juliema aTRAM issues - Githubissues

juliema / aTRAM

BSD 3-Clause "New" or "Revised" License

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issues

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Could you help me figure out what causes the error?

#320 luckyvivi opened 1 year ago
0
atram_preprocessor.py taking a lot of time to load .fastq.gz files

#319 RominaSSBatista closed 1 year ago
1
TypeError: 'NoneType' object is not subscriptable

#318 RominaSSBatista closed 1 year ago
1
[Question] How to use aTRAM stitcher? (no tutorial available / help menu unclear)

#317 ClaraKoehne opened 1 year ago
0
Only using one CPU for atram_preprocessor.py

#316 mchaney1 opened 1 year ago
0
## How to continue the uncompleted tasks?

#315 laiqiang0728 opened 2 years ago
5
[Errno 2] No such file or directory

#314 danielyao12 opened 2 years ago
2
using a different genetic code on stitcher

#313 jacksonhturner opened 2 years ago
1
stitcher does not recognise contig file

#312 Upasana1991 opened 2 years ago
0
how to merge many .fa files to one single target file containing list of amino acids

#311 Upasana1991 opened 2 years ago
2
conda installation

#310 jacksonhturner closed 2 years ago
0
Dist utils is being removed in Python 3.12

#309 rafelafrance opened 2 years ago
0
Abyss assembler issue: Missing files in temp directory

#308 rafelafrance opened 2 years ago
18
Install in conda environment

#307 RvV1979 opened 2 years ago
2
meaning of node number?

#306 juliadupin opened 2 years ago
0
Spack

#305 rdemoya closed 3 years ago
0
timeout error in atram.py

#304 senramvx opened 3 years ago
2
Missing modules

#303 senramvx closed 2 years ago
6
reciprocal blast search and e-value cutoffs

#302 rdemoya closed 3 years ago
0
Catch TimeoutExpired error for subprocesses #298

#301 rafelafrance closed 3 years ago
0
Open database in readonly mode for atram.py

#300 rafelafrance closed 3 years ago
1
atram_preprocessor TypeError: 'NoneType' object is not subscriptable

#299 n-oury closed 3 years ago
6
ERROR: Exception: [Errno 2] No such file or directory: '/tmp/atram_bku5sgqt/lib_des-1S_uce-5k-probes.fasta_01_owavb3if/trinity.Trinity.fasta'

#298 liugang9988 opened 3 years ago
10
assembling large number of loci (UCEs)

#297 MareikeJaniak closed 3 years ago
4
add --np flag to abyss to tell it how many cpus to use

#296 juliema closed 3 years ago
3
Preprocessing step very slow after update to v2.3.3

#295 MareikeJaniak closed 3 years ago
5
sqlite3.OperationalError: disk I/O error

#294 nomascus closed 3 years ago
10
add new parameter to abyss optios

#293 juliema closed 3 years ago
1
make library shuffle and option -- not the default

#292 juliema closed 3 years ago
0
upgrade to latest Spades version

#291 juliema opened 4 years ago
0
'NoneType' object has no attribute 'debug'

#290 tandermann closed 3 years ago
2
'stitcher' required files are not documented

#289 sestaton closed 4 years ago
29
--timeout 0 exits immediately

#288 sestaton closed 4 years ago
2
LOGGER variable is not inherited to child processes

#287 Ulises-Rosas closed 4 years ago
7
aTRAM/2.3.0 spades and python2 compatibility issues

#286 HeatherKates closed 3 years ago
1
Change integer arguments to be explicit as to what is acceptable

#285 rafelafrance closed 4 years ago
0
v2.3.0 --gzip option not working

#284 HeatherKates closed 4 years ago
4
Abyss is erroring out

#283 rafelafrance closed 4 years ago
1
Too many files open

#282 rafelafrance closed 4 years ago
1
Run --query-split jobs in parallel

#281 rafelafrance closed 4 years ago
0
an alternative way for installation was setted up

#280 Ulises-Rosas closed 4 years ago
3
Add more parameter options for abyss-pe

#279 adsweet closed 4 years ago
4
add in the --careful option for SPAdes

#278 juliema closed 4 years ago
0
Look at shrinking logger output

#277 rafelafrance closed 4 years ago
1
incompatibility issue with python 3.7?

#276 juliema closed 4 years ago
2
blast only atram not working

#275 juliema closed 4 years ago
0
Find an alternative to SQLite

#274 rafelafrance closed 4 years ago
0
Allow wildcards and lists of files in the preprocessor input files.

#273 rafelafrance closed 4 years ago
0
atram_preprocessor.py error with multiple fastq files

#272 MareikeJaniak closed 4 years ago
5
atram.py, nothing is assembling. spades error

#271 HeatherKates closed 4 years ago
3