Closed bilalSarwar2020 closed 5 years ago
Can you send us the log file?
Also can you please try with the new version of CRISPREsso available here: https://github.com/pinellolab/crispresso2
On Tue, Feb 5, 2019 at 12:59 PM bilalSarwar2020 notifications@github.com wrote:
Dear Luca Pinello I am using CRISPRessoPooled.py script to analyzed the paired ends reads data by Illumina. the read length is 150 bp. the amplicon size is 180bp long. below is the command that I am used several time. it ends up with an error at last of the analysis I am new to the Linux environment. Kindly help me to resolve this issue. thanks ERROR: Flash failed to run, please check the log file.
$ python CRISPRessoPooled.py -r1 /home/bilal/Sir_Qayyum_data/6297_1_1.fastq.gz -r2 /home/bilal/Sir_Qayyum_data/6297_1_2.fastq.gz -f /home/bilal/Sir_Qayyum_data/CRISPResso-master/cat.csv
-Analysis of CRISPR/Cas9 outcomes from POOLED deep sequencing data- ) ) ( _______________________ ( __)__ | __ __ __ __ __ | __)__ C\| \ ||__)/ \/ \| |_ | \ | C\| \ \ / || \__/\__/|__|__|__/ | \ / \___/ |_______________________| \___/ [Luca Pinello 2015, send bugs, suggestions or *green coffee* to lucapinello AT gmail DOT com] Version 1.0.13 INFO @ Tue, 05 Feb 2019 22:43:54: Checking dependencies... INFO @ Tue, 05 Feb 2019 22:43:54: All the required dependencies are present! INFO @ Tue, 05 Feb 2019 22:43:54: Only the Amplicon description file was provided. The analysis will be perfomed using only the provided amplicons sequences. INFO @ Tue, 05 Feb 2019 22:43:54: Creating Folder CRISPRessoPooled_on_6297_1_1_6297_1_2 WARNING @ Tue, 05 Feb 2019 22:43:54: Folder CRISPRessoPooled_on_6297_1_1_6297_1_2 already exists. INFO @ Tue, 05 Feb 2019 22:43:54: Merging paired sequences with Flash... CRITICAL @ Tue, 05 Feb 2019 22:43:54: ERROR: Flash failed to run, please check the log file. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/lucapinello/CRISPResso/issues/51>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABB_6hZGZbWuCVvmdU7qwAxPe0pOaI63ks5vKcaJgaJpZM4ajwkS> .
Dear Luca Pinello Thanks for getting me back. Probably the FLASH was not at the right PATH. I got a clue from your response to issue #49 and after fixing it run successfuly but with the empty output files in the result folder. i attached all the files including the log files. kindly help me
Regards stressed
. CRISPRessoPooled_RUNNING_LOG.txt MAPPING_STATISTICS.txt REPORT_READS_ALIGNED_TO_AMPLICONS.txt SAMPLES_QUANTIFICATION_SUMMARY.txt
Do you have bowtie2 installed and in the path?
On Wed, Feb 6, 2019 at 10:50 AM bilalSarwar2020 notifications@github.com wrote:
Dear Luca Pinello Thanks for getting me back. Probably the FLASH was not at the right PATH. I got a clue from your response to issue #49 https://github.com/lucapinello/CRISPResso/issues/49 and after fixing it run successfuly but with the empty output files in the result folder. i attached all the files including the log files. kindly help me
Regards stressed
. CRISPRessoPooled_RUNNING_LOG.txt https://github.com/lucapinello/CRISPResso/files/2837017/CRISPRessoPooled_RUNNING_LOG.txt MAPPING_STATISTICS.txt https://github.com/lucapinello/CRISPResso/files/2837018/MAPPING_STATISTICS.txt REPORT_READS_ALIGNED_TO_AMPLICONS.txt https://github.com/lucapinello/CRISPResso/files/2837019/REPORT_READS_ALIGNED_TO_AMPLICONS.txt SAMPLES_QUANTIFICATION_SUMMARY.txt https://github.com/lucapinello/CRISPResso/files/2837020/SAMPLES_QUANTIFICATION_SUMMARY.txt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lucapinello/CRISPResso/issues/51#issuecomment-461073360, or mute the thread https://github.com/notifications/unsubscribe-auth/ABB_6iVCnHdRe1eU-SNhUm8-HhsgjdxLks5vKvmrgaJpZM4ajwkS .
YES Version 2.2.6 installed
bilal@Plant-Genomics:~$ bowtie2 --version /usr/bin/bowtie2-align-s version 2.2.6 64-bit Built on lgw01-12 Mon Dec 28 11:09:46 UTC 2015 Compiler: gcc version 5.3.1 20151219 (Ubuntu 5.3.1-4ubuntu1) Options: -O3 -m64 -msse2 -funroll-loops -g3 -Wl,-Bsymbolic-functions -Wl,-z,relro -DPOPCNT_CAPABILITY -DWITH_TBB Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
Can you please try with the new version of CRISPResso and install it via conda?
See the instructions here: https://github.com/pinellolab/crispresso2
On Wed, Feb 6, 2019 at 11:06 AM bilalSarwar2020 notifications@github.com wrote:
YES Version 2.2.6 installed
bilal@Plant-Genomics:~$ bowtie2 --version /usr/bin/bowtie2-align-s version 2.2.6 64-bit Built on lgw01-12 Mon Dec 28 11:09:46 UTC 2015 Compiler: gcc version 5.3.1 20151219 (Ubuntu 5.3.1-4ubuntu1) Options: -O3 -m64 -msse2 -funroll-loops -g3 -Wl,-Bsymbolic-functions -Wl,-z,relro -DPOPCNT_CAPABILITY -DWITH_TBB Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lucapinello/CRISPResso/issues/51#issuecomment-461079640, or mute the thread https://github.com/notifications/unsubscribe-auth/ABB_6m4OmoeIjWl4Mw5ueC2KNYVSmvomks5vKv1ogaJpZM4ajwkS .
Dear Luca Pinello I am using CRISPRessoPooled.py script to analyzed the paired ends reads data by Illumina. the read length is 150 bp. the amplicon size is 180bp long. below is the command that I am used several time. it ends up with an error at last of the analysis I am new to the Linux environment. Kindly help me to resolve this issue. thanks
ERROR: Flash failed to run, please check the log file.
$ python CRISPRessoPooled.py -r1 /home/bilal/Sir_Qayyum_data/6297_1_1.fastq.gz -r2 /home/bilal/Sir_Qayyum_data/6297_1_2.fastq.gz -f /home/bilal/Sir_Qayyum_data/CRISPResso-master/cat.csv