[2023-03-18 23:27:53,695] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,695] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,695] [INFO] DQC Reference Directory: /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference
[2023-03-18 23:27:55,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,548] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stg4be8d1cf-d0d2-4c88-8d6f-c7dee90f3f9d/OceanDNA-b32985.fa | prodigal -d OceanDNA-b32985/cds.fna -a OceanDNA-b32985/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:20,275] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:20,275] [INFO] Task started: HMMsearch
[2023-03-18 23:28:20,275] [INFO] Running command: hmmsearch --tblout OceanDNA-b32985/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/reference_markers.hmm OceanDNA-b32985/protein.faa > /dev/null
[2023-03-18 23:28:20,536] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:20,537] [INFO] Found 6/6 markers.
[2023-03-18 23:28:20,566] [INFO] Query marker FASTA was written to OceanDNA-b32985/markers.fasta
[2023-03-18 23:28:20,567] [INFO] Task started: Blastn
[2023-03-18 23:28:20,567] [INFO] Running command: blastn -query OceanDNA-b32985/markers.fasta -db /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/reference_markers.fasta -out OceanDNA-b32985/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:21,419] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:21,420] [INFO] Selected 30 target genomes.
[2023-03-18 23:28:21,420] [INFO] Target genome list was writen to OceanDNA-b32985/target_genomes.txt
[2023-03-18 23:28:21,446] [INFO] Task started: fastANI
[2023-03-18 23:28:21,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be8d1cf-d0d2-4c88-8d6f-c7dee90f3f9d/OceanDNA-b32985.fa --refList OceanDNA-b32985/target_genomes.txt --output OceanDNA-b32985/fastani_result.tsv --threads 1
[2023-03-18 23:28:43,034] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:43,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:43,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:43,050] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:43,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:43,050] [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
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	79.3542	505	1368	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.5687	173	1368	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	77.4223	309	1368	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.0093	185	1368	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	76.9207	204	1368	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.8701	180	1368	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.3512	201	1368	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.2757	194	1368	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.2668	188	1368	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.1859	199	1368	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.1691	199	1368	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	76.1395	112	1368	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1079	113	1368	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	76.0343	153	1368	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	76.0292	79	1368	95	below_threshold
Elstera cyanobacteriorum	strain=TH019	GCA_002251735.1	2022747	2022747	type	True	75.9439	81	1368	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.9375	100	1368	95	below_threshold
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	75.9246	82	1368	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.7164	128	1368	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	75.676	59	1368	95	below_threshold
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	75.676	59	1368	95	below_threshold
Niveispirillum lacus	strain=1-14	GCA_002251795.1	1981099	1981099	type	True	75.5801	91	1368	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	75.5591	88	1368	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.4937	107	1368	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	75.4446	92	1368	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	75.4427	89	1368	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	75.4219	89	1368	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.3638	82	1368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:43,051] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32985/tc_result.tsv
[2023-03-18 23:28:43,051] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:43,051] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:43,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/checkm_data
[2023-03-18 23:28:43,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:43,157] [INFO] Task started: CheckM
[2023-03-18 23:28:43,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32985/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32985/checkm_input OceanDNA-b32985/checkm_result
[2023-03-18 23:29:43,591] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:43,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:43,595] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:43,595] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:43,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32985/markers.fasta)
[2023-03-18 23:29:43,596] [INFO] Task started: Blastn
[2023-03-18 23:29:43,596] [INFO] Running command: blastn -query OceanDNA-b32985/markers.fasta -db /var/lib/cwl/stgc78b67d5-dffe-459a-a660-8b9752108a72/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32985/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:45,234] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:45,235] [INFO] Selected 18 target genomes.
[2023-03-18 23:29:45,235] [INFO] Target genome list was writen to OceanDNA-b32985/target_genomes_gtdb.txt
[2023-03-18 23:29:45,253] [INFO] Task started: fastANI
[2023-03-18 23:29:45,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be8d1cf-d0d2-4c88-8d6f-c7dee90f3f9d/OceanDNA-b32985.fa --refList OceanDNA-b32985/target_genomes_gtdb.txt --output OceanDNA-b32985/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:59,080] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:59,090] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:29:59,090] [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_017792345.1	s__GCA-2696645 sp017792345	95.2949	1237	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	conclusive
GCA_012926505.1	s__GCA-2696645 sp012926505	79.3492	506	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	77.5334	175	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017963645.1	s__Marivibrio halodurans	77.4322	308	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709955.1	s__GCA-2696645 sp002709955	77.3927	318	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.86	99.71	0.96	0.91	10	-
GCA_002696645.1	s__GCA-2696645 sp002696645	77.2447	305	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.85	99.85	0.96	0.96	2	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	76.9207	204	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844765.1	s__SPJV01 sp006844765	76.3458	98	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__SPJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	76.3178	58	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.2406	198	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	76.0546	113	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173055.1	s__Zavarzinia compransoris	76.0367	154	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003385955.1	s__Aestuariispira insulae	75.9371	116	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Aestuariispira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	75.9036	70	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924985.1	s__CAIXEA01 sp903924985	75.7236	58	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.91	0.93	0.93	2	-
GCF_000504425.1	s__Rhodopseudomonas palustris_C	75.6205	90	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	95.77	95.77	0.90	0.90	2	-
GCF_014199205.1	s__Roseomonas pecuniae	75.4332	93	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:59,090] [INFO] GTDB search result was written to OceanDNA-b32985/result_gtdb.tsv
[2023-03-18 23:29:59,090] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:59,092] [INFO] DFAST_QC result json was written to OceanDNA-b32985/dqc_result.json
[2023-03-18 23:29:59,093] [INFO] DFAST_QC completed!
[2023-03-18 23:29:59,093] [INFO] Total running time: 0h2m5s