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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory #19

Closed LOYON2019 closed 5 years ago

LOYON2019 commented 5 years ago

Hi, I got this issue, could you know how to figure out this? thank you. I use the new version of JUM-JUM_v2.0.2. working fold is under fastq, JUM is also under fastq.

root@debian:/mnt/hgfs/rawdata/fastq/N2F# bash ../JUM/JUM_2-2.sh ../JUM 6 3 N2F Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

qqwang-berkeley commented 5 years ago

Hi there,

Could you confirm that you are using the newest manual for JUM v2.0.2: https://github.com/qqwang-berkeley/JUM/wiki/3.1.-Manual-running-JUM-(v2.0.2-and-up)

Since this version there is only JUM_A.sh, JUM_B.sh and JUM_C.sh. No more JUM_2-2, 2-1 etc.

If so, could you send me the results from running "ls -l -t" in your working folder fastq and ../JUM?

Qingqing

On Thu, Jan 17, 2019 at 3:15 PM LOYON2019 notifications@github.com wrote:

Hi, I got this issue, could you know how to figure out this? thank you. I use the new version of JUM-JUM_v2.0.2. working fold is under fastq, JUM is also under fastq.

root@debian:/mnt/hgfs/rawdata/fastq/N2F# bash ../JUM/JUM_2-2.sh ../JUM 6 3 N2F Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

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LOYON2019 commented 5 years ago

root@debian:/mnt/hgfs/rawdata/fastq/JUM# ls -l -t total 103 drwxrwxrwx 1 root root 28672 Jan 16 13:08 bin -rwxrwxrwx 1 root root 577 Jul 14 2018 JUM_2-1.sh -rwxrwxrwx 1 root root 2444 Jul 14 2018 JUM_2-2.sh -rwxrwxrwx 1 root root 17637 Jul 14 2018 JUM_2-3.sh -rwxrwxrwx 1 root root 16625 Jul 14 2018 JUM_3.sh -rwxrwxrwx 1 root root 10345 Jul 14 2018 JUM_4.sh -rwxrwxrwx 1 root root 1070 Jul 14 2018 LICENSE -rwxrwxrwx 1 root root 24045 Jul 14 2018 Old JUM manual for 1.3.7-1.3.11 -rwxrwxrwx 1 root root 1409 Jul 14 2018 README.md root@debian:/mnt/hgfs/rawdata/fastq/JUM#

LOYON2019 commented 5 years ago

I download from https://github.com/qqwang-berkeley/JUM/releases the Source code (zip) https://github.com/qqwang-berkeley/JUM/archive/JUM_v2.0.2.zip

qqwang-berkeley commented 5 years ago

I see what is going on.

You need to download from the JUM_2.0.2.tar.gz link (the one marked with 31.5KB) on the release page, NOT the Source code (zip) NOR Source code (tar.gz).

Something is weird. The three links should give you the same folder but the latter two did not give the correct version. I will fix it.

But at the same time, try downloading JUM2.0.2 again with the correct link and I think you should be all set.

On Thu, Jan 17, 2019 at 5:18 PM LOYON2019 notifications@github.com wrote:

root@debian:/mnt/hgfs/rawdata/fastq/JUM# ls -l -t total 103 drwxrwxrwx 1 root root 28672 Jan 16 13:08 bin -rwxrwxrwx 1 root root 577 Jul 14 2018 JUM_2-1.sh -rwxrwxrwx 1 root root 2444 Jul 14 2018 JUM_2-2.sh -rwxrwxrwx 1 root root 17637 Jul 14 2018 JUM_2-3.sh -rwxrwxrwx 1 root root 16625 Jul 14 2018 JUM_3.sh -rwxrwxrwx 1 root root 10345 Jul 14 2018 JUM_4.sh -rwxrwxrwx 1 root root 1070 Jul 14 2018 LICENSE -rwxrwxrwx 1 root root 24045 Jul 14 2018 Old JUM manual for 1.3.7-1.3.11 -rwxrwxrwx 1 root root 1409 Jul 14 2018 README.md root@debian:/mnt/hgfs/rawdata/fastq/JUM#

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LOYON2019 commented 5 years ago

I got the same issue after download the JUM_2.0.2.tar.gz. however, I do see the file "prepare_count_file_after_STAR_2_pass_mapping.pl" in my JUM folder.

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_2-1.sh root@debian:/mnt/hgfs/rawdata/fastq/N2F# bash /mnt/hgfs/rawdata/fastq/JUM/JUM_2-2.sh /mnt/hgfs/rawdata/fastq/JUM 6 3 N2F Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

LOYON2019 commented 5 years ago

root@debian:/mnt/hgfs/rawdata/fastq/JUM# ls -l -t total 215 -rwxrwxrwx 1 root root 2450 Jul 25 19:18 JUM_2-2.sh -rwxrwxrwx 1 root root 10367 Jul 25 19:17 JUM_C.sh -rwxrwxrwx 1 root root 20102 Jul 25 19:10 JUM_A.sh -rwxrwxrwx 1 root root 19729 Jul 25 19:08 JUM_B.sh -rwxrwxrwx 1 root root 1766 Jul 25 18:16 Identify_junctions_exist_in_certain_number_of_input_files.pl -rwxrwxrwx 1 root root 581 Jul 25 18:08 JUM_2-1.sh -rwxrwxrwx 1 root root 2007 Jul 25 13:38 preparing_intron_retention_count_table_short_intron.pl -rwxrwxrwx 1 root root 3617 Jul 25 13:37 preparing_intron_retention_count_table_long_intron.pl -rwxrwxrwx 1 root root 1169 Jul 24 19:02 count_intron_read_long_intron_retention_step2_updated.pl -rwxrwxrwx 1 root root 3145 Jul 24 19:02 determining_rightful_long_intron_retention_event_updated.pl -rwxrwxrwx 1 root root 2303 Jul 24 19:02 extract_intron_retention_event_coordinate_from_samples_conditional_union.pl -rwxrwxrwx 1 root root 5098 Jul 24 19:02 final_process_A3SS_output.pl -rwxrwxrwx 1 root root 5146 Jul 24 19:02 final_process_A5SS_output.pl -rwxrwxrwx 1 root root 2856 Jul 24 19:02 final_process_cassette_exon_output1.pl -rwxrwxrwx 1 root root 2856 Jul 24 19:02 final_process_cassette_exon_output1_update.pl -rwxrwxrwx 1 root root 984 Jul 24 19:02 final_process_cassette_exon_output2.pl -rwxrwxrwx 1 root root 3977 Jul 24 19:02 final_process_composite_output.pl -rwxrwxrwx 1 root root 2604 Jul 24 19:02 final_process_IR_output_long.pl -rwxrwxrwx 1 root root 2253 Jul 24 19:02 final_process_IR_output_short.pl -rwxrwxrwx 1 root root 10312 Jul 24 19:02 final_process_MXE_output.pl -rwxrwxrwx 1 root root 1653 Jul 24 19:02 first_processing_generate_JUM_reference_for_profiled_total_alternative_splicing_event_junction.pl -rwxrwxrwx 1 root root 3250 Jul 24 19:02 generate_JUM_format_annotation_file_for_profiled_alternative_splicing_event_junction.pl -rwxrwxrwx 1 root root 2572 Jul 24 19:02 identify_gene_name_for_JUM_output_1.pl -rwxrwxrwx 1 root root 2186 Jul 24 19:02 identify_gene_name_for_JUM_output_2.pl -rwxrwxrwx 1 root root 1111 Jul 24 19:02 identify_gene_name_for_JUM_output_3.pl -rwxrwxrwx 1 root root 1446 Jul 24 19:02 Identify_intron_retention_event_exist_in_all_samples.pl -rwxrwxrwx 1 root root 1691 Jul 24 19:02 Identify_junctions_exist_in_all_samples.pl -rwxrwxrwx 1 root root 1168 Jul 24 19:02 making_junction_count_file_matching_annotation_for_JUM_in_intron_retention.pl -rwxrwxrwx 1 root root 1251 Jul 24 19:02 making_junction_count_file_matching_annotation_for_JUM.pl -rwxrwxrwx 1 root root 1263 Jul 24 19:02 output_reformat_JUM_1.pl -rwxrwxrwx 1 root root 2880 Jul 24 19:02 output_reformat_JUM_2.pl -rwxrwxrwx 1 root root 2883 Jul 24 19:02 output_reformat_JUM_3.pl -rwxrwxrwx 1 root root 2299 Jul 24 19:02 output_reformat_JUM_4.pl -rwxrwxrwx 1 root root 1225 Jul 24 19:02 prepare_count_file_after_STAR_2_pass_mapping.pl -rwxrwxrwx 1 root root 2417 Jul 24 19:02 prepare_significant_long_intron_retention_event.pl -rwxrwxrwx 1 root root 4163 Jul 24 19:02 preparing_intron_retention_event_for_JUM_combine.pl -rwxrwxrwx 1 root root 6803 Jul 24 19:02 process_raw_AS_differential_output.pl -rwxrwxrwx 1 root root 2036 Jul 24 19:02 profile_AS_events_sharing_3_prime_ss.pl -rwxrwxrwx 1 root root 2036 Jul 24 19:02 profile_AS_events_sharing_5_prime_ss.pl -rwxrwxrwx 1 root root 2738 Jul 24 19:02 profile_overhang_from_STAR_output_step_1.pl -rwxrwxrwx 1 root root 1689 Jul 24 19:02 profile_overhang_from_STAR_output_step_2.pl -rwxrwxrwx 1 root root 1496 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_1.pl -rwxrwxrwx 1 root root 1351 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_2.pl -rwxrwxrwx 1 root root 8888 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_3_updated.pl -rwxrwxrwx 1 root root 1686 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_4.pl -rwxrwxrwx 1 root root 2424 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_5.pl -rwxrwxrwx 1 root root 2461 Jul 24 19:02 profiling_splicing_patterns_from_AS_events_6.pl -rwxrwxrwx 1 root root 3317 Jul 24 19:02 profiling_splicing_patterns_from_AS_events.pl -rwxrwxrwx 1 root root 1106 Jul 24 19:02 R_script_JUM.R -rwxrwxrwx 1 root root 1861 Jul 24 19:02 screening_A5SS_A3SS_events.pl -rwxrwxrwx 1 root root 3082 Jul 24 19:02 screening_cassette_exon_events.pl -rwxrwxrwx 1 root root 2161 Jul 24 19:02 screening_intron_retention_event_for_deltachange_consistency.pl -rwxrwxrwx 1 root root 1831 Jul 24 19:02 screening_intron_retention_event_for_no_inner_junction.pl -rwxrwxrwx 1 root root 5090 Jul 24 19:02 screening_MXE_events.pl -rwxrwxrwx 1 root root 1698 Jul 24 19:02 second_processing_generate_JUM_reference_for_profiled_total_alternative_splicing_event_junction.pl -rwxrwxrwx 1 root root 592 Jul 24 19:02 vary_for_replicate.pl -rwxrwxrwx 1 root root 1435 Jul 24 19:02 count_reads_for_intron_retention_sam.pl -rwxrwxrwx 1 root root 2052 Jul 24 19:02 determining_rightful_total_cassette_exon_event.pl -rwxrwxrwx 1 root root 65 Jul 24 19:02 experiment_design.txt -rwxrwxrwx 1 root root 4929 Jul 24 19:02 extract_intron_retention_event_coordinate_conditional_union_splicing_junction_gff.pl -rwxrwxrwx 1 root root 1549 Jul 24 19:02 count_intron_read_long_intron_retention_step1.pl -rwxrwxrwx 1 root root 1350 Jul 24 19:02 count_intron_read_long_intron_retention_step3.pl root@debian:/mnt/hgfs/rawdata/fastq/JUM#

qqwang-berkeley commented 5 years ago

I see that you are still running the old command style for JUM.

Starting from JUM_2.0.2, you should run JUM with JUM_A.sh, JUM_B.sh, and JUM_C.sh (instead of JUM_2-1.sh, JUM_2-2.sh etc.) Please see this tutorial: https://github.com/qqwang-berkeley/JUM/wiki/3.1.-Manual-running-JUM-(v2.0.2-and-up)

Could you run JUM_A.sh as shown in the manual above and let me know if it works? (Here JUM_A.sh did all the substeps for you and changed the way parameters are fed to the subcommands)

On Thu, Jan 17, 2019 at 5:49 PM LOYON2019 notifications@github.com wrote:

I got the same issue after download the JUM_2.0.2.tar.gz. however, I do see the file "prepare_count_file_after_STAR_2_pass_mapping.pl" in my JUM folder.

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_2-1.sh root@debian:/mnt/hgfs/rawdata/fastq/N2F# bash /mnt/hgfs/rawdata/fastq/JUM/JUM_2-2.sh /mnt/hgfs/rawdata/fastq/JUM 6 3 N2F Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

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LOYON2019 commented 5 years ago

Hi, thanks for the response, I got a new issue. see below "bash: JUM/JUM_2-2.sh: No such file or directory"

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A.sh --Folder JUM --JuncThreshold 5 --Condition1_fileNum_threshold 3 --Condition2_fileNum_threshold 3 --IRthreshold 5 --Readlength 150 --Thread 3 --Condition1SampleName N2S1,N2S2,N2S3 --Condition2SampleName N2F1,N2F2,N2F3 Sample names are: N2S1 N2S2 N2S3 N2F1 N2F2 N2F3 bash: JUM/JUM_2-2.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq#

qqwang-berkeley commented 5 years ago

OK, Now I see what is going on.

Yes the errors you have encountered is because during the latest upgrade of JUM 2.0.2, I used a user-provided argument management function that is only compatible to newer versions of the Linux system. It is not compatible with Mac OSX that is BSD-derived, and likely for earlier versions of Linux. So basically, the folder name, file name, threshold etc. you fed JUM is not accepted by Linux so that is why you have been having issues.

I have generated a modified version of JUM2.0.2 (see attached) that bypasses the fancy user argument function but go back to the old and classic (although a bit dull) one that was used in JUM 2.0, and is stable and compatible with all versions of Linux as well as Mac OSX.

You can follow everything as on the manual, except that you should ignore the descriptions for parameters such as "--Folder" etc for all three JUM_A.sh/JUM_B.sh/JUM_C.sh scripts; instead just simply give the parameters. For example, you need to run JUM_A.sh as:

bash /user/home/JUM_2.0.2/JUM_A.sh /user/home/JUM_2.0.2 5 2 2 5 100 3 ctrl1,ctrl2,ctrl3 treat1,treat2,treat3

Just be careful that you include all the input parameters and they are in the right order (9 parameters for JUM_A.sh, 8 for JUM_B.sh and 6 for JUM_C.sh - this is the reason I updated the user input to the fancy new system which is not compatible with mac or older versions of linux... to help users ease the process of parameter feeding).

Please let me know if this version works for you and if you have any questions. I will need to add this version to the GitHub page.

Qingqing

On Mon, Jan 21, 2019 at 6:00 PM LOYON2019 notifications@github.com wrote:

Hi, thanks for the response, I got a new issue. see below "bash: JUM/JUM_2-2.sh: No such file or directory"

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A.sh --Folder JUM --JuncThreshold 5 --Condition1_fileNum_threshold 3 --Condition2_fileNum_threshold 3 --IRthreshold 5 --Readlength 150 --Thread 3 --Condition1SampleName N2S1,N2S2,N2S3 --Condition2SampleName N2F1,N2F2,N2F3 Sample names are: N2S1 N2S2 N2S3 N2F1 N2F2 N2F3 bash: JUM/JUM_2-2.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq#

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LOYON2019 commented 5 years ago

Hi Qingqing, thanks for the help, you are right, I use Debian 8. could you let me where I can get the modified version of JUM2.0.2? thank you.

qqwang-berkeley commented 5 years ago

I attached it with the previous email. Did you get it? If not, I will send it again.

On Tue, Jan 22, 2019 at 2:05 PM LOYON2019 notifications@github.com wrote:

Hi Qingqing, thanks for the help, you are right, I use Debian 8. could you let me where I can get the modified version of JUM2.0.2? thank you.

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LOYON2019 commented 5 years ago

No, could you send again, thanks.

qqwang-berkeley commented 5 years ago

OK. I have uploaded the package to the JUM GitHub page.

Check here: https://github.com/qqwang-berkeley/JUM/releases/tag/JUMv2.0.2_short_user_argument_BSD

On Tue, Jan 22, 2019 at 2:09 PM LOYON2019 notifications@github.com wrote:

No, could you send again, thanks.

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LOYON2019 commented 5 years ago

Hi Qingqing, Seems have the same issue. see below:

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 Sample names are: N2S1 N2S2 N2S3 N2F1 N2F2 N2F3 bash: JUM/JUM_2-2.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A_sorted_adjusted.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 bash: /JUM_2-1.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq#

qqwang-berkeley commented 5 years ago

this is really bizarre. You checked that JUM_2-2.sh is in the :/mnt/hgfs/rawdata/fastq/JUM directory, right?

What about providing the full path of /mnt/hgfs/rawdata/fastq/JUM as the first parameter when running JUM_A.sh (the path for all JUM scripts)?

On Wed, Jan 23, 2019 at 5:03 PM LOYON2019 notifications@github.com wrote:

Hi Qingqing, Seems have the same issue. see below:

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 Sample names are: N2S1 N2S2 N2S3 N2F1 N2F2 N2F3 bash: JUM/JUM_2-2.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A_sorted_adjusted.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 bash: /JUM_2-1.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq#

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qqwang-berkeley commented 5 years ago

Just want to quickly follow up. Did JUM work for you now?

On Mon, Jan 28, 2019 at 9:34 PM Qingqing Wang qingqing_wang@berkeley.edu wrote:

this is really bizarre. You checked that JUM_2-2.sh is in the :/mnt/hgfs/rawdata/fastq/JUM directory, right?

What about providing the full path of /mnt/hgfs/rawdata/fastq/JUM as the first parameter when running JUM_A.sh (the path for all JUM scripts)?

On Wed, Jan 23, 2019 at 5:03 PM LOYON2019 notifications@github.com wrote:

Hi Qingqing, Seems have the same issue. see below:

root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 Sample names are: N2S1 N2S2 N2S3 N2F1 N2F2 N2F3 bash: JUM/JUM_2-2.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq# bash JUM/JUM_A_sorted_adjusted.sh JUM 5 3 3 5 150 4 N2S1,N2S2,N2S3 N2F1,N2F2,N2F3 bash: /JUM_2-1.sh: No such file or directory root@debian:/mnt/hgfs/rawdata/fastq#

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