Issue to run on real data #21
Comments
|
Hi Tomas,
Looks like you have special characters in your TE name (i.e. #). TEMP2 will create intermediate files naming by your TE name, and special characters will cause issues on reading these intermediate files. Can you re-name the TEs, such as replcae # with _ and let me know if it works?
Best,
Tianxiong
… On Jan 10, 2024, at 4:49 AM, Tomas carrasco ***@***.***> wrote:
Hi thank you so much for this tool.
I'm writing again because I cant manage to make it run on my real data.
I create a conda env with Python2.7, I notice that on previous issues gawk was necessary and is installed. Nonetheless continue to fail. Here the packages on my conda env:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
bedops 2.4.41 h4ac6f70_1 bioconda
bedtools 2.31.1 hf5e1c6e_0 bioconda
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
bwa 0.7.17 he4a0461_11 bioconda
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.25.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2019.11.28 py27h8c360ce_1 conda-forge
clustalw 2.1 h4ac6f70_9 bioconda
curl 8.5.0 hca28451_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gatk 3.8 hdfd78af_11 bioconda
gawk 5.3.0 ha916aea_0 conda-forge
gcc_impl_linux-64 13.2.0 h338b0a0_3 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 13.2.0 h76e1118_3 conda-forge
gmp 6.3.0 h59595ed_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gxx_impl_linux-64 13.2.0 h338b0a0_3 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
htslib 1.19 h81da01d_0 bioconda
icu 73.2 h59595ed_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 13.2.0 ha9c7c90_103 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsanitizer 13.2.0 h7e041cc_3 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-devel_linux-64 13.2.0 ha9c7c90_103 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
openjdk 8.0.382 hd590300_0 conda-forge
openssl 3.2.0 hd590300_1 conda-forge
pango 1.50.14 ha41ecd1_2 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pixman 0.43.0 h59595ed_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
python 2.7.18 h42bf7aa_3
python_abi 2.7 1_cp27mu conda-forge
r-base 4.3.2 hb8ee39d_1 conda-forge
r-bitops 1.0_7 r43h57805ef_2 conda-forge
r-catools 1.18.2 r43ha503ecb_2 conda-forge
r-cli 3.6.2 r43ha503ecb_0 conda-forge
r-colorspace 2.1_0 r43h57805ef_1 conda-forge
r-crayon 1.5.2 r43hc72bb7e_2 conda-forge
r-ellipsis 0.3.2 r43h57805ef_2 conda-forge
r-fansi 1.0.6 r43h57805ef_0 conda-forge
r-farver 2.1.1 r43ha503ecb_2 conda-forge
r-ggplot2 3.4.4 r43hc72bb7e_0 conda-forge
r-glue 1.6.2 r43h57805ef_2 conda-forge
r-gplots 3.1.3 r43hc72bb7e_2 conda-forge
r-gsalib 2.2.1 r43hc72bb7e_2 conda-forge
r-gtable 0.3.4 r43hc72bb7e_0 conda-forge
r-gtools 3.9.5 r43h57805ef_0 conda-forge
r-isoband 0.2.7 r43ha503ecb_2 conda-forge
r-kernsmooth 2.23_22 r43h13b3f57_0 conda-forge
r-labeling 0.4.3 r43hc72bb7e_0 conda-forge
r-lattice 0.22_5 r43h57805ef_0 conda-forge
r-lifecycle 1.0.4 r43hc72bb7e_0 conda-forge
r-magrittr 2.0.3 r43h57805ef_2 conda-forge
r-mass 7.3_60 r43h57805ef_1 conda-forge
r-matrix 1.6_4 r43h316c678_0 conda-forge
r-mgcv 1.9_1 r43h316c678_0 conda-forge
r-munsell 0.5.0 r43hc72bb7e_1006 conda-forge
r-nlme 3.1_164 r43h61816a4_0 conda-forge
r-pillar 1.9.0 r43hc72bb7e_1 conda-forge
r-pkgconfig 2.0.3 r43hc72bb7e_3 conda-forge
r-plyr 1.8.9 r43ha503ecb_0 conda-forge
r-r6 2.5.1 r43hc72bb7e_2 conda-forge
r-rcolorbrewer 1.1_3 r43h785f33e_2 conda-forge
r-rcpp 1.0.12 r43h7df8631_0 conda-forge
r-reshape 0.8.9 r43hc72bb7e_2 conda-forge
r-rlang 1.1.2 r43ha503ecb_0 conda-forge
r-scales 1.3.0 r43hc72bb7e_0 conda-forge
r-tibble 3.2.1 r43h57805ef_2 conda-forge
r-utf8 1.2.4 r43h57805ef_0 conda-forge
r-vctrs 0.6.5 r43ha503ecb_0 conda-forge
r-viridislite 0.4.2 r43hc72bb7e_1 conda-forge
r-withr 2.5.2 r43hc72bb7e_0 conda-forge
readline 8.2 h8228510_1 conda-forge
samtools 1.19 h50ea8bc_0 bioconda
sed 4.8 he412f7d_0 conda-forge
setuptools 44.0.0 py27_0 conda-forge
sqlite 3.44.2 h2c6b66d_0 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h0c5db8f_5 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
The error is:
cat RunTEMP2Clean_230957.err
[bam_sort_core] merging from 80 files and 40 in-memory blocks...
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 85224 reads
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 17768650 reads
pass1 - making usageList (570 chroms): 286 millis
pass2 - checking and writing primary data (338482 records, 6 fields): 1464 millis
gawk: cmd. line:1: (FILENAME=Awka_Nigeria_10.unpair.uniq.transposon.fixLTR.bed FNR=2) fatal: cannot redirect to `Awka_Nigeria_10.supportReads/seq_10543#LINE/I.-.bed': No such file or directory
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
[main_samview] region "seq_11258#Satellite" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_17149#Satelite" specifies an unknown reference name. Continue anyway.
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_22908#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_8603#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_18651#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_11654#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_12632#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_9794#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_11404#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_2247#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_557#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_22490#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_11542#LTR/Ty3.sam: No such file or directory
/beegfs/data/tcarrasco/Programs/TEMP2/bin/TEMP2_insertion.sh: line 293: Awka_Nigeria_10.transposonMapping/seq_10597#LTR/Ty3.sam: No such file or directory
[main_samview] region "seq_3671#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_8560#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_13666#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_3486#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_22889#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_22681#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_3502#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_3199#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_863#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_3168#MITE" specifies an unknown reference name. Continue anyway.
[main_samview] region "seq_22348#MITE" specifies an unknown reference name. Continue anyway.
... Lots of them...
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
Error in `[.data.frame`(soma, , 3) : undefined columns selected
Calls: [ -> [.data.frame
Execution halted
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
Error in read.table(Args[6], header = F, row.names = NULL) :
no lines available in input
Execution halted
pass1 - making usageList (1 chroms): 7 millis
pass2 - checking and writing primary data (1 records, 6 fields): 7 millis
On the out file I do have (I took the freedom to add more of the require software on the check):
Testing required softwares:
bwa: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/bwa
samtools: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/samtools
bedtools: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/bedtools
Rscript: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/Rscript
gawk: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/gawk
bedops: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/bedops
awk: /beegfs/data/tcarrasco/Programs/Conda/envs/TEMP-P2.7/bin/awk
------ Start pipeline ------
bam file not specified, map raw reads tp genome via bwa mem Mon Jan 8 12:46:38 UTC 2024
transform sam to sorted bam and index it Mon Jan 8 14:43:05 UTC 2024
get concordant-uniq-split reads Mon Jan 8 15:27:21 UTC 2024
check fragment length Mon Jan 8 15:33:08 UTC 2024
insert size set to 95 quantile: 498
WARNING: standard deviation of insert size is higher than 100 (120)
get mate seq of the uniq-unpaired Mon Jan 8 15:33:15 UTC 2024
map paired split uniqMappers and unpaired uniqMappers to transposons Mon Jan 8 16:12:39 UTC 2024
merge fragments in genome and transposon Mon Jan 8 16:15:11 UTC 2024
merge support reads in the same direction within 498 - 150 Mon Jan 8 16:19:16 UTC 2024
merge support reads in different direction within 2 X 498 - 150 Mon Jan 8 16:19:18 UTC 2024
filter candidate insertions which overlap with the same transposon insertion or in high depth region Mon Jan 8 16:19:18 UTC 2024
filter candidate insertions in high depth region Mon Jan 8 16:19:44 UTC 2024
average read number for 200bp bins is 37.718, set read number cutoff to 188.59
Filtered insertion number: 1 - 0 (overlap rmsk) 0 (short insertion) - 0 (high depth) = 1
generate the overall distribution of transposon mapping reads, first map all reads to transposon Mon Jan 8 16:20:16 UTC 2024
sam to bed and bedGraph, multiple mappers are divided by their map times Mon Jan 8 16:20:16 UTC 2024
estimate de novo insertion number for each transposon using singleton reads Mon Jan 8 16:35:41 UTC 2024
generate distribution figures for singleton supporting reads Mon Jan 8 16:35:42 UTC 2024
filter unreliable singleton insertions, also filter 2p insertions overlapped with similar reference transposon copies Mon Jan 8 16:35:45 UTC 2024
Calculate frequency of each transposon insertion Mon Jan 8 16:35:45 UTC 2024
get TSD, remove redundant insertions and recalculate de novo insertion rate Mon Jan 8 16:35:46 UTC 2024
calculate de novo insertion rate per genome Mon Jan 8 16:35:46 UTC 2024
clean tmp files Mon Jan 8 16:35:47 UTC 2024
Done, Congras!!!🍺🍺🍺
And just to check this are the files that manage to print:
-rw-r--r-- 1 tcarrasco gei 1,4K janv. 9 13:44 RunTEMP2.slurm
-rw-r--r-- 1 tcarrasco gei 14G janv. 9 16:07 Awka_Nigeria_10.sorted.bam
-rw-r--r-- 1 tcarrasco gei 4,0M janv. 9 16:27 Awka_Nigeria_10.sorted.bam.bai
-rw-r--r-- 1 tcarrasco gei 12M janv. 9 17:19 Awka_Nigeria_10.supportReadsUnfiltered.bb
drwxr-xr-x 2 tcarrasco gei 4 janv. 9 17:19 Awka_Nigeria_10.supportReads
-rw-r--r-- 1 tcarrasco gei 0 janv. 9 17:20 Awka_Nigeria_10.spike.bed
drwxr-xr-x 2 tcarrasco gei 824 janv. 9 17:35 Awka_Nigeria_10.transposonMapping
-rw-r--r-- 1 tcarrasco gei 64K janv. 9 17:35 RunTEMP2Clean_230957.err
-rw-r--r-- 1 tcarrasco gei 14K janv. 9 17:35 Awka_Nigeria_10.insertion.bb
-rw-r--r-- 1 tcarrasco gei 23K janv. 9 17:35 Awka_Nigeria_10.soma.summary.txt
-rw-r--r-- 1 tcarrasco gei 317 janv. 9 17:35 Awka_Nigeria_10.insertion.bed
drwxr-xr-x 4 tcarrasco gei 54 janv. 9 17:36 tmpTEMP2
-rw-r--r-- 1 tcarrasco gei 9,0K janv. 9 17:36 RunTEMP2Clean_230957.out
—
Reply to this email directly, view it on GitHub <#21>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDFWGVT3PHH467HBU53YNZPZLAVCNFSM6AAAAABBUPN44OVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TGOJYHAZDSMI>.
You are receiving this because you are subscribed to this thread.
|
|
Hi Tianxiong, Thanks for your response, sadly I have the same error. And like that for a while, at the end of the error it shows: Nontheless the out file says that everything is ok, Do you have any idea what else to modify? Thank you so much |
|
Something have to be wrong before the spike file, here the file size: |
|
and the temporary files: |
|
Hi Tomas,
It looks like there is still special characters in your TE name (e.g. seq_10543_LINE/I). As I understand it is I element belong to LINE family. However, “/“ as TE name will make the system think the previous part is a folder, and TEMP2 searches a file call “I” in folder “seq_10543_LINE”, which is not implementalble.
I would suggest substitue all special characters with “_” or “.”.
Best,
Tianxiong
Tianxiong Yu
Postdoctoral Research Assistant
Weng Lab, Albert Sherman Center AS5-1079
Program in Bioinformatics and Integrative Biology
UMass Chan Medical School
… On Jan 17, 2024, at 4:11 AM, Tomas carrasco ***@***.***> wrote:
and the temporary files:
ls tmpTEMP2
total 104G
-rw-r--r-- 1 tcarrasco gei 96K janv. 16 13:57 Awka_Nigeria_10.bwamem.log
-rw-r--r-- 1 tcarrasco gei 21K janv. 16 14:25 Awka_Nigeria_10.tmp.header
-rw-r--r-- 1 tcarrasco gei 10M janv. 16 14:48 Awka_Nigeria_10.pair.uniq.split.bam
-rw-r--r-- 1 tcarrasco gei 29M janv. 16 14:49 Awka_Nigeria_10.pair.uniq.split.fastq
-rw-r--r-- 1 tcarrasco gei 3,2M janv. 16 14:49 Awka_Nigeria_10.pair.uniq.split.bed
-rw-r--r-- 1 tcarrasco gei 51 janv. 16 14:49 Awka_Nigeria_10.fragL
-rw-r--r-- 1 tcarrasco gei 30G janv. 16 15:02 Awka_Nigeria_10.unpair.sam
-rw-r--r-- 1 tcarrasco gei 2,4G janv. 16 15:22 Awka_Nigeria_10.unpair.uniq.1.fastq
-rw-r--r-- 1 tcarrasco gei 2,3G janv. 16 15:22 Awka_Nigeria_10.unpair.uniq.2.fastq
-rw-r--r-- 1 tcarrasco gei 838M janv. 16 15:37 Awka_Nigeria_10.unpair.uniq.bed
-rw-r--r-- 1 tcarrasco gei 12K janv. 16 15:37 Awka_Nigeria_10.tmp.te.size
-rw-r--r-- 1 tcarrasco gei 754K janv. 16 15:37 Awka_Nigeria_10.tmp.te.index.sa
-rw-r--r-- 1 tcarrasco gei 377K janv. 16 15:37 Awka_Nigeria_10.tmp.te.index.pac
-rw-r--r-- 1 tcarrasco gei 1,5M janv. 16 15:37 Awka_Nigeria_10.tmp.te.index.bwt
-rw-r--r-- 1 tcarrasco gei 20K janv. 16 15:37 Awka_Nigeria_10.tmp.te.index.ann
-rw-r--r-- 1 tcarrasco gei 114K janv. 16 15:37 Awka_Nigeria_10.tmp.te.index.amb
-rw-r--r-- 1 tcarrasco gei 32M janv. 16 15:37 Awka_Nigeria_10.pair.uniq.split.transposon.sam
-rw-r--r-- 1 tcarrasco gei 1,7G janv. 16 15:40 Awka_Nigeria_10.unpair.uniq.transposon.sam
-rw-r--r-- 1 tcarrasco gei 119K janv. 16 15:40 Awka_Nigeria_10.pair.uniq.split.transposon.bed
-rw-r--r-- 1 tcarrasco gei 40M janv. 16 15:45 Awka_Nigeria_10.unpair.uniq.transposon.bed
-rw-r--r-- 1 tcarrasco gei 119K janv. 16 15:45 Awka_Nigeria_10.pair.uniq.split.transposon.fixLTR.bed
-rw-r--r-- 1 tcarrasco gei 40M janv. 16 15:45 Awka_Nigeria_10.unpair.uniq.transposon.fixLTR.bed
-rw-r--r-- 1 tcarrasco gei 15K janv. 16 15:45 Awka_Nigeria_10.tmp.chr.size
drwxr-xr-x 2 tcarrasco gei 4 janv. 16 15:45 Awka_Nigeria_10.supportReads
-rw-r--r-- 1 tcarrasco gei 108 janv. 16 15:45 Awka_Nigeria_10.final.bed
-rw-r--r-- 1 tcarrasco gei 101M janv. 16 15:46 Awka_Nigeria_10.tmp.rmsk.bed
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 15:46 Awka_Nigeria_10.removed.bed
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 15:46 Awka_Nigeria_10.removed.1p1.bed
-rw-r--r-- 1 tcarrasco gei 43K janv. 16 15:46 Awka_Nigeria_10.tmp.random.bed
-rw-r--r-- 1 tcarrasco gei 31K janv. 16 15:46 Awka_Nigeria_10.TPregion.bed
-rw-r--r-- 1 tcarrasco gei 41M janv. 16 15:46 Awka_Nigeria_10.singleton.cov
-rw-r--r-- 1 tcarrasco gei 138 janv. 16 15:46 Awka_Nigeria_10.insertion.raw.bed
-rw-r--r-- 1 tcarrasco gei 63G janv. 16 16:08 Awka_Nigeria_10.transposon.sam
-rw-r--r-- 1 tcarrasco gei 96K janv. 16 16:08 Awka_Nigeria_10.transposon.bwamem.log
-rw-r--r-- 1 tcarrasco gei 3,8G janv. 16 16:15 Awka_Nigeria_10.transposon.bam
-rw-r--r-- 1 tcarrasco gei 40K janv. 16 16:19 Awka_Nigeria_10.transposon.bam.bai
-rw-r--r-- 1 tcarrasco gei 40K janv. 16 16:20 Awka_Nigeria_10.parafile
drwxr-xr-x 2 tcarrasco gei 824 janv. 16 16:25 Awka_Nigeria_10.transposonMapping
-rw-r--r-- 1 tcarrasco gei 40K janv. 16 16:25 Awka_Nigeria_10.parafile.completed
-rw-r--r-- 1 tcarrasco gei 8,8M janv. 16 16:25 Awka_Nigeria_10.transposon.sense.bdg
-rw-r--r-- 1 tcarrasco gei 8,8M janv. 16 16:25 Awka_Nigeria_10.transposon.anti.bdg
-rw-r--r-- 1 tcarrasco gei 284M janv. 16 16:26 Awka_Nigeria_10.transposon.bed
-rw-r--r-- 1 tcarrasco gei 21K janv. 16 16:26 Awka_Nigeria_10.soma.rate.bed
-rw-r--r-- 1 tcarrasco gei 25 janv. 16 16:26 Awka_Nigeria_10.singleton.sense.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.singleton.anti.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.2p.sense.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.2p.anti.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.1p1.sense.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.1p1.anti.bdg
-rw-r--r-- 1 tcarrasco gei 0 janv. 16 16:26 Awka_Nigeria_10.tmp2
-rw-r--r-- 1 tcarrasco gei 114 janv. 16 16:26 Awka_Nigeria_10.tmp1
-rw-r--r-- 1 tcarrasco gei 114 janv. 16 16:26 Awka_Nigeria_10.insertion.filtered.bed
-rw-r--r-- 1 tcarrasco gei 29 janv. 16 16:26 Awka_Nigeria_10.tmp.bed
-rw-r--r-- 1 tcarrasco gei 21K janv. 16 16:26 Awka_Nigeria_10.tmp
—
Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDAQMEDJ7WLWGMUUQ5TYO6IVXAVCNFSM6AAAAABBUPN44OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJVGM4DSNRTGQ>.
You are receiving this because you commented.
|
|
Dear Tianxiong Yu Thank you so much for helping me to debug this. I think we are progressing but get is not there. There is a new error: Nonetheless, the good news, this seems to be the only case of failure because: Although it concern me that the file .spike.bed is empty. Here the file size, it is everything ok? Again than you so much! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi thank you so much for this tool.
I'm writing again because I cant manage to make it run on my real data.
I create a conda env with Python2.7, I notice that on previous issues gawk was necessary and is installed. Nonetheless continue to fail. Here the packages on my conda env:
The error is:
On the out file I do have (I took the freedom to add more of the require software on the check):
And just to check this are the files that manage to print:
The text was updated successfully, but these errors were encountered: