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wenbostar / pepmap

GNU General Public License v3.0
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missing output file #4

Open wsnoble opened 1 year ago

wsnoble commented 1 year ago

I am getting the peptide_map_detail.txt file but no peptide_map.txt.

java -jar /net/noble/vol1/home/noble/pepmap-2.0.0.jar -i peptides.11647.tmp -d /net/noble/vol1/data/crux-datasets/2017tran-denovo/genomes/Solanum-lycopersicum.fasta -i2l -o pepmap-output.11647.tmp

Here is the stdout:

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2023-09-28 20:43:33 [INFO ] main.java.PeptideMapper[print_parameters:490] - Mapping parameter:
pepmap version: 2.0.0
Database: /net/noble/vol1/data/crux-datasets/2017tran-denovo/genomes/Solanum-lycopersicum.fasta
Input peptide file for mapping: peptides.11647.tmp
Don't distinguish I and L: true
The number of mismatch: 0
The max ratio of X in a match: 0.0
The min length of peptide: 0
2023-09-28 20:43:34 [INFO ] main.java.PeptideMapper[run:73] - Don't distinguish I and L during peptide mapping.
2023-09-28 20:43:34 [INFO ] main.java.PeptideMapper[run:86] - Start indexing fasta file

2023-09-28 20:43:37 [INFO ] main.java.PeptideMapper[run:98] - Indexing took 0.723005692 seconds and consumes 30.827902 MB
2023-09-28 20:43:37 [INFO ] main.java.PeptideMapper[run:108] - Total number of valid unique peptides in input file 'peptides.11647.tmp': 4073
2023-09-28 20:43:37 [INFO ] main.java.PeptideMapper[run:109] - Total number of invalid unique peptides in input file 'peptides.11647.tmp': 0
2023-09-28 20:43:37 [INFO ] main.java.PeptideMapper[run:110] - Total number of proteins in database '/net/noble/vol1/data/crux-datasets/2017tran-denovo/genomes/Solanum-lycopersicum.fasta': 34656
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[run:125] - Use 24 CPUs!
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 21 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 30 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 30 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 38 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 43 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 45 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 56 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 14 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 10 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 120 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 24 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 39 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 65 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 38 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 21 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 17 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 67 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 75 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 69 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 33 proteins ...
2023-09-28 20:43:38 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 41 proteins ...
2023-09-28 20:43:39 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 47 proteins ...
2023-09-28 20:43:39 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 22 proteins ...
2023-09-28 20:43:39 [INFO ] main.java.PeptideMapper[get_proteins:460] - Need to extract protein sequences for 12 proteins ...
2023-09-28 20:43:40 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 30 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 30 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 56 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 45 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 120 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 41 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 38 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 21 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 24 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 65 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 38 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 75 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 21 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 33 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 10 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 14 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 39 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 69 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 43 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 67 proteins!
2023-09-28 20:43:41 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 17 proteins!
2023-09-28 20:43:42 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 47 proteins!
2023-09-28 20:43:42 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 22 proteins!
2023-09-28 20:43:42 [INFO ] main.java.PeptideMapper[get_proteins:481] - Found protein sequences for 12 proteins!

2023-09-28 20:43:42 [INFO ] main.java.PeptideMapper[run:158] - Mapping 4073 peptides took 3.668598308 seconds
2023-09-28 20:43:42 [INFO ] main.java.PeptideMapper[run:197] - Mapping result saved to file: pepmap-output.11647.tmp/peptide_map_detail.txt
2023-09-28 20:43:42 [INFO ] main.java.PepMap[main:65] - Total time used: 0.16 min

peptides.11647.tmp.txt Solanum-lycopersicum.fasta.txt

wenbostar commented 1 year ago

I just did an update and the peptide_map.txt file is generated in the latest version. For the previous version that is the one you're using, this file is not generated when multiple threads are used in the case with > 1000 peptides for mapping.