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A WGS de novo assembler based on the FMD-index for large genomes

C 93.92% C++ 0.74% D 3.67% Perl 1.66%

bioinformatics denovo-assembly genomics

fermi's People

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joshuashen honglongwu traymond bioinformaticsarchive taoliu avilella snewhouse swang8 lingrui ssunkara liyaoyao0324 mingcheninsz wook2014 zhr190405

fermi's Issues

Re: Error 127

Hi,

I am running fermi on 150bp paired-end reads from the HiSeq platform.

I generated a makefile and tried to run it using the following command: make -f ../path_to/assemble.mak -j 16

I received the following error message:

/bin/sh: fermi: command not found
make: *** [fmdef.raw.fmd] Error 127

Any guidance would be much appreciated.

Thanks,
freuv

Undefined symbol when compiling

Hello,

Please advise on what to do with the following error:

Undefined symbols for achitecture x86_64:
"_ld_set", referenced from:
   _bcr_append in bcr.o

Symbols not found for achitecture x86_64. Does this mean I can't run Fermi on my mac?

The inline function ld_set is defined in bcr.c so, not sure why it is not being found in the bcr_append function.

I understand inline is used to make references to that function faster during compilation but, if I remove that modifier, compilation works just fine. Not sure why this modifier is causing this error.

empty fmdef.p4.fa.gz and fmdef.p5.fq.gz output

Hello
I run Fermi to assemble a plant genome using paired-end illumina reads
The files p0-p3 were generated successfully, but the other two (p4-p5) are empty.
By looking at the log file, I can see that the command that failed is:
"scaf -Pt 16 fmdef.ec.fmd fmdef.p3.mag.gz perl -ne 'print "$1 $2\n" if /avg = (\S+) std = (\S+)/' fmdef.p3.mag.gz.log 2> fmdef.p4.fa.gz.log | gzip -1 > fmdef.p4.fa.gz"
If I understand correctly, it failed due to missing avg and std values, because the fmdef.p3.mag.gz.log is empty.
Any suggestion what can be done?
Thanks
Mali

p3.mag.gz stalled and then fail

I'm using fermi to assemble a very large animal genome with a single 180-bp Illumina HiSeq library. In this case, with the default parameters FERMI runs smoothly up to the generation of a rather large (7.1 TiB so far) p3.mag.gz file and later it fails probably due to disk space issues.

So my questions are: What is the p3.mag.gz? and how can I optimise this step?

Thank you

Please add a license

What is a the license? Please consider adding a LICENSE file to the GitHub repository.
For instructions, see https://help.github.com/articles/adding-a-license-to-a-repository/

fermi pe2cofq seems to exit early

Given two files of 25M pairs:

$ wc -l data/left.fastq 
100318080 data/left.fastq
$ wc -l data/right.fastq 
100318080 data/right.fastq

pe2confq only returns 1694 reads when I was expecting 50M:

$ fermi pe2cofq data/left.fastq data/right.fastq | wc -l
[M::main] Version: 1.0-r718
[M::main] CMD: fermi pe2cofq data/left.fastq data/right.fastq
[M::main] Real time: 0.003 sec; CPU: 0.004 sec; RSS: 0.797 MB
6776

The reads are fairly standard fastq (sanger) format:

$ head -n 4 data/left.fastq 
@HWI-ST890:123:D0BC2ACXX:7:1101:1240:2122/1
GTGAATATGTAGTCTACATCATGACAACCGATATCAATACACGCTGCTAAATCCTAACTCGTCAATCAACACTTCATCTTGATGCCCCTCCTCTTCTCTG
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIIJJJIJJJJJJJJJJJJJJJJJJJJJJJIHHHFFFFFFDEEEEEEDDDDDDDDDDDDDDDDDDDDDD
$ head -n 4 data/right.fastq 
@HWI-ST890:123:D0BC2ACXX:7:1101:1240:2122/2
GACTGGATGGGCTGTTGAAAGGTATTTTCCGAACGTGGGACGGGCAGGTGTTCTTCTGGACGGCATGCTTTGCACTATTCACGGGCGCGCAGTTCATGTT
+
CBCFFFEFHHHHHJJJJIIJJJCFIIJJIJJJIJJJIJJGIJJJIGHH6CCBEFFFFCECEDDDDDDDDEDDCEDDDDEEEDDDBDDDDDBDBDDDEDDC

Fermi compiled with:

$ gcc --version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3

Cannot reproduce example in README

Hello,

I am following the README and running into an error at the final step. I'm able to generate the FASTQ file for C.elegans and then get to the Fermi part.

fermi-x.y/run-fermi.pl -ct8 -e fermi-x.y/fermi SRR065390.fastq > fmdef.mak gives me a fmdef.mak file
fmdef.txt

but, the final step that generates the contigs returns an empty file. This is the command make -f fmdef.mak -j 8 > fmdef.log 2>&1

Should I expect some intermediary output?

Thanks.

Option -n non-existent in samtools bam2fq -n

Hi,
I'm having problems running this new version because run-fermi.pl generates a make file that calls to samtools bam2fq -n file.bam.

Seems that there's no option -n in "samtools bam2fq".

Your work is great, thank you!

fermi -make command issue

Hello Dr.Li,

I am trying to use FERMI for a plant genome assembly using Illumina PE sequences.
I ran the run_fermi.pl with the below command

/work/rn13ow/fermi-1.1/run-fermi.pl -Pt2 -e /work/rn13ow/fermi-1.1/fermi -k50 /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq > fmdef.mak &

after generating the index - fmdex.mak
the make is given below

fmdef.mak file

FERMI=/work/rn13ow/fermi-1.1/fermi
UNITIG_K=50
OVERLAP_K=60

all:fmdef.p5.fq.gz

Construct the FM-index for raw sequences

fmdef.raw.fmd:/work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq
($(FERMI) pe2cofq /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq) | $(FERMI) ropebwt -a bcr -v3 -btNf fmdef.raw.tmp - > $@ 2> $@.log

Error correction

fmdef.ec.fq.gz:fmdef.raw.fmd
($(FERMI) pe2cofq /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq) | $(FERMI) correct -pt 2 $< - 2> $@.log | gzip -1 > $@

Construct the FM-index for corrected sequences

fmdef.ec.fmd:fmdef.ec.fq.gz
$(FERMI) fltuniq $< 2> fmdef.fltuniq.log | $(FERMI) ropebwt -a bcr -v3 -btf fmdef.ec.tmp - > $@ 2> [email protected]

Generate unitigs

fmdef.ec.rank:fmdef.ec.fmd
$(FERMI) seqrank -t 2 $< > $@ 2> $@.log

fmdef.p0.mag.gz:fmdef.ec.rank fmdef.ec.fmd
$(FERMI) unitig -t 2 -l $(UNITIG_K) -r $^ 2> $@.log | gzip -1 > $@

fmdef.p1.mag.gz:fmdef.p0.mag.gz
$(FERMI) clean $< 2> [email protected] | gzip -1 > $@
fmdef.p2.mag.gz:fmdef.p1.mag.gz
$(FERMI) clean -CAOFo $(OVERLAP_K) $< 2> $@.log | gzip -1 > $@

Generate scaftigs

fmdef.p3.mag.gz:fmdef.ec.rank fmdef.ec.fmd fmdef.p2.mag.gz
$(FERMI) remap -t 2 -r $^ 2> [email protected] | gzip -1 > $@
fmdef.p4.fa.gz:fmdef.ec.fmd fmdef.p3.mag.gz
$(FERMI) scaf -Pt 2 $^ perl -ne 'print "$$1 $$2\n" if /avg = (\S+) std = (\S+)/' fmdef.p3.mag.gz.log 2> [email protected] | gzip -1 > $@

fmdef.p5.fq.gz:fmdef.ec.rank fmdef.ec.fmd fmdef.p4.fa.gz
$(FERMI) remap -c2 -t 2 -D perl -ne 'print "$$1\n" if /avg = \S+ std = \S+ cap = (\S+)/' fmdef.p3.mag.gz.log -r $^ 2> $@.log | gzip -1 > $@

when I try to run the make command to start the assembly,I get the error message
make -f fmdef.mak -j 2 &>run_fermi_4PE_L5A.log11 &

"make: *** No rule to make target /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq', needed byfmdef.raw.fmd'. Stop."

I am not sure about the rule and how to specify it. I have followed the command as listed in the Readme file and have also tried the -B option, getting the same message.

I would appreciate it very much if you could let me know how to get around this issue.

Thanks and Regards,
Radesh

no output from 'fermi clean'

Dear Dr. Li,

I ran fermi with commands shown in documentation but failed at the 'fermi clean' step with no log info and no output. What are the possible reasons and how to troubleshoot? Thank you!

run-fermi.pl -ct12 -e ~/Downloads/fermi/fermi *.fastq.gz > ilmn_fermi_asbl.mak
make -f ilmn_fermi_asbl.mak -j 12 > ilmn_fermi_asbl.log 2>&1

Version: 1.1-r751-beta
input: illumina hiseq pe reads, 50x coverage human
memory on machine: 128Gb

$ du -h * #file size of all output files
44G     fmdef.ec.fmd
12K     fmdef.ec.fmd.log
134G    fmdef.ec.fq.gz
188K    fmdef.ec.fq.gz.log
20G     fmdef.ec.rank
4.0K    fmdef.ec.rank.log
4.0K    fmdef.fltuniq.log
531G    fmdef.p0.mag.gz
4.0K    fmdef.p0.mag.gz.log
0       fmdef.p1.mag.gz
0       fmdef.p1.mag.gz.log
4.0K    fmdef.p2.mag.gz
4.0K    fmdef.p2.mag.gz.log
4.0K    fmdef.p3.mag.gz
4.0K    fmdef.p3.mag.gz.log
4.0K    fmdef.p4.fa.gz
4.0K    fmdef.p4.fa.gz.log
4.0K    fmdef.p5.fq.gz
4.0K    fmdef.p5.fq.gz.log
68G     fmdef.raw.fmd
12K     fmdef.raw.fmd.log
4.0K    ilmn_fermi_asbl.log
8.0K    ilmn_fermi_asbl.mak

fermi hangs on a very small dataset

I've run fermi on a very small dataset containing 22 fasta records using the following cmd:

run-fermi.pl -k 200 -p cdhitout_0.85 <reads.fa>  | make -f -

however fermi hangs indefinitely. When I look at top I can see that fermi ropebwt is constantly in the sleep state:

45288 uqcskenn  20   0 24188  740  584 S    3  0.0   1:08.84 fermi ropebwt -a bcr -v3 -btf cdhitout_0.85.ec.tmp -                                                                                         
45447 uqcskenn  20   0 24188  740  584 S    2  0.0   1:08.00 fermi ropebwt -a bcr -v3 -btf cdhitout_0.90.ec.tmp -

I've tried using both the git HEAD and with release 1.1

<reads.fa> contains:

>M00920:10:000000000-A292A:1:1101:2305:13136:1
CTTCTGGTGAAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGACCCGGGAACGTATTCACCGCGACATGCTGATCCGCGATTACTAGCGATTCCGACTTCACGCAGTCGAGTTGCAGACTGCGATCCGGACTACGATCGGCTTTGTGAGATTCGCTCCGCCTCGCGGCTTGGCAACCCTCTGTACCGACCATTGTATGACGTGTGAAGCCCTACCCATAAGGGCCATGAGGACTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCTCGTTAAAGTGCCCAACCAAATGATGGCAATTAACGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACAT
>M00920:10:000000000-A292A:1:1101:24216:16298:1
CCCTTATCCTTAGTTACCAGCACCTCGGGTGGGCACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAGGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGGCCAGGGCTACACACGTGCTACAATGGTCGGTACAAAGGGTTGCCAAGCCGCGAGGTGGAGCTAATCCCATAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGTGAATCAGAATGTCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCATCACACCATGGGAGTGGGTTGCTCCAGAAGTAGCTAGTCTAACCGCAAGGGGGACGGTTACCA
>M00920:10:000000000-A292A:1:1110:4340:7240:1
CAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGAACGGCAGCGGGGGCTTCGGCCCGCCGGCGAGTGGCGAACGGGTGAGTAATGCATCGGAACGTACCCATGTTGTGGGGGATAACGTAGCGAAAGCTACGCTAATACCGCATAAGCCCTGAGGGGGAAAGCGGGGGATTCTTCGGAACCTCGCGCAATTGGAGCGGCCGATGTCAGATTAGCTAGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCGGACTCCTCCGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGGGTGATC
>M00920:10:000000000-A292A:1:1110:21042:16009:1
ACCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCACACTCGAGCCTTGCAGTCACAAACGCATTTCCCAGGTTAAGCCCGGGGATTTCACATCTGTCTTACAAAGCCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGTGCTTGTTCTTCAGTTCCCGTCATTGACAGTCTATGTTAGACCCCGCCGTTTCGTTCCTGCCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGAATGGCTGGATCAGGGT
>M00920:10:000000000-A292A:1:1101:19922:4365:1
ATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGACAGACCAGGTCCAGGGGGCTGCCTTCGCCTTCGATGTTCCTCCTGATATCTACGTATTTCACTGCTACACCCGGATTTCCACCCCCCTCTACCGCACTCTAGGCACACAGTCACAAACGCATTTCCCAGGTTAAGCCCGGGGGTTTCAAATCTGAATTATTTAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTCGGTATGACCGCGACTGCCAGCGGGTAGGAAGGCGGTACTTTTTATTCCGGTGCCGACATCCTCCCCGGATATTCACCGCGGCTATTTCTTTCCGTCCGACAGAGGTGTAAAACCCGAAGGCGAGCTTG
>M00920:10:000000000-A292A:1:1101:18095:13295:1
GGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGGAAGCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCGGTGGGGAAGAAATTGCACGGGTTAATACCCTGTGTAGATGACGGTACCCGACTAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGGTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGAGACTGCCAAGCTGGAGTGTGGCAGAGGGGGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATCAGGAG
>M00920:10:000000000-A292A:1:2102:3086:14182:1
GTAGTGACCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCACACTCCAGCCTGGCAGTCTCAAATGCAGTTCCCAGGTTGAGCCCGGGGCTTTCACATCTGACTTACCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTAACGCGGCTGCTGGCACGTAGTTCGCCGGTGCTTCTTAGTCGGGTACCGTCATCTACACAGGATATTAGCCCGTGCAATTTCTTCCCCACCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGCATGGCTGGATCAGGCTTCCGCCC
>M00920:10:000000000-A292A:1:2108:13711:22806:1
GATTAAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGTGGACGGGTGAGTAAAGCATCGGAACGTATCCTGAAGTGGAGTATAACGTAGCGAAAGTTACGCTAATACCGCATAGTCTGTGAGCAGGAAAGCAGGGGATCGCAAGACCTTGCGCTCTGGGAGCGGCCGATGTCGGATTAGCTAGTTGGGGGGGTAAAGGCCTACCAAGGCGCGGCTCCGTAGCGGGGATTGGAGTATGAAACGCCACACTGTGACTGAGAAACGGCCCGGACTCCTACGTGAGGAAGCAGCGGTGAATTTTTTCCAATGGGTTCAAGCC
>M00920:10:000000000-A292A:1:2110:11377:9313:1
GCATCGGAACGTGCCCTGGAATGGGGGATAACGTAGCGAAAGTTACGCTAATACCGCATATTCTGTGAGCAGGAAAGCAGGGGATCGCAAGACCTTGCGTTCTGGGATCGGCCGATGTCGTATGAGCTAGTTGGTGGGGAAAAGGCCTACCACGGCGACGATCCGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCCGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCGGTGGGGAAGAAATTGCATGGGTTAATTCCC
>M00920:10:000000000-A292A:1:1105:17264:25408:1
GAATTACTGGGCGTAAAGCGTGCGCAGGCGGCGCCATAAGACAGACGTGAAATCCCCGGGCTTAACCTGGGAACTGCGTTTGTGACTGTGGTGCTCGAGTGTGGCAGAGGGGGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAACACCGATGGCGAAGGCAGCCCCCTGGGTCAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGCGAACTAGGTGTTGGGGAAGGAGACGTTCTTAGTACCGCAGCTAACGCGTGAAGTTCGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATGGACA
>M00920:10:000000000-A292A:1:2105:19316:26848:1
ATCCGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGCTCTCTCTAACATAGGGAGTTAATGACGGTACCTGAAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCACAGGCGGCGCCATAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAAC
>M00920:10:000000000-A292A:1:1111:13173:15398:1
TGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTGCCAGAGATGGCTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCACCGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGCTGAAGTCAAGTCATCATGGCCCTTATGGGTAGGGCGTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAAGCCGCGAGGTGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGC
>M00920:10:000000000-A292A:1:1102:8010:26367:1
GCCTTACACATGCAAGTCGAACGGCAGCGGAACTTCGGGTGCCGGCGAGTGGCGAACGGGTGAGTAATGCATCGGAACGTGCCATTGAGTGGGGGATAACGTAGCGAAAGTTGCGCTAATACCGCATATTCTGTGAGCAGGAAAGCAGGGGACCGCAAGGCCTTGCGCTCTTTGAGCGGCCGATGTCAGATTAGCTAGTTGGTGAGGTAAAGGCTTACCAAGGCGACGATCTGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGT
>M00920:10:000000000-A292A:1:1106:8344:21464:1
GTTCCTACCATTGTAGCACGTGTGTAGCCCTGGGCATAAAGGCCATGATGACTTGACATCATCCCCTCCTTCCTCGCGTCTTACGACGGCAGTTTCTTTAGAGTTCCCAGCTTAACCTGTTGGCAACTAAAGATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACACCTCACGGCACGAGCTGACGACAGCCATGCAGCACCTGTGTGACGGCTCCCTTTCGGGCACCCTCAACTCTCATCGAGGTTCCGTCCATGTCAAGGGTAGGTAAGGTTTTTCGCGTTGCATCGAATTAATCCACATCATCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTTAATC
>M00920:10:000000000-A292A:1:1109:11262:3539:1
TTTACCCACCCAACACCTAGTTGACATAGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTACCCACGCTTTCGTGCATGAGCGTCAGTATCGGCCCAGGGGGCTGCCTTCGCCATAGGTGTTCCTCCCCATCTCTACGCTTTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCGTACTCTAGTGAGGCAGTCACAAACGCAGTTCCCAGGTTACGCCCGGGGATTTCACGCCTGTCTTACCAATCCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGTGCTTCTTATGCCGGTACCG
>M00920:10:000000000-A292A:1:1113:21063:11515:1
ACACAGGGTATTAACCCATGCGATTTCTTCCCGGCCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGCATGGCTGGATCAGGGTTGCCCCCATTGTCCAAAATTCCCCACTGCTGCCTCCCGGAGGAGTCTGGCCCGTGTCTCAGTTCCAGTGTGGCGGATCATCCTCTCAGACCCGCTCCAGATCGTCGCCTTGGTAAGCCGTTACCTCACCAACTAGCTAATCTGACATAGGCCGCTCAAAGAGCGCAAGGCCTTGCGGTCCCCTGCTTTCCTGCTCACAGAATATGCGGTATTAGCGCAACTTTCGCTACGTTATCCCCCACTCAATGGCACGTTCCGATGCATTACTCACC
>M00920:10:000000000-A292A:1:2109:18065:11577:1
CCTTTGTATTGTCCATTGTAGCACGTGTGTAGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCAACTTAGAGTGCCCAACTTAATGATGGCAACTAAGCTTAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCAGTGTGACGGCTCCCTTTCGGGCACCCTCAACTCTCATCGAGGTTCCGTCCATGTCAAGGGTAGGTAAGGTTTTTCGCGTTGCATCGAATTAATCCACATCATCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTTAATC
>M00920:10:000000000-A292A:1:2113:10809:18271:1
GTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTCACCTACCCTTGACATGGACGGAACCTCGATGAGAGTTGAGGGTGCCCGAAAGGGAGCCGTCACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAA
>M00920:10:000000000-A292A:1:2101:18998:6292:1
GTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTAGCAGAGATGCTTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAAGGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAAGCCGCGAGGTGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGAC
>M00920:10:000000000-A292A:1:2108:17778:22051:1
ATCCACAGAACTTAGCAGAGATGCTTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTGTCCTTAGTTACCAGCACCTCGGGTGGGCACTCTAAGGAGACTGCCGGTGACAAACCGGGGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGGCCAGGGCTACACACGTGCTACAATGGTCGGTACAAAGGGTTGCCAAGCCGCGAGGTGGAGCTAATCCCATAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGTGAATC
>M00920:10:000000000-A292A:1:1104:5131:15907:1
GTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCGACTAGTCGTTCGGAGCAGCAATGCACTGAGTGACGCAGCTAACGCGTGAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTCTGGAGCCTTGGTGAGAGCCGAGGGTGCCTTCGGGAGCCAGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGT
>M00920:10:000000000-A292A:1:1113:7839:16644:1
CGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTACAGGCCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCTGATCTCTACGCATTTCACTGCTACACCAGGAATTCCACACACTTCTGCCGTACTCTAGCCTTGCAGTCACAAACGCAGTTCCCAGGTTAAGCCCGGGGATTTCACATCTGTCTTACAAAAACGCCTCCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTTTTACCGCGGCTGCTGGCACGTTTTTAGCCGGTGCTTCTTAGTCCGGTACCGTCATCCATGGCCTATGTTAGAGAC

SRA Toolkit commands in the README

Hi Heng Li

It might be good to update the README with respect to downloading C. elegans

The following doesn't work:

$ fastq-dump --split-spot SRR065390.lite.sra
fastq-dump.2.8.1 err: item not found while constructing within virtual database module - the path 'SRR065390.lite.sra' cannot be opened as database or table

The following does work:

$  fastq-dump --split-spot SRR065390

Thanks!

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