[2023-03-14 12:03:55,345] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference
[2023-03-14 12:03:56,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,864] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,864] [INFO] Running command: cat /var/lib/cwl/stgc6d79927-ed93-4f0d-9c1a-03918061d355/OceanDNA-b20955.fa | prodigal -d OceanDNA-b20955/cds.fna -a OceanDNA-b20955/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:44,953] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:44,954] [INFO] Task started: HMMsearch
[2023-03-14 12:04:44,954] [INFO] Running command: hmmsearch --tblout OceanDNA-b20955/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/reference_markers.hmm OceanDNA-b20955/protein.faa > /dev/null
[2023-03-14 12:04:45,287] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:45,288] [INFO] Found 6/6 markers.
[2023-03-14 12:04:45,343] [INFO] Query marker FASTA was written to OceanDNA-b20955/markers.fasta
[2023-03-14 12:04:45,344] [INFO] Task started: Blastn
[2023-03-14 12:04:45,345] [INFO] Running command: blastn -query OceanDNA-b20955/markers.fasta -db /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/reference_markers.fasta -out OceanDNA-b20955/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:45,934] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:45,936] [INFO] Selected 45 target genomes.
[2023-03-14 12:04:45,936] [INFO] Target genome list was writen to OceanDNA-b20955/target_genomes.txt
[2023-03-14 12:04:45,961] [INFO] Task started: fastANI
[2023-03-14 12:04:45,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d79927-ed93-4f0d-9c1a-03918061d355/OceanDNA-b20955.fa --refList OceanDNA-b20955/target_genomes.txt --output OceanDNA-b20955/fastani_result.tsv --threads 1
[2023-03-14 12:05:23,718] [INFO] Task succeeded: fastANI
[2023-03-14 12:05:23,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:05:23,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:05:23,741] [INFO] Found 43 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:05:23,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:05:23,742] [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
Magnetofaba australis	strain=IT-1	GCA_002109495.1	1472297	1472297	type	True	75.2027	77	2606	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.103	130	2606	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	75.0163	150	2606	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.0137	151	2606	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	74.9928	162	2606	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9791	348	2606	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	74.9625	150	2606	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	74.9604	63	2606	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	74.9438	151	2606	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	74.9342	174	2606	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	74.9266	165	2606	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.8696	143	2606	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	74.8632	196	2606	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	74.8605	60	2606	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.8129	217	2606	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	74.8075	210	2606	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	74.7948	209	2606	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	74.7913	126	2606	95	below_threshold
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	74.7888	56	2606	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7863	267	2606	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	74.7818	81	2606	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	74.7768	86	2606	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	74.7749	188	2606	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	74.7746	218	2606	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.7709	272	2606	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	74.7648	136	2606	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	74.7499	162	2606	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	74.7494	94	2606	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	74.7486	234	2606	95	below_threshold
Arthrobacter bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	74.74	67	2606	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	74.7382	301	2606	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	74.7346	217	2606	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.7325	302	2606	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	74.732	256	2606	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	74.7314	117	2606	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	74.7306	152	2606	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	74.7104	217	2606	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	74.6972	134	2606	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	74.6775	74	2606	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	74.6773	202	2606	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	74.6761	73	2606	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	74.6723	60	2606	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	74.5514	57	2606	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:05:23,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20955/tc_result.tsv
[2023-03-14 12:05:23,747] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:05:23,747] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:05:23,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/checkm_data
[2023-03-14 12:05:23,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:05:23,785] [INFO] Task started: CheckM
[2023-03-14 12:05:23,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20955/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20955/checkm_input OceanDNA-b20955/checkm_result
[2023-03-14 12:07:24,399] [INFO] Task succeeded: CheckM
[2023-03-14 12:07:24,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:07:24,427] [INFO] ===== Completeness check finished =====
[2023-03-14 12:07:24,428] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:07:24,428] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20955/markers.fasta)
[2023-03-14 12:07:24,429] [INFO] Task started: Blastn
[2023-03-14 12:07:24,429] [INFO] Running command: blastn -query OceanDNA-b20955/markers.fasta -db /var/lib/cwl/stg2ede175a-9145-476b-99e9-0d4f8d03ed52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20955/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:07:25,295] [INFO] Task succeeded: Blastn
[2023-03-14 12:07:25,306] [INFO] Selected 41 target genomes.
[2023-03-14 12:07:25,306] [INFO] Target genome list was writen to OceanDNA-b20955/target_genomes_gtdb.txt
[2023-03-14 12:07:25,356] [INFO] Task started: fastANI
[2023-03-14 12:07:25,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d79927-ed93-4f0d-9c1a-03918061d355/OceanDNA-b20955.fa --refList OceanDNA-b20955/target_genomes_gtdb.txt --output OceanDNA-b20955/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:07:56,415] [INFO] Task succeeded: fastANI
[2023-03-14 12:07:56,434] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:07:56,435] [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_016927815.1	s__JAFGLY01 sp016927815	76.7205	278	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__JAFGLY01;g__JAFGLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	76.1617	343	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694325.1	s__J125 sp003694325	75.9762	257	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	75.9573	267	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959175.1	s__CAJBVW01 sp903959175	75.7735	303	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	75.7272	403	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152105.1	s__UBA2385 sp013152105	75.717	194	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343455.1	s__UBA2385 sp002343455	75.6395	421	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921785.1	s__SXON01 sp903921785	75.5999	301	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.5539	299	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_016845285.1	s__BH17 sp016845285	75.5242	215	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__BH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226595.1	s__M1803 sp006226595	75.4884	272	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.2966	407	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	75.2867	202	2606	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCF_002109495.1	s__Magnetofaba australis	75.174	80	2606	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetococcaceae;g__Magnetofaba	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867695.1	s__VGIY01 sp016867695	74.983	99	2606	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__WJJG01;g__VGIY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702545.1	s__JADJTL01 sp016702545	74.8979	172	2606	d__Bacteria;p__Myxococcota;c__Polyangia;o__GCA-2747355;f__GCA-2747355;g__JADJTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	74.8719	240	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_003094615.1	s__Caulobacter radicis	74.8663	195	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	-
GCA_018623495.1	s__JAAZVP01 sp018623495	74.8617	125	2606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008595.1	s__Giesbergeria suum	74.8609	60	2606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612475.1	s__D16-63 sp003612475	74.859	77	2606	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050235.1	s__UTPRO1 sp002050235	74.8476	90	2606	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__UTPRO1	95.0	99.98	99.98	0.96	0.96	2	-
GCA_017881055.1	s__JADGRF01 sp017881055	74.8476	99	2606	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703145.1	s__Ottowia sp016703145	74.7964	155	2606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCF_003722335.1	s__Caulobacter flavus	74.7942	209	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCA_903914415.1	s__Fen-1342 sp903914415	74.7838	75	2606	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__Fen-1342	95.0	99.57	99.48	0.90	0.90	3	-
GCF_011683915.1	s__Pelagibius litoralis	74.7774	87	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	74.7667	277	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_015490435.1	s__WFXV01 sp015490435	74.7652	69	2606	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002898275.1	s__HRBIN40 sp002898275	74.7356	72	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	74.7246	155	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155635.1	s__NIES-981 sp000155635	74.7173	112	2606	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000755.1	s__Youhaiella tibetensis	74.6742	74	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCA_011390475.1	s__SLRI01 sp011390475	74.6437	88	2606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:07:56,438] [INFO] GTDB search result was written to OceanDNA-b20955/result_gtdb.tsv
[2023-03-14 12:07:56,439] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:07:56,445] [INFO] DFAST_QC result json was written to OceanDNA-b20955/dqc_result.json
[2023-03-14 12:07:56,445] [INFO] DFAST_QC completed!
[2023-03-14 12:07:56,445] [INFO] Total running time: 0h4m1s