OceanDNA-b27494/protein.faa > /dev/null
[2023-03-18 02:03:16,270] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:03:16,271] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg935eaa0a-632a-4479-ba35-4baeedf91cc8/OceanDNA-b27494.fa]
[2023-03-18 02:03:16,298] [INFO] Query marker FASTA was written to OceanDNA-b27494/markers.fasta
[2023-03-18 02:03:16,299] [INFO] Task started: Blastn
[2023-03-18 02:03:16,299] [INFO] Running command: blastn -query OceanDNA-b27494/markers.fasta -db /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/reference_markers.fasta -out OceanDNA-b27494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:03:17,084] [INFO] Task succeeded: Blastn
[2023-03-18 02:03:17,085] [INFO] Selected 16 target genomes.
[2023-03-18 02:03:17,085] [INFO] Target genome list was writen to OceanDNA-b27494/target_genomes.txt
[2023-03-18 02:03:17,095] [INFO] Task started: fastANI
[2023-03-18 02:03:17,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg935eaa0a-632a-4479-ba35-4baeedf91cc8/OceanDNA-b27494.fa --refList OceanDNA-b27494/target_genomes.txt --output OceanDNA-b27494/fastani_result.tsv --threads 1
[2023-03-18 02:03:36,481] [INFO] Task succeeded: fastANI
[2023-03-18 02:03:36,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:03:36,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:03:36,492] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 02:03:36,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 02:03:36,492] [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	97.8143	1028	1148	95	conclusive
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	85.9382	825	1148	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	85.601	814	1148	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	84.3739	785	1148	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.6968	523	1148	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.6251	533	1148	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.5925	544	1148	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	79.5318	533	1148	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.5094	530	1148	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.4917	527	1148	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	79.4855	414	1148	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.4517	533	1148	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	79.2571	386	1148	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	79.245	523	1148	95	below_threshold
Bradyrhizobium canariense	strain=BTA-1	GCA_019402665.1	255045	255045	suspected-type	True	79.021	503	1148	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.9988	522	1148	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:03:36,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27494/tc_result.tsv
[2023-03-18 02:03:36,492] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:03:36,493] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:03:36,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/checkm_data
[2023-03-18 02:03:36,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:03:36,499] [INFO] Task started: CheckM
[2023-03-18 02:03:36,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27494/checkm_input OceanDNA-b27494/checkm_result
[2023-03-18 02:04:31,332] [INFO] Task succeeded: CheckM
[2023-03-18 02:04:31,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:04:31,335] [INFO] ===== Completeness check finished =====
[2023-03-18 02:04:31,336] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:04:31,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27494/markers.fasta)
[2023-03-18 02:04:31,337] [INFO] Task started: Blastn
[2023-03-18 02:04:31,337] [INFO] Running command: blastn -query OceanDNA-b27494/markers.fasta -db /var/lib/cwl/stgf9d312c2-15de-472e-8a2d-b3c1f91c0c0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:04:32,878] [INFO] Task succeeded: Blastn
[2023-03-18 02:04:32,879] [INFO] Selected 8 target genomes.
[2023-03-18 02:04:32,879] [INFO] Target genome list was writen to OceanDNA-b27494/target_genomes_gtdb.txt
[2023-03-18 02:04:32,890] [INFO] Task started: fastANI
[2023-03-18 02:04:32,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg935eaa0a-632a-4479-ba35-4baeedf91cc8/OceanDNA-b27494.fa --refList OceanDNA-b27494/target_genomes_gtdb.txt --output OceanDNA-b27494/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:04:41,044] [INFO] Task succeeded: fastANI
[2023-03-18 02:04:41,049] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:04:41,049] [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_000314675.2	s__Afipia broomeae	97.8371	1027	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	conclusive
GCF_000497575.1	s__Afipia sp000497575	90.2352	887	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCA_017474385.1	s__Afipia sp017474385	89.2236	728	1148	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	85.9221	827	1148	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	85.8044	783	1148	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	85.5877	815	1148	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	84.3616	786	1148	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	83.5634	782	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:04:41,050] [INFO] GTDB search result was written to OceanDNA-b27494/result_gtdb.tsv
[2023-03-18 02:04:41,050] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:04:41,051] [INFO] DFAST_QC result json was written to OceanDNA-b27494/dqc_result.json
[2023-03-18 02:04:41,051] [INFO] DFAST_QC completed!
[2023-03-18 02:04:41,051] [INFO] Total running time: 0h1m48s