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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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No candidate is found in the file(s) you specified #139

Closed xlmming closed 1 year ago

xlmming commented 1 year ago

Hi，shujun, Today i use ltr_finder to create CIDE.scn : ltr_finder -w 2 -C -D 15000 -d 1000 -L 7000 -l 100 -p 20 -M 0.85 CIDE.fa >CIDEscn . And then run LTR_retriever -genome CIDE.fa -infinder CIDE.scn -threads 20 I get this ERROR: No candidate is found in the file(s) you specified. Can you help me ? I will be really appreciate.

error details: ##########################

LTR_retriever v2.9.0

########################## Contributors: Shujun Ou, Ning Jiang For LTR_retriever, please cite: Ou S and Jiang N (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422. For LAI, please cite: Ou S, Chen J, Jiang N (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018;46(21):e126. Parameters: -genome CIDE.fa -infinder CIDE.scn -threads 20 2022年 11月 12日 星期六 02:52:24 CST Dependency checking: All passed! 2022年 11月 12日 星期六 02:52:42 CST LTR_retriever is starting from the Init step. 2022年 11月 12日 星期六 02:52:48 CST The longest sequence ID in the genome contains 17 characters, which is longer than the limit (15) Trying to reformat seq IDs... Attempt 1... 2022年 11月 12日 星期六 02:52:56 CST Seq ID conversion successful! 2022年 11月 12日 星期六 02:52:56 CST Start to convert inputs... ERROR: No candidate is found in the file(s) you specified.

details of CIDE.mcn: Program : LTR_FINDER Version : 1.07

Predict protein Domains 2.415 second

Sequence: CM034325.1 Len:44834621 index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity [ 1] CM034325.1 396646-398818 261,266 2173 TTAGC N-N 396943-396957 N-N N-N N-N N-N - 6 0.629,0.5 0.917 [ 2] CM034325.1 567483-572452 245,245 4970 CTATG N-N 567728-567742 N-N N-N N-N N-N - 6 0.557,0.471 0.984 [ 3] CM034325.1 867272-876772 213,202 9501 GTCTGA N-N 876552-876566 N-N N-N N-N N-N + 6 0.514,0.586 0.921 [ 4] CM034325.1 897162-902327 445,453 5166 GCAGT N-N 901860-901874 N-N N-N N-N N-N + 6 0.514,0.514 0.974 [ 5] CM034325.1 1075449-1091365 1415,1399 15917 CTAAAG N-N 1089871-1089885 N-N N-N N-N N-N + 6 0.457,0.414 0.97 [ 6] CM034325.1 1136935-1142108 453,453 5174 GCAGT N-N 1141641-1141655 1139044-1139499 N-N N-N N-N + 7 0.629,0.514 0.991 [ 7] CM034325.1 1357325-1375452 1843,1852 18128 CCAC N-N 1373559-1373573 N-N N-N N-N N-N + 6 0.543,0.414 0.952 [ 8] CM034325.1 1902462-1909845 1113,1117 7384 GTAAC N-N 1908656-1908670 N-N N-N N-N N-N + 6 0.529,0.486 0.996 [ 9] CM034325.1 1948907-1957341 651,651 8435 CTAT N-N 1949558-1949572 N-N N-N N-N N-N - 6 0.543,0.529 1 [10] CM034325.1 2080640-2089589 1341,1335 8950 N N-N 2081981-2081995 2084943-2085446 N-N N-N N-N - 6 0.5,0.5 0.94 [11] CM034325.1 2114560-2119502 385,385 4943 GTAGC N-N 2119056-2119070 N-N N-N N-N N-N + 6 0.571,0.557 0.979 [12] CM034325.1 2128653-2136043 545,508 7391 TAGA N-N 2129210-2129224 N-N N-N N-N N-N - 6 0.514,0.543 0.93 [13] CM034325.1 2257548-2260141 213,218 2594 AAATGC N-N 2259842-2259856 N-N N-N N-N N-N + 6 0.429,0.443 0.895 [14] CM034325.1 2307319-2315109 959,959 7791 GTCTC N-N 2314135-2314149 N-N N-N N-N N-N + 6 0.514,0.529 0.998 [15] CM034325.1 2356261-2364695 651,651 8435 CTAT N-N 2356912-2356926 2360265-2360768 N-N N-N N-N - 7 0.557,0.529 1 [16] CM034325.1 2415814-2418900 452,452 3087 AAAAG N-N 2418434-2418448 N-N N-N N-N N-N + 6 0.657,0.529 1 [17] CM034325.1 2637159-2642101 385,385 4943 GTAGC N-N 2641655-2641669 N-N N-N N-N N-N + 6 0.571,0.586 0.979 [18] CM034325.1 2693924-2698866 385,385 4943 GTAGC N-N 2698420-2698434 N-N N-N N-N N-N + 6 0.571,0.586 0.979 [19] CM034325.1 2750438-2755380 385,385 4943 GTAGC N-N 2754934-2754948 N-N N-N N-N N-N + 6 0.571,0.586 0.979 [20] CM034325.1 2764025-2771415 545,508 7391 TAGA N-N 2764582-2764596 N-N N-N N-N N-N - 6 0.514,0.543 0.93 [21] CM034325.1 2791706-2806977 660,668 15272 TTCTCA N-N 2806276-2806290 N-N N-N N-N N-N + 6 0.514,0.5 0.94

oushujun commented 1 year ago

Please remove the -w 2 parameter and try again. Or use LTR_FINDER_parallel as instructed in the readme.

Shujun

xlmming commented 1 year ago

Dear Shujun， Today I do remove the -w 2 parameter and run again，it really make sence. Thank you very much! ming