[2023-03-18 04:38:00,446] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,446] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference
[2023-03-18 04:38:01,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,561] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,562] [INFO] Running command: cat /var/lib/cwl/stg89e3e6a6-bd7c-48e0-9d76-7808b6ccfae0/OceanDNA-b31536.fa | prodigal -d OceanDNA-b31536/cds.fna -a OceanDNA-b31536/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:15,696] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:15,697] [INFO] Task started: HMMsearch
[2023-03-18 04:38:15,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b31536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/reference_markers.hmm OceanDNA-b31536/protein.faa > /dev/null
[2023-03-18 04:38:15,891] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:15,891] [INFO] Found 6/6 markers.
[2023-03-18 04:38:15,916] [INFO] Query marker FASTA was written to OceanDNA-b31536/markers.fasta
[2023-03-18 04:38:15,917] [INFO] Task started: Blastn
[2023-03-18 04:38:15,917] [INFO] Running command: blastn -query OceanDNA-b31536/markers.fasta -db /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/reference_markers.fasta -out OceanDNA-b31536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:16,712] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:16,713] [INFO] Selected 23 target genomes.
[2023-03-18 04:38:16,714] [INFO] Target genome list was writen to OceanDNA-b31536/target_genomes.txt
[2023-03-18 04:38:16,728] [INFO] Task started: fastANI
[2023-03-18 04:38:16,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e3e6a6-bd7c-48e0-9d76-7808b6ccfae0/OceanDNA-b31536.fa --refList OceanDNA-b31536/target_genomes.txt --output OceanDNA-b31536/fastani_result.tsv --threads 1
[2023-03-18 04:38:31,278] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:31,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:31,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:31,292] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:31,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:38:31,292] [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
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	88.9221	575	730	95	below_threshold
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	86.9912	515	730	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	78.5003	119	730	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.165	184	730	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	77.7882	172	730	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.5616	141	730	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	77.539	173	730	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.5274	159	730	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.421	149	730	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.2478	169	730	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.2425	176	730	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.2181	161	730	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.1776	161	730	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	77.1523	125	730	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	77.1407	101	730	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.1218	150	730	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.0883	127	730	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	77.0875	182	730	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	77.0422	80	730	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	76.9817	187	730	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	76.9392	154	730	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	76.9365	189	730	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	76.6991	128	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:38:31,292] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31536/tc_result.tsv
[2023-03-18 04:38:31,292] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:31,292] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:31,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/checkm_data
[2023-03-18 04:38:31,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:31,298] [INFO] Task started: CheckM
[2023-03-18 04:38:31,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31536/checkm_input OceanDNA-b31536/checkm_result
[2023-03-18 04:39:09,299] [INFO] Task succeeded: CheckM
[2023-03-18 04:39:09,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:39:09,302] [INFO] ===== Completeness check finished =====
[2023-03-18 04:39:09,302] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:39:09,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31536/markers.fasta)
[2023-03-18 04:39:09,303] [INFO] Task started: Blastn
[2023-03-18 04:39:09,303] [INFO] Running command: blastn -query OceanDNA-b31536/markers.fasta -db /var/lib/cwl/stg0fb178bc-5c61-4e49-828a-77a809a4ce32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:10,667] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:10,668] [INFO] Selected 12 target genomes.
[2023-03-18 04:39:10,668] [INFO] Target genome list was writen to OceanDNA-b31536/target_genomes_gtdb.txt
[2023-03-18 04:39:10,675] [INFO] Task started: fastANI
[2023-03-18 04:39:10,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e3e6a6-bd7c-48e0-9d76-7808b6ccfae0/OceanDNA-b31536.fa --refList OceanDNA-b31536/target_genomes_gtdb.txt --output OceanDNA-b31536/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:39:18,482] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:18,490] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:39:18,490] [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_013911755.1	s__Sphingosinicella sp013911755	99.8535	693	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016793845.1	s__Sphingosinicella sp016793845	89.09	459	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	88.9221	575	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_014199685.1	s__Sphingosinicella soli	86.9912	515	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890385.1	s__Tardibacter chloracetimidivorans	78.5003	119	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.1462	185	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	77.4258	161	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	77.2181	161	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	77.1725	124	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503355.1	s__Sphingomonas sp005503355	77.1015	173	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018982925.1	s__Glacieibacterium sp018982925	77.0148	170	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	76.9411	154	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:39:18,490] [INFO] GTDB search result was written to OceanDNA-b31536/result_gtdb.tsv
[2023-03-18 04:39:18,490] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:39:18,492] [INFO] DFAST_QC result json was written to OceanDNA-b31536/dqc_result.json
[2023-03-18 04:39:18,492] [INFO] DFAST_QC completed!
[2023-03-18 04:39:18,492] [INFO] Total running time: 0h1m18s