Files

1. 1. General files that are created during processing ##

processing time is set to be up to 6 hours except for SnpCgh microarray which is limited to 1 hour of processing \nnote: the original uploaded file and the files inside it (in case of an archive) is deleted by process_input_files.php

1. **process_log.text** - log file for the project processing. 2. **working.txt** - generated at the start of processing contain the processing start timestamp, used to indicate front end that the installation still running. 3. **working_done.txt** - when the installation is done the file working.txt changes name to working_done.txt 4. **condensed_log.txt** - condensed process log contains process levels to be displayed in the UI during processing 5. **completed.txt** - created when processing is done, contain the timestamp of when the processing was done. 6. **error.txt** - will be created in case an error occurred during processing. contain the following errors:

   * Error : FASTA file uploaded as input. Upload FASTQ, or ZIP or GZ archives.
   * 

7. **zipTemp.txt** - contain the output of the unzip of zip files uploaded 8. **gzTemp.txt** - containt the output of the gzip (unpacking) of the files uploaded

1. 1. Files created during Whole Genome NGS - Single end read (including intermediate files that my be deleted during the process) ##

1. **parent.txt** - used to save the name of the directory of the project 2. **dataType.txt** - contains number to describe the data type uploaded:

    *  SnpCgh microarray - 1:0

3. **upload_size_1.txt** - saves the size (in bytes) of the uploaded file 4. **datafiles.txt** - contains the name of the datafiles to work on. 5. **data.sam** - the sam file created from the user input

   * If the user inserted bam file - the it's created by scripts_seqModules/bam2sam.sh (the original bam file and the .bai file is deleted)
   *  

6. **data_r1.b.fastq, data_r2.b.fastq, data_r2.c.fastq** - temp files created by scripts_seqModules/sam2fastq.sh when converting sam files to fastq (these files are deleted by scripts_seqModules/sam2fastq.sh) 7. **data_r1.fastq, data_r2.fastq** - final files created by scripts_seqModules/sam2fastq.sh when converting sam file to paired-FASTQ files

1. 1. Files created during Whole Genome NGS - Paired end read (including intermediate files that my be deleted during the process) ##

In addition to the files that are created in single end read:

1. **upload_size_2.txt** - saves the size of the second uploaded file (in bytes)