Autometa Nextflow outputs and cached files #158

chasemc · 2021-05-06T16:34:54Z

chasemc
May 6, 2021

This is an example of outputs/chached files of the Autometa pipeline as it currently stands.

[82/2c5022] process > AUTOMETA:LENGTH_FILTER (filtering metagenome: metagenome)                               [100%] 1 of 1 ✔
[f3/2d16ee] process > AUTOMETA:KMER_COVERAGE (Calculating k-mer coverage for metagenome)                      [100%] 1 of 1 ✔
[75/a7f913] process > AUTOMETA:ORFS (Calling orfs for metagenome)                                             [100%] 8 of 8 ✔
[be/6826b8] process > AUTOMETA:MARKERS (Finding markers for metagenome)                                       [100%] 1 of 1 ✔
[d4/a54032] process > AUTOMETA:TAXON_ASSIGNMENT:DIAMOND (diamond blastp on metagenome)                        [100%] 1 of 1 ✔
[74/d948ac] process > AUTOMETA:TAXON_ASSIGNMENT:LCA (Assigning LCA to metagenome)                             [100%] 1 of 1 ✔
[79/8d8c5b] process > AUTOMETA:TAXON_ASSIGNMENT:MAJORITY_VOTE (Performing taxon majority vote on metagenome)  [100%] 1 of 1 ✔
[48/2b24a4] process > AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS (Splitting votes into kingdoms for metagenome) [100%] 1 of 1 ✔
[a3/6b4f03] process > AUTOMETA:KMERS (counting kmers for metagenome)                                          [100%] 1 of 1 ✔
[be/a2856e] process > AUTOMETA:BINNING (Performing Autometa binning)                                          [100%] 1 of 1 ✔
[9f/7baa53] process > AUTOMETA:UNCLUSTERED_RECRUITMENT (Performing Autometa unclustered recruitment)          [100%] 1 of 1 ✔
[56/a965a4] process > AUTOMETA:BINNING_SUMMARY (Binning summary for metagenome)                               [100%] 1 of 1 ✔

AUTOMETA:LENGTH_FILTER

Directory /work/82/2c50226fc67a53b482a2dbaf5ce7fc contains 1 symlink and 3 files

metagenome.fna.gz (symlink)
metagenome.filtered.fna
metagenome.gc_content.tsv

contig	gc_content	length
NODE_1_length_1389215_cov_225.275	68.58160903819783	1389215
NODE_2_length_1166739_cov_224.155	60.45499464747471	1166739

metagenome.stats.tsv

assembly	nseqs	size (bp)	N50 (bp)	N10 (bp)	N90 (bp)	length_weighted_gc_content (%)	largest_seq
~/Autometa/nextflow/work/82/2c50226fc67a53b482a2dbaf5ce7fc/metagenome.filtered.fna	2059	78034179	96188	686892	14855	54.38916195940243	NODE_1_length_1389215_cov_225.275

AUTOMETA:KMER_COVERAGE

Directory /work/f3/2d16ee09ea11890d95a364d90492ac contains 1 symlink and 1 files

metagenome.filtered.fna (symlink)
metagenome.coverages.tsv

contig	coverage
NODE_1_length_1389215_cov_225.275	225.275
NODE_2_length_1166739_cov_224.155	224.155

AUTOMETA:ORFS

Directory /work/75/a7f913adb91087ac75e67d9f63e32b contains 1 symlink and 2 files

metagenome.filtered.2.fna (symlink)

>NODE_14_length_480305_cov_222.789
CAAAGAACGTGTCGGAGGCTTGGTGGGGCGTTGTTATATCAATACAGAGGGGCATACGAT
AAGCGGGTGTTTCAGCGATGCTGACGTTACAGCTTCAGGAGATAACACCGGAGGCCTCAT

metagenome.orfs.faa

>NODE_14_length_480305_cov_222.789_1 # 2 # 781 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.422
KERVGGLVGRCYINTEGHTISGCFSDADVTASGDNTGGLIGMFRSTKAFSVANCYSTGNI
SGKNYTGGIIGRLDDNTGFSISNCYSAGNIASTGNDSRTGGILTKASSVKATVSNCYYIN

metagenome.orfs.fna

>NODE_14_length_480305_cov_222.789_1 # 2 # 781 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.422
AAAGAACGTGTCGGAGGCTTGGTGGGGCGTTGTTATATCAATACAGAGGGGCATACGATAAGCGGGTGTT
TCAGCGATGCTGACGTTACAGCTTCAGGAGATAACACCGGAGGCCTCATCGGTATGTTCCGTTCGACCAA

AUTOMETA:MARKERS

Directory /work/be/6826b861f1427869d2f47ec92f12bc contains 1 symlink and 2 files

metagenome.orfs.faa (currently not cached so no symlink, but might change to symlink in future)

>NODE_673_length_25618_cov_223.34_1 # 3 # 119 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.521
ITWRCYDERLIITRCVREKFRAVIITAPGGAIIQKLNW*

metagenome.hmmscan.tsv (not a tsv- domtblout?)

#                                                                             --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name        accession  query name                         accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
#------------------- ----------               -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
Ribosomal_L12        PF00542.14 NODE_674_length_25598_cov_223.537_13 -            5.3e-32  103.1   7.3   5.3e-32  103.1   7.3   2.2   2   0   0   2   2   2   1 Ribosomal protein L7/L12 C-terminal domain
Ribosomal_L22        PF00237.14 NODE_674_length_25598_cov_223.537_13 -             0.0026   11.1   2.7     0.053    6.9   0.3   2.2   1   1   1   2   2   2   2 Ribosomal protein L22p/L17e

metagenome.markers.tsv

contig	orf	sacc	sname	score	cutoff
NODE_674_length_25598_cov_223.537	NODE_674_length_25598_cov_223.537_13	PF00542.14	Ribosomal_L12	103.1	44.0
NODE_674_length_25598_cov_223.537	NODE_674_length_25598_cov_223.537_14	PF00466.15	Ribosomal_L10	63.0	37.3

AUTOMETA:TAXON_ASSIGNMENT:DIAMOND

Directory /work/d4/a540329889754b3bc387bfdfe67d7a contains 1 symlink and 1 files

metagenome.orfs.faa (symlink)
metagenome.blastp.tsv (blast table format 6)
NODE_673_length_25618_cov_223.34_2 KMV72573.1 100 164 0 0 2 165 1 164 2.62e-118 331

AUTOMETA:TAXON_ASSIGNMENT:LCA

Directory /work/74/d948ac2f013262e69f9e2d61bccf96 contains 1 symlink and 1 files

metagenome.blastp.tsv (symlink)
NODE_673_length_25618_cov_223.34_2 KMV72573.1 100 164 0 0 2 165 1 164 2.62e-118 331
metagenome.lca.tsv

qseqid	name	rank	lca
NODE_673_length_25618_cov_223.34_2	bacteria symbiont bfo1 of frankliniella occidentalis	species	1628855
NODE_673_length_25618_cov_223.34_3	bacteria symbiont bfo1 of frankliniella occidentalis	species	1628855

AUTOMETA:TAXON_ASSIGNMENT:MAJORITY_VOTE

Directory /work/79/8d8c5b5f86a0de68a6f3b967bf2143 contains 1 symlink and 1 files

metagenome.lca.tsv (symlink)

qseqid	name	rank	lca
NODE_673_length_25618_cov_223.34_2	bacteria symbiont bfo1 of frankliniella occidentalis	species	1628855
NODE_673_length_25618_cov_223.34_3	bacteria symbiont bfo1 of frankliniella occidentalis	species	1628855

metagenome.votes.tsv

contig	taxid
NODE_673_length_25618_cov_223.34	1628855
NODE_674_length_25598_cov_223.537	1619088

AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS

Directory /work/48/2b24a416d54b23bb0521df140dbc83 contains 2 symlink and 3 files

metagenome.votes.tsv (symlink)

contig	taxid
NODE_673_length_25618_cov_223.34	1628855
NODE_674_length_25598_cov_223.537	1619088

metagenome.filtered.fna (symlink)

>NODE_1_length_1389215_cov_225.275
CGCCGTAGGGGGAAGTCTCGTAGGGCGAATTCACTGACAAGATCTCCATAACTCGTGACG

metagenome.archaea.fna
- empty
metagenome.bacteria.fna

>NODE_1_length_1389215_cov_225.275
CGCCGTAGGGGGAAGTCTCGTAGGGCGAATTCACTGACAAGATCTCCATAACTCGTGACG

metagenome.taxonomy.tsv

contig	taxid	superkingdom	phylum	class	order	family	genus	species
NODE_673_length_25618_cov_223.34	1628855	bacteria	proteobacteria	gammaproteobacteria	enterobacterales	erwiniaceae	unclassified	bacteria symbiont bfo1 of frankliniella occidentalis
NODE_674_length_25598_cov_223.537	1619088	bacteria	unclassified	unclassified	unclassified	unclassified	unclassified	candidate division ws6 bacterium gw2011_gwb1_33_6

AUTOMETA:KMERS (counting kmers for metagenome)

Directory /work/a3/6b4f030b6090a147d09644bbdf3c33 contains 1 symlink and 3 files

metagenome.bacteria.fna (symlink)

>NODE_1_length_1389215_cov_225.275
CGCCGTAGGGGGAAGTCTCGTAGGGCGAATTCACTGACAAGATCTCCATAACTCGTGACG

metagenome.kmers.embedded.tsv

contig	x_1	x_2
NODE_1_length_1389215_cov_225.275	16.187662019452603	-14.559610216974583
NODE_2_length_1166739_cov_224.155	20.07298060133192	2.449826893640892

metagenome.kmers.normalized.tsv

contig	AAAAA	AAAAT	AAAAC	AAAAG	AAATA	AAATT	AAATC	AAATG	AAACA	AAACT	AAACC	AAACG	AAAGA	AAAGT	AAAGC	AAAGG	AATAA	AATAT	AATAC	AATAG	AATTA	AATTC	AATTG	AATCA	AATCT	AATCC	AATCG	AATGA	AATGT	AATGC	AATGG	AACAA	AACAT	AACAC	AACAG	AACTA	AACTT	AACTC	AACTG	AACCA	AACCT	AACCC	AACCG	AACGA	AACGT	AACGC	AACGG	AAGAA	AAGAT	AAGAC	AAGAG	AAGTA	AAGTC	AAGTG	AAGCA	AAGCT	AAGCC	AAGCG	AAGGA	AAGGT	AAGGC	AAGGG	ATAAA	ATAAT	ATAAC	ATAAG	ATATA	ATATC	ATATG	ATACA	ATACT	ATACC	ATACG	ATAGA	ATAGT	ATAGC	ATAGG	ATTAA	ATTAC	ATTAG	ATTTA	ATTTC	ATTTG	ATTCA	ATTCT	ATTCC	ATTCG	ATTGA	ATTGT	ATTGC	ATTGG	ATCAA	ATCAT	ATCAC	ATCAG	ATCTA	ATCTC	ATCTG	ATCCA	ATCCT	ATCCC	ATCCG	ATCGA	ATCGT	ATCGC	ATCGG	ATGAA	ATGAC	ATGAG	ATGTA	ATGTC	ATGTG	ATGCA	ATGCT	ATGCC	ATGCG	ATGGA	ATGGT	ATGGC	ATGGG	ACAAA	ACAAC	ACAAG	ACATA	ACATC	ACATG	ACACA	ACACT	ACACC	ACACG	ACAGA	ACAGT	ACAGC	ACAGG	ACTAA	ACTAC	ACTAG	ACTTA	ACTTC	ACTTG	ACTCA	ACTCT	ACTCC	ACTCG	ACTGA	ACTGC	ACTGG	ACCAA	ACCAC	ACCAG	ACCTA	ACCTC	ACCTG	ACCCA	ACCCT	ACCCC	ACCCG	ACCGA	ACCGT	ACCGC	ACCGG	ACGAA	ACGAC	ACGAG	ACGTA	ACGTC	ACGTG	ACGCA	ACGCT	ACGCC	ACGCG	ACGGA	ACGGC	ACGGG	AGAAA	AGAAC	AGAAG	AGATA	AGATC	AGATG	AGACA	AGACT	AGACC	AGACG	AGAGA	AGAGC	AGAGG	AGTAA	AGTAC	AGTAG	AGTTA	AGTTC	AGTTG	AGTCA	AGTCC	AGTCG	AGTGA	AGTGC	AGTGG	AGCAA	AGCAC	AGCAG	AGCTA	AGCTC	AGCTG	AGCCA	AGCCT	AGCCC	AGCCG	AGCGA	AGCGC	AGCGG	AGGAA	AGGAC	AGGAG	AGGTA	AGGTC	AGGTG	AGGCA	AGGCC	AGGCG	AGGGA	AGGGC	AGGGG	TAAAA	TAAAC	TAAAG	TAATA	TAATC	TAATG	TAACA	TAACC	TAACG	TAAGA	TAAGC	TAAGG	TATAA	TATAC	TATAG	TATTC	TATTG	TATCA	TATCC	TATCG	TATGA	TATGC	TATGG	TACAA	TACAC	TACAG	TACTA	TACTC	TACTG	TACCA	TACCC	TACCG	TACGA	TACGC	TACGG	TAGAA	TAGAC	TAGAG	TAGTC	TAGTG	TAGCA	TAGCC	TAGCG	TAGGA	TAGGC	TAGGG	TTAAA	TTAAC	TTAAG	TTATC	TTATG	TTACA	TTACC	TTACG	TTAGA	TTAGC	TTAGG	TTTAC	TTTAG	TTTTC	TTTTG	TTTCA	TTTCC	TTTCG	TTTGA	TTTGC	TTTGG	TTCAA	TTCAC	TTCAG	TTCTC	TTCTG	TTCCA	TTCCC	TTCCG	TTCGA	TTCGC	TTCGG	TTGAC	TTGAG	TTGTC	TTGTG	TTGCA	TTGCC	TTGCG	TTGGA	TTGGC	TTGGG	TCAAC	TCAAG	TCATC	TCATG	TCACA	TCACC	TCACG	TCAGA	TCAGC	TCAGG	TCTAC	TCTAG	TCTTC	TCTTG	TCTCA	TCTCC	TCTCG	TCTGC	TCTGG	TCCAC	TCCAG	TCCTC	TCCTG	TCCCA	TCCCC	TCCCG	TCCGA	TCCGC	TCCGG	TCGAC	TCGAG	TCGTC	TCGTG	TCGCA	TCGCC	TCGCG	TCGGC	TCGGG	TGAAC	TGAAG	TGATC	TGATG	TGACA	TGACC	TGACG	TGAGC	TGAGG	TGTAC	TGTAG	TGTTC	TGTTG	TGTCC	TGTCG	TGTGC	TGTGG	TGCAC	TGCAG	TGCTC	TGCTG	TGCCA	TGCCC	TGCCG	TGCGC	TGCGG	TGGAC	TGGAG	TGGTC	TGGTG	TGGCC	TGGCG	TGGGC	TGGGG	CAAAC	CAAAG	CAATC	CAATG	CAACC	CAACG	CAAGC	CAAGG	CATAC	CATAG	CATTC	CATCC	CATCG	CATGC	CATGG	CACAC	CACAG	CACTC	CACTG	CACCC	CACCG	CACGC	CACGG	CAGAC	CAGAG	CAGTC	CAGCC	CAGCG	CAGGC	CAGGG	CTAAC	CTAAG	CTATC	CTACC	CTACG	CTAGC	CTAGG	CTTAC	CTTTC	CTTCC	CTTCG	CTTGC	CTTGG	CTCAC	CTCAG	CTCTC	CTCCC	CTCCG	CTCGC	CTCGG	CTGAC	CTGTC	CTGCC	CTGCG	CTGGC	CTGGG	CCAAC	CCATC	CCACC	CCACG	CCAGC	CCAGG	CCTAC	CCTTC	CCTCC	CCTCG	CCTGC	CCCAC	CCCTC	CCCCC	CCCCG	CCCGC	CCCGG	CCGAC	CCGTC	CCGCC	CCGCG	CCGGC	CGAAC	CGATC	CGACC	CGACG	CGAGC	CGTAC	CGTTC	CGTCC	CGTGC	CGCAC	CGCTC	CGCCC	CGCCG	CGCGC	CGGAC	CGGTC	CGGCC	CGGGC	GAAAC	GAATC	GAACC	GAAGC	GATAC	GATCC	GATGC	GACAC	GACTC	GACCC	GACGC	GAGAC	GAGCC	GAGGC	GTAAC	GTACC	GTAGC	GTTCC	GTTGC	GTCAC	GTCCC	GTCGC	GTGCC	GTGGC	GCACC	GCAGC	GCTCC	GCCCC	GCCGC	GCGCC	GGACC	GGCCC
NODE_1_length_1389215_cov_225.275	-2.1352182204228463	-1.9062437487978434	-0.9760959822622621	-1.2534341839644734	-1.6104550888130742	-1.73561823176708	-0.4822951960490072	-0.9908836824166416	-1.1720885445105211	-1.0385571518859984	0.02088650560587353	-0.5072398000730035	-1.315876437302233	-1.3288467877448604	-0.5542519820700581	-0.87995212170936	-2.8824326222530674	-1.6035585097540137	-0.7372958213078366	-1.6492606632348692	-2.409347326469924	0.10648637006687701	-0.6023203851110805	-0.9890232167637217	-1.1051811795145912	0.10212635070279824	0.23846279425492953	-1.4717468080090177	-1.0784030604331982	-0.4634371774146105	-0.6201552527471146	-0.5675774366672075	-0.4214729783155784	0.16911972139861364	0.28475996866327347	-1.3499557509550955	-0.7621690860529765	0.4283806979408189	0.30636574737785527	-0.20700764846693412	-0.28386665399254574	0.3487132952069477	0.8165804975756743	0.2186601669587498	-0.16618565394667884	0.8055204770007383	0.6318729618577401	-0.21898383951364964	-0.2940190254565638	-0.12148547502877195	-0.7489238593029557	-0.9138536733850412	-0.23985416223922995	-0.6541454529756665	-0.5712426820655035	-0.3136917910552685	0.33890929511032664	0.22750978223573246	-0.2611693564382769	0.13346532089551807	0.4152315626699602	-0.276547316650276	-3.216438766379087	-2.9201729502359144	-1.8344640664037126	-2.5947505498012866	-2.7442822837722503	-0.07347625584241137	-1.331461168318931	-1.4627512451004399	-1.6528642707381678	-0.2866252764316255	-0.6541454529756665	-1.4747634015484434	-1.5116906741406617	-0.9138536733850412	-1.1609896514424722	-3.4702192871551865	-1.450881669545056	-2.959393663389196	-3.087227034899081	-0.12226642001184346	-1.2534341839644734	-0.8520127530201185	-1.0021197556835675	0.14787998489770257	0.68309275115503	-1.072324014356816	-1.2804296883064852	-0.2460243008093857	-0.5118428001449644	-0.16781964123833393	0.04298315288346382	0.7858661241608479	0.638101228922888	-1.2342489432431247	0.5890736370079954	0.5479639141013503	0.17203432561869453	0.1364855587697341	0.3846453044330109	1.2387101331237573	1.2569718553838385	0.68239418319089	1.498513181620004	1.4284493566061256	-0.2729076402028264	0.150857063607387	-0.40890736795521393	-0.9190395104174067	0.3053474173509548	-0.16781964123833393	-0.4267556107800056	-0.03694918560503715	0.7952735312627436	0.5763346112305656	-0.15159868541479507	0.33298042398804806	0.5782752289558385	-0.1467832667999285	-1.4075848637917316	0.17899491056631828	-0.22416072769318351	-1.459770616962302	0.6125773724790179	-0.17438242115085742	-0.8916873779277809	-1.0307750114439436	1.1280381720079453	0.19277239600662202	-0.8185434935807163	-0.5997983156783705	0.8709853529984399	0.16678190619008468	-3.3065898633733846	-0.18098855582797482	-2.2796695031613914	-2.5061971524598414	0.2605482596610027	-0.63439497555825	-0.7801067867396437	-1.282920349618937	0.1370885132649383	0.8499319438006075	-0.5494500520746507	0.5747794009637592	0.4835852522879145	-0.03551549360318836	1.1879649341185219	1.2061339626891445	-0.7953046476490752	0.8938696468320279	1.0890233002769494	0.2785001673147668	0.14907188015203449	0.6204146956703785	1.4764896440753963	1.4181228158067998	0.9786868763582398	1.8975204882450474	1.8142245071269782	0.5736114039456341	1.1488538040018963	0.919279362357396	-0.5199493876779527	0.8027362524643331	0.5906067917736226	0.28891150550300826	0.4418037182729595	1.5221766016209473	1.4272887828208798	0.20015669539419023	1.643640910468474	0.6207863738013996	-1.1199027913399509	0.18762805771102117	0.05155557596965539	-0.9724329745035251	0.9933873345111179	0.14728350411652208	-1.0642756811739875	-1.5370888647462722	0.6753815317315397	0.24605914114686422	-1.586522322601446	-0.033368802260025025	-0.7074003565112105	-2.0783847456596805	-0.0434263583040673	-0.5639255762484364	-2.095098226633421	0.7940243118623117	-0.07273248488956675	-1.058281657233777	0.28006879508739324	0.5786629009901568	-0.9001548290268794	0.2422681807443171	-0.05504595163705733	-0.17933292631071357	1.2050986587349868	1.3220757162933707	-1.3133024333070598	0.6428379839990683	0.9905671813793424	0.08258586133011477	-0.3405390410914566	0.7031418153851385	1.4841983269428407	0.6461041817856895	1.6278840697573074	1.2833709039511783	0.2368274709141988	0.4891113024821688	0.1615017531188012	-0.34638701097387975	1.0035759096570545	1.037460566444284	-0.2940190254565638	1.1206265715447514	1.2743262930780088	-0.7785996274490724	0.78397397600881	-0.32224291204451877	-3.492692143007245	-2.424851513005889	-2.7660222704086563	-3.087227034899081	-1.8519317594441034	-2.540683328531011	-2.3940798543391355	-1.1720885445105211	-1.6279075387643003	-2.870162529661253	-2.0404398140955573	-2.164893988568963	-3.780374215459026	-2.4566002113204695	-2.335239354316202	-0.7953046476490752	-1.4657407839488057	-1.3797279092887658	-0.5542519820700581	0.20185304864236864	-1.7395475099069697	-1.0405121867218017	-1.3553033572816906	-1.2879203600356428	-0.4535956545698192	-0.6742938847361698	-1.747452689414083	-0.48005805865065093	-0.43206629771724325	-0.6581427934082867	-0.18763862189799205	0.47157824697419076	-0.08771403850518375	0.2790233166858403	0.17841670875778418	-1.4104137199922093	-0.9277427855457084	-1.1720885445105211	-0.735851777735603	-1.2680685914829113	-1.6456699951041407	-0.318433383627851	-0.3503047437027813	-1.427556996978647	-0.4278154942920488	-1.2705286173237735	-3.61332013079586	-2.8460649780821927	-3.251530086190357	-1.9062437487978434	-2.2932751552171697	-2.2270257696759694	-1.0153900926044641	-0.8916873779277809	-3.6659638642812817	-2.4728607321922498	-2.7021707984221233	-2.051135103212305	-3.4482403804364115	-0.5222776774375438	-1.6747629560458053	-0.7130262503933787	-0.08169445674679758	0.5646111475345065	-1.4075848637917316	-0.606115456079632	-0.87995212170936	-0.6648407420924144	0.3359492534818499	-0.0017094574727345834	0.09460751828877093	-0.21554741001506855	0.18877353320855034	0.14907188015203449	0.8214570692635508	0.9856771960851506	1.23268238732624	1.301030149525437	-0.27018655008846565	-0.6594787989510289	0.12434948748750847	-0.6111980591430979	-0.5118428001449644	0.6307698177855827	0.5986175155197015	-0.6304912620777765	0.4238660175862924	-0.5246114007837641	0.2379179835631644	-0.2424938470100032	0.7728645140266857	0.05940388309579133	-0.7968372149988533	1.5861680509935843	0.6399257140120969	-0.7401901793342012	1.0737844635954172	0.3300027542941235	-0.11061580279186822	-2.401684453724355	0.5322536211950316	-0.1293225057360522	-1.0662816999008533	0.45329301832071534	0.9946665978300079	0.6377359321151728	0.39401305443661094	0.6862302820537833	0.9956888314993972	0.6841396889578635	0.8008757868114135	-0.2620674256499613	0.15914603942634198	1.0871602349965563	0.5936660675822056	1.458000115121977	1.6437745199282225	1.767049756716771	1.4898242208250092	1.508045849132816	1.0068649701806245	0.311441900409716	2.0135628392923377	2.0202782870032365	2.3649162834330943	1.263637239794228	0.5105002495591944	0.08639781003753211	1.301030149525437	0.518764759409088	-0.7801067867396437	1.1484153997861941	0.6938586130815892	0.7341416022609344	-0.23985416223922995	-0.17438242115085742	-0.44600754227932693	0.8287276253743895	0.044306779813972075	0.7371232178539519	1.102886738579059	0.5602778730761689	0.2857994697963783	0.8750280960153987	0.8011861048899316	1.3332551601334692	1.467128211171237	0.07106204622318077	1.198030022234125	1.8600273169647936	1.8340801510703977	1.4909144787010915	0.8208487967387132	0.3482253713133935	1.2974476058615403	1.3838921429682551	1.5146042498234962	1.5185490281145124	0.8944350977942244	0.07106204622318077	-0.5761506673776957	-0.87995212170936	-0.3318307131996724	-0.6824683171757278	0.4698511308281156	0.879915269750145	0.29716322844669346	0.5407436661278631	-1.098937662874906	-1.136997224699251	-0.24690886521912003	0.7328135808174151	1.5040593366468809	0.5249186249834661	0.491651524000527	0.29613547912704047	0.19048928999205347	-0.08620574259329875	0.23518946890996045	1.329603521969493	2.250820821603868	1.2852847801334624	1.2367049188966195	0.19448131126159082	-0.6111980591430979	0.22475268095790712	1.2431075017927324	1.859489074850502	1.2516469241544768	0.6955842390490592	-2.401684453724355	-3.2338305090909563	-0.5910208298571471	0.17957277825070309	0.4754533863767855	-1.6035585097540137	-1.796242853583515	-1.4687392869450624	-0.2756361548560303	0.4369028396732485	1.1484153997861941	0.46508612289517887	0.2594821614790051	0.5253275393216114	-0.22243211879256566	-0.48341564434549683	0.10212635070279824	0.9329707043757657	1.5293925078562196	1.8081221037393789	0.518764759409088	0.41340424375126156	1.2205167871625517	1.5610897144317017	1.3983402787156411	0.8214570692635508	0.26745033112818173	0.9042790810979036	1.6624369634920029	1.2561847636470214	1.716297115414014	1.308530653467875	0.07491809213227033	0.6622770410312903	0.4810244314262409	1.6968497927828963	1.4876401325932957	0.6318729618577401	0.39912815510338157	0.04033063143433255	1.2610939536732597	2.006430207506499	1.8745574871305155	1.8208496506680223	1.4807446343419013	2.2673560912994204	2.582601640112567	2.2691448085509243	1.5402678478179002	1.9667966546611868	2.006616115668403	2.167185939904531	1.9682464205363404	0.3982000807908277	1.0989782383740874	1.2799166690830905	1.6056487315081163	1.6169654407447758	1.3310657777591954	1.8046019729256724	2.824308434442879	2.5164560321096343	1.4439051065602255	1.8302069652402018	2.3355848018933263	2.1377862321072456	0.2308083008943974	0.46247742576359196	0.8395352958686984	0.6439279023630938	-0.2276269356696698	1.2502617453438991	1.0777924849929563	0.6442909446615086	0.14069862548903792	0.9908238878369194	1.4961931743927142	0.26850797268631743	0.9677149794569911	0.8907539383208628	-0.8866411098601565	0.29767670727697415	0.1882009594740411	0.8244928943030752	0.7949613726836519	0.8561184416581065	0.4882631260106249	1.754929836495418	1.4044690006570144	1.3644740571111535	1.9229030811111598	1.7978679407443283	0.6435647282171011	0.8305370347944684	2.5282760415374126	2.23452568711258	1.015416330137715	1.386314708610574

metagenome.kmers.tsv

contig	AAAAA	AAAAT	AAAAC	AAAAG	AAATA	AAATT	AAATC	AAATG	AAACA	AAACT	AAACC	AAACG	AAAGA	AAAGT	AAAGC	AAAGG	AATAA	AATAT	AATAC	AATAG	AATTA	AATTC	AATTG	AATCA	AATCT	AATCC	AATCG	AATGA	AATGT	AATGC	AATGG	AACAA	AACAT	AACAC	AACAG	AACTA	AACTT	AACTC	AACTG	AACCA	AACCT	AACCC	AACCG	AACGA	AACGT	AACGC	AACGG	AAGAA	AAGAT	AAGAC	AAGAG	AAGTA	AAGTC	AAGTG	AAGCA	AAGCT	AAGCC	AAGCG	AAGGA	AAGGT	AAGGC	AAGGG	ATAAA	ATAAT	ATAAC	ATAAG	ATATA	ATATC	ATATG	ATACA	ATACT	ATACC	ATACG	ATAGA	ATAGT	ATAGC	ATAGG	ATTAA	ATTAC	ATTAG	ATTTA	ATTTC	ATTTG	ATTCA	ATTCT	ATTCC	ATTCG	ATTGA	ATTGT	ATTGC	ATTGG	ATCAA	ATCAT	ATCAC	ATCAG	ATCTA	ATCTC	ATCTG	ATCCA	ATCCT	ATCCC	ATCCG	ATCGA	ATCGT	ATCGC	ATCGG	ATGAA	ATGAC	ATGAG	ATGTA	ATGTC	ATGTG	ATGCA	ATGCT	ATGCC	ATGCG	ATGGA	ATGGT	ATGGC	ATGGG	ACAAA	ACAAC	ACAAG	ACATA	ACATC	ACATG	ACACA	ACACT	ACACC	ACACG	ACAGA	ACAGT	ACAGC	ACAGG	ACTAA	ACTAC	ACTAG	ACTTA	ACTTC	ACTTG	ACTCA	ACTCT	ACTCC	ACTCG	ACTGA	ACTGC	ACTGG	ACCAA	ACCAC	ACCAG	ACCTA	ACCTC	ACCTG	ACCCA	ACCCT	ACCCC	ACCCG	ACCGA	ACCGT	ACCGC	ACCGG	ACGAA	ACGAC	ACGAG	ACGTA	ACGTC	ACGTG	ACGCA	ACGCT	ACGCC	ACGCG	ACGGA	ACGGC	ACGGG	AGAAA	AGAAC	AGAAG	AGATA	AGATC	AGATG	AGACA	AGACT	AGACC	AGACG	AGAGA	AGAGC	AGAGG	AGTAA	AGTAC	AGTAG	AGTTA	AGTTC	AGTTG	AGTCA	AGTCC	AGTCG	AGTGA	AGTGC	AGTGG	AGCAA	AGCAC	AGCAG	AGCTA	AGCTC	AGCTG	AGCCA	AGCCT	AGCCC	AGCCG	AGCGA	AGCGC	AGCGG	AGGAA	AGGAC	AGGAG	AGGTA	AGGTC	AGGTG	AGGCA	AGGCC	AGGCG	AGGGA	AGGGC	AGGGG	TAAAA	TAAAC	TAAAG	TAATA	TAATC	TAATG	TAACA	TAACC	TAACG	TAAGA	TAAGC	TAAGG	TATAA	TATAC	TATAG	TATTC	TATTG	TATCA	TATCC	TATCG	TATGA	TATGC	TATGG	TACAA	TACAC	TACAG	TACTA	TACTC	TACTG	TACCA	TACCC	TACCG	TACGA	TACGC	TACGG	TAGAA	TAGAC	TAGAG	TAGTC	TAGTG	TAGCA	TAGCC	TAGCG	TAGGA	TAGGC	TAGGG	TTAAA	TTAAC	TTAAG	TTATC	TTATG	TTACA	TTACC	TTACG	TTAGA	TTAGC	TTAGG	TTTAC	TTTAG	TTTTC	TTTTG	TTTCA	TTTCC	TTTCG	TTTGA	TTTGC	TTTGG	TTCAA	TTCAC	TTCAG	TTCTC	TTCTG	TTCCA	TTCCC	TTCCG	TTCGA	TTCGC	TTCGG	TTGAC	TTGAG	TTGTC	TTGTG	TTGCA	TTGCC	TTGCG	TTGGA	TTGGC	TTGGG	TCAAC	TCAAG	TCATC	TCATG	TCACA	TCACC	TCACG	TCAGA	TCAGC	TCAGG	TCTAC	TCTAG	TCTTC	TCTTG	TCTCA	TCTCC	TCTCG	TCTGC	TCTGG	TCCAC	TCCAG	TCCTC	TCCTG	TCCCA	TCCCC	TCCCG	TCCGA	TCCGC	TCCGG	TCGAC	TCGAG	TCGTC	TCGTG	TCGCA	TCGCC	TCGCG	TCGGC	TCGGG	TGAAC	TGAAG	TGATC	TGATG	TGACA	TGACC	TGACG	TGAGC	TGAGG	TGTAC	TGTAG	TGTTC	TGTTG	TGTCC	TGTCG	TGTGC	TGTGG	TGCAC	TGCAG	TGCTC	TGCTG	TGCCA	TGCCC	TGCCG	TGCGC	TGCGG	TGGAC	TGGAG	TGGTC	TGGTG	TGGCC	TGGCG	TGGGC	TGGGG	CAAAC	CAAAG	CAATC	CAATG	CAACC	CAACG	CAAGC	CAAGG	CATAC	CATAG	CATTC	CATCC	CATCG	CATGC	CATGG	CACAC	CACAG	CACTC	CACTG	CACCC	CACCG	CACGC	CACGG	CAGAC	CAGAG	CAGTC	CAGCC	CAGCG	CAGGC	CAGGG	CTAAC	CTAAG	CTATC	CTACC	CTACG	CTAGC	CTAGG	CTTAC	CTTTC	CTTCC	CTTCG	CTTGC	CTTGG	CTCAC	CTCAG	CTCTC	CTCCC	CTCCG	CTCGC	CTCGG	CTGAC	CTGTC	CTGCC	CTGCG	CTGGC	CTGGG	CCAAC	CCATC	CCACC	CCACG	CCAGC	CCAGG	CCTAC	CCTTC	CCTCC	CCTCG	CCTGC	CCCAC	CCCTC	CCCCC	CCCCG	CCCGC	CCCGG	CCGAC	CCGTC	CCGCC	CCGCG	CCGGC	CGAAC	CGATC	CGACC	CGACG	CGAGC	CGTAC	CGTTC	CGTCC	CGTGC	CGCAC	CGCTC	CGCCC	CGCCG	CGCGC	CGGAC	CGGTC	CGGCC	CGGGC	GAAAC	GAATC	GAACC	GAAGC	GATAC	GATCC	GATGC	GACAC	GACTC	GACCC	GACGC	GAGAC	GAGCC	GAGGC	GTAAC	GTACC	GTAGC	GTTCC	GTTGC	GTCAC	GTCCC	GTCGC	GTGCC	GTGGC	GCACC	GCAGC	GCTCC	GCCCC	GCCGC	GCGCC	GGACC	GGCCC
NODE_1_length_1389215_cov_225.275	170	214	544	412	288	254	892	536	447	511	1476	870	387	382	830	599	80	290	691	277	129	1608	791	537	478	1601	1835	331	491	909	777	819	948	1712	1922	374	674	2219	1964	1175	1088	2049	3272	1799	1224	3236	2720	1161	1077	1280	683	579	1137	751	816	1056	2029	1815	1113	1652	2190	1096	57	77	230	107	92	1343	381	334	276	1085	751	330	318	579	452	44	338	74	65	1279	412	616	530	1676	2863	494	401	1130	866	1222	1509	3173	2737	420	2606	2501	1717	1657	2124	4991	5083	2861	6472	6034	1100	1681	960	576	1962	1222	943	1393	3203	2573	1242	2017	2578	1248	353	1729	1155	335	2668	1214	592	515	4468	1753	637	793	3455	1708	52	1206	147	117	1876	766	662	400	1658	3383	834	2569	2345	1395	4744	4831	652	3535	4297	1910	1678	2689	6331	5972	3848	9646	8875	2566	4562	3626	859	3227	2610	1930	2249	6627	6027	1766	7483	2690	471	1744	1522	546	3905	1675	498	310	2841	1849	295	1398	712	180	1384	822	177	3199	1344	501	1913	2579	587	1842	1368	1208	4826	5425	388	2750	3894	1570	1028	2921	6380	2759	7366	5219	1832	2358	1699	1022	3945	4081	1077	4435	5172	663	3167	1047	43	127	90	65	226	113	131	447	283	81	187	165	32	123	139	652	333	363	830	1769	253	510	372	398	918	736	251	894	938	748	1198	2317	1324	1911	1728	352	571	447	692	406	278	1051	1018	346	942	405	38	83	55	214	145	155	523	592	36	121	96	185	45	857	270	708	1332	2543	353	788	599	743	2023	1443	1589	1165	1746	1678	3288	3875	4961	5312	1103	747	1637	784	866	2717	2631	769	2209	855	1834	1134	3132	1534	651	7065	2742	689	4232	2011	1294	130	2462	1270	497	2275	3910	2736	2144	2872	3914	2866	3221	1112	1695	4289	2618	6215	7484	8466	6416	6534	3958	1974	10833	10906	15394	5117	2409	1576	5312	2429	662	4560	2894	3013	1137	1214	925	3312	1511	3022	4357	2532	1924	3469	3222	5486	6272	1552	4792	9291	9053	6423	3286	2048	5293	5771	6577	6603	3537	1552	812	599	1037	730	2313	3486	1946	2483	481	463	1129	3009	6508	2444	2364	1944	1749	1326	1829	5466	13734	5229	4981	1756	784	1810	5013	9286	5056	2899	130	56	800	1730	2326	290	239	332	1097	2238	4560	2302	1874	2445	1157	891	1601	3676	6675	8821	2429	2186	4901	6890	5855	3288	1889	3572	7625	5079	8047	5352	1558	2804	2339	7892	6402	2720	2155	1505	5104	10756	9427	8934	6358	13963	19138	13988	6748	10338	10758	12632	10353	2153	4340	5201	7204	7286	5474	8790	24371	17913	6128	9018	14949	12266	1821	2296	3348	2753	1151	5049	4249	2754	1664	3895	6457	1891	3806	3524	595	1947	1745	3298	3202	3404	2356	8364	5891	5660	9894	8731	2752	3318	18126	13512	3992	5785

AUTOMETA:BINNING (Performing Autometa binning)

Directory /work/be/a2856ecdf279c8afe2cafe40e4f909 contains 5 symlink and 2 files

metagenome.bacteria.binning.tsv.gz

contig	cluster	completeness	purity	coverage_stddev	gc_content_stddev
NODE_22_length_427389_cov_223.136	bin_0001	100.0	97.84172661870504	1.5578037044291226	1.2465668323617285
NODE_57_length_203554_cov_224.112	bin_0001	100.0	97.84172661870504	1.5578037044291226	1.2465668323617285

metagenome.bacteria.main.tsv.gz

contig	cluster	completeness	purity	coverage_stddev	gc_content_stddev	coverage	gc_content	length	superkingdom	phylum	class	order	family	genus	species	taxid	x_1	x_2
NODE_22_length_427389_cov_223.136	bin_0001	100.0	97.84172661870504	1.5578037044291226	1.2465668323617285	223.136	39.0873419765132	427389	bacteria	firmicutes	bacilli	lactobacillales	enterococcaceae	enterococcus	enterococcus faecalis	1351	5.352314819581879	36.2754397093081

See above process outputs for what's contained in these symlinks

metagenome.coverages.tsv (symlink)
metagenome.gc_content.tsv (symlink)
metagenome.kmers.embedded.tsv (symlink)
metagenome.markers.tsv (symlink)
metagenome.taxonomy.ts (symlink)

AUTOMETA:UNCLUSTERED_RECRUITMENT (Performing Autometa unclustered recruitment)

Directory /work/9f/7baa5342eb4907a9b60ae0dc676489 contains 4 symlink and 3 files

metagenome.bacteria.binning.tsv.gz
metagenome.bacteria.recruitment.main.tsv.gz

contig	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	coverage	phylum_actinobacteria	phylum_candidatus kryptonia	phylum_chloroflexi	phylum_deinococcus-thermus	phylum_firmicutes	phylum_proteobacteria	phylum_unclassified	phylum_verrucomicrobia	class_actinomycetia	class_alphaproteobacteria	class_bacilli	class_clostridia	class_dehalococcoidia	class_deinococci	class_epsilonproteobacteria	class_gammaproteobacteria	class_unclassified	class_verrucomicrobiae	order_aeromonadales	order_bacillales	order_campylobacterales	order_corynebacteriales	order_deinococcales	order_enterobacterales	order_eubacteriales	order_lactobacillales	order_pseudomonadales	order_rhodobacterales	order_thiotrichales	order_unclassified	order_verrucomicrobiales	family_aeromonadaceae	family_akkermansiaceae	family_bacillaceae	family_clostridiaceae	family_deinococcaceae	family_enterococcaceae	family_erwiniaceae	family_eubacteriaceae	family_francisellaceae	family_helicobacteraceae	family_moraxellaceae	family_nocardiaceae	family_rhodobacteraceae	family_unclassified	genus_acinetobacter	genus_aeromonas	genus_akkermansia	genus_caloranaerobacter	genus_candidatus kryptonium	genus_clostridium	genus_deinococcus	genus_enterococcus	genus_eubacterium	genus_francisella	genus_helicobacter	genus_neobacillus	genus_nocardia	genus_phaeobacter	genus_unclassified	species_acinetobacter haemolyticus	species_aeromonas veronii	species_akkermansia muciniphila cag:154	species_bacteria symbiont bfo1 of frankliniella occidentalis	species_caloranaerobacter sp. tr13	species_candidate division ws6 bacterium gw2011_gwb1_33_6	species_candidatus kryptonium thompsoni	species_clostridium sp. cag:356	species_dehalococcoidia bacterium sm23_28_1	species_deinococcus maricopensis	species_enterococcus faecalis	species_eubacterium sp. cag:274	species_francisella salina	species_helicobacter acinonychis	species_neobacillus bataviensis	species_nocardia brasiliensis	species_parcubacteria group bacterium gw2011_gwa2_38_13b	species_phaeobacter inhibens	species_unclassified
NODE_1_length_1389215_cov_225.275	-16.72810671448208	-1.9402180341205129	-1.2471084716922451	-5.426541914858616	2.2320218775355456	-1.7443993280949865	-2.460619347034904	0.7313565823208961	0.3124247655955997	1.5568784924915249	1.1851261478123267	0.18481026652166685	0.49161754640158783	-0.8449283785854781	-0.22936800125962686	-0.8637824350679385	-0.03198029467255098	0.3358520699185528	0.13919239037326075	0.581002277411783	1.162712125967487	0.37073865337065687	-0.9273428296493713	-1.148341268131118	0.050415876274372426	-0.2603226260363084	-0.36120880593214233	-0.035068631586136746	-0.09804612382045796	-0.3166948660940281	-0.23922048958516068	-0.620206689422632	-0.039137539224967315	-0.10560045776411187	0.25131611810451976	-0.3691321852556475	0.16579452058786673	-0.3061319065459438	-0.17463917546781518	-0.0589156053080491	-0.224354416843927	0.07157227953765415	0.1636294233475792	-0.025459784599107062	-0.09764808085457995	-0.04784889591527386	0.13564380837094095	-0.15760525444692816	-0.17658183367151345	0.21365341620562048	225.275	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0

metagenome.bacteria.recruitment.tsv.gz

contig	cluster	recruited_cluster
NODE_22_length_427389_cov_223.136	bin_0001	bin_0001
NODE_57_length_203554_cov_224.112	bin_0001	bin_0001

See above process outputs for what's contained in these symlinks

metagenome.coverages.tsv (symlink)
metagenome.kmers.normalized.tsv (symlink)
metagenome.markers.tsv (symlink)
metagenome.taxonomy.tsv (symlink)

AUTOMETA:BINNING_SUMMARY (Binning summary for metagenome)

Directory /work/56/a965a4956cb86cc75bdb37304fbb5a contains 4 symlink and 2 files and 1 directory

metabins/
- Directory of nucleotide.fna files, one for each bin and one unclustered.fna
metabin_stats.tsv

cluster	nseqs	seqs_pct	size (bp)	size_pct	N90	N50	N10	length_weighted_gc_content	min_gc_content	max_gc_content	std_gc_content	length_weighted_coverage	min_coverage	max_coverage	std_coverage	completeness	purity	num_total_markers	num_unique_markers (expected 139)	num_single_copy_markers
bin_0001	42	2.075098814229249	2688938	3.4537303581896377	37429	97904	427389	38.93124348720573	34.73900212118417	40.6484393902734	1.2465668323617285	223.23632662560453	217.828	226.542	1.557803704429123	100.0	97.84172661870504	142	139	136

metabin_taxonomy.tsv

cluster	taxid	superkingdom	phylum	class	order	family	genus	species
bin_0001	1351	bacteria	firmicutes	bacilli	lactobacillales	enterococcaceae	enterococcus	enterococcus faecalis

See above process outputs for what's contained in these symlinks

metagenome.bacteria.main.tsv.gz (symlink? I messed up this file)
metagenome.filtered.fna (symlink)
metagenome.markers.tsv (symlink)

chasemc · 2021-05-06T16:42:05Z

chasemc
May 6, 2021
Author

For some reason Github squishes the large tables, when "Previewing" the tables appear fine

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Autometa Nextflow outputs and cached files #158

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Autometa Nextflow outputs and cached files #158

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chasemc May 6, 2021

AUTOMETA:LENGTH_FILTER

AUTOMETA:KMER_COVERAGE

AUTOMETA:ORFS

AUTOMETA:MARKERS

AUTOMETA:TAXON_ASSIGNMENT:DIAMOND

AUTOMETA:TAXON_ASSIGNMENT:LCA

AUTOMETA:TAXON_ASSIGNMENT:MAJORITY_VOTE

AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS

AUTOMETA:KMERS (counting kmers for metagenome)

AUTOMETA:BINNING (Performing Autometa binning)

AUTOMETA:UNCLUSTERED_RECRUITMENT (Performing Autometa unclustered recruitment)

AUTOMETA:BINNING_SUMMARY (Binning summary for metagenome)

Replies: 1 comment

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chasemc May 6, 2021 Author

chasemc
May 6, 2021

chasemc
May 6, 2021
Author