[2023-03-18 04:30:02,799] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:30:02,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:30:02,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference
[2023-03-18 04:30:03,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:30:03,997] [INFO] Task started: Prodigal
[2023-03-18 04:30:03,997] [INFO] Running command: cat /var/lib/cwl/stg35da9b1a-7890-404f-a80e-1c28a94c7598/OceanDNA-b32146.fa | prodigal -d OceanDNA-b32146/cds.fna -a OceanDNA-b32146/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:30:19,673] [INFO] Task succeeded: Prodigal
[2023-03-18 04:30:19,674] [INFO] Task started: HMMsearch
[2023-03-18 04:30:19,674] [INFO] Running command: hmmsearch --tblout OceanDNA-b32146/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/reference_markers.hmm OceanDNA-b32146/protein.faa > /dev/null
[2023-03-18 04:30:19,851] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:30:19,852] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg35da9b1a-7890-404f-a80e-1c28a94c7598/OceanDNA-b32146.fa]
[2023-03-18 04:30:19,872] [INFO] Query marker FASTA was written to OceanDNA-b32146/markers.fasta
[2023-03-18 04:30:19,873] [INFO] Task started: Blastn
[2023-03-18 04:30:19,873] [INFO] Running command: blastn -query OceanDNA-b32146/markers.fasta -db /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/reference_markers.fasta -out OceanDNA-b32146/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:30:20,660] [INFO] Task succeeded: Blastn
[2023-03-18 04:30:20,660] [INFO] Selected 18 target genomes.
[2023-03-18 04:30:20,661] [INFO] Target genome list was writen to OceanDNA-b32146/target_genomes.txt
[2023-03-18 04:30:20,669] [INFO] Task started: fastANI
[2023-03-18 04:30:20,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg35da9b1a-7890-404f-a80e-1c28a94c7598/OceanDNA-b32146.fa --refList OceanDNA-b32146/target_genomes.txt --output OceanDNA-b32146/fastani_result.tsv --threads 1
[2023-03-18 04:30:33,386] [INFO] Task succeeded: fastANI
[2023-03-18 04:30:33,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:30:33,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:30:33,398] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:30:33,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:30:33,398] [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
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	88.9574	644	871	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.8607	691	871	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	85.2406	626	871	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	84.7746	589	871	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	84.6356	665	871	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.467	650	871	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	83.9757	586	871	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	83.962	597	871	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	83.9441	599	871	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.1077	584	871	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.0896	582	871	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	83.0692	587	871	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	82.9515	603	871	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	76.7978	176	871	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.5665	125	871	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	76.5308	142	871	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	76.4976	109	871	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	76.4887	110	871	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:30:33,398] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32146/tc_result.tsv
[2023-03-18 04:30:33,398] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:30:33,399] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:30:33,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/checkm_data
[2023-03-18 04:30:33,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:30:33,404] [INFO] Task started: CheckM
[2023-03-18 04:30:33,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32146/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32146/checkm_input OceanDNA-b32146/checkm_result
[2023-03-18 04:31:14,287] [INFO] Task succeeded: CheckM
[2023-03-18 04:31:14,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.53%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:31:14,289] [INFO] ===== Completeness check finished =====
[2023-03-18 04:31:14,289] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:31:14,290] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32146/markers.fasta)
[2023-03-18 04:31:14,290] [INFO] Task started: Blastn
[2023-03-18 04:31:14,290] [INFO] Running command: blastn -query OceanDNA-b32146/markers.fasta -db /var/lib/cwl/stgd09e157f-8d7a-4073-9c78-d74a3d2e31f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32146/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:31:15,737] [INFO] Task succeeded: Blastn
[2023-03-18 04:31:15,738] [INFO] Selected 24 target genomes.
[2023-03-18 04:31:15,738] [INFO] Target genome list was writen to OceanDNA-b32146/target_genomes_gtdb.txt
[2023-03-18 04:31:15,758] [INFO] Task started: fastANI
[2023-03-18 04:31:15,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg35da9b1a-7890-404f-a80e-1c28a94c7598/OceanDNA-b32146.fa --refList OceanDNA-b32146/target_genomes_gtdb.txt --output OceanDNA-b32146/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:31:35,638] [INFO] Task succeeded: fastANI
[2023-03-18 04:31:35,651] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:31:35,651] [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_003609835.1	s__Sphingopyxis sp003609835	89.4421	658	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013985.1	s__Sphingopyxis alaskensis	88.9574	644	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595975.1	s__Sphingopyxis sp014595975	88.1655	626	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	85.8598	651	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	85.8082	660	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	85.7405	657	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCA_005503215.1	s__Sphingopyxis sp005503215	85.6451	664	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	85.2441	626	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	85.1878	646	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427105.1	s__Sphingopyxis sp001427105	84.8477	642	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001468265.1	s__Sphingopyxis sp001468265	84.8383	641	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012274265.1	s__Sphingopyxis microcysteis	84.7746	589	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCA_017745175.1	s__Sphingopyxis sp017745175	84.7366	611	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803645.1	s__Sphingopyxis fribergensis	84.651	664	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	84.6416	657	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	84.5805	598	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830555.1	s__Sphingopyxis sp001830555	84.4493	625	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108295.1	s__Sphingopyxis sp900108295	84.3638	618	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307295.1	s__Sphingopyxis macrogoltabida_B	84.0094	623	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205675.1	s__Sphingopyxis bauzanensis	83.978	596	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002277025.1	s__Sphingopyxis sp002277025	83.8759	628	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001990265.1	s__Sphingopyxis sp001990265	83.7629	576	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454115.1	s__Sphingopyxis sp002454115	83.7073	585	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCF_016734905.1	s__Sphingopyxis sp016734905	83.2315	563	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:31:35,652] [INFO] GTDB search result was written to OceanDNA-b32146/result_gtdb.tsv
[2023-03-18 04:31:35,652] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:31:35,654] [INFO] DFAST_QC result json was written to OceanDNA-b32146/dqc_result.json
[2023-03-18 04:31:35,654] [INFO] DFAST_QC completed!
[2023-03-18 04:31:35,654] [INFO] Total running time: 0h1m33s