SorenKarst
commented
3 years ago Hi William,
Thank you for reporting this bug in v0.3.2 of the pipeline. It is a mistake in the umi_binning.sh script that makes the workflow break if absolute paths are used. A fix has been implemented in the development branch of the pipeline, which can be installed as described here in issue #36 .
Alternatively, you can use a relative path for your output directory, which should work.
P.s. I replied to your e-mail you sent a while ago, but I can see my response bounced. Can you send me a new e-mail I can send the response to?
All the best Søren
walexandertsu
So I have longread_umi installed and mostly working. I also have a dataset that produces acceptable numbers of clusters of UMIs, and I can see the UMIs stored in the files "umi_ref_b1.fa" and "umi_ref_b2.fa." However, the pipeline breaks at the next step, where it tries to create new directories in umi_binning > read_binning>bins:
[main] Version: 0.7.17-r1188 [main] CMD: bwa samse -n 10000000 /var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/reads_tf_umi2.fa /var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/umi2_map.sai /var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/umi_ref_b2.fa [main] Real time: 23.828 sec; CPU: 22.785 sec [10:48:34] ### Read-UMI match filtering ### [10:48:34] Reading UMI1 match file... [10:48:46] Reading UMI2 match file... [10:49:01] UMI match filtering... [10:49:02] Read orientation filtering... [10:49:02] UMI match error filtering... [10:49:02] UMI bin/cluster size ratio filtering... [10:49:02] Print UMI matches... [10:49:02] Done. mkdir: cannot create directory ‘.//var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job1/1’: No such file or directory gawk: cmd. line:28: (FILENAME=- FNR=21) fatal: can't redirect to
/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job1/1/umi42889bins.fastq' (No such file or directory) mkdir: cannot create directory ‘.//var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job2/1’: No such file or directory gawk: cmd. line:28: (FILENAME=- FNR=621) fatal: can't redirect to/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job2/1/umi168704bins.fastq' (No such file or directory) mkdir: cannot create directory ‘.//var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job3/1’: No such file or directory gawk: cmd. line:28: (FILENAME=- FNR=345) fatal: can't redirect to/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job3/1/umi2785bins.fastq' (No such file or directory) mkdir: cannot create directory ‘.//var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job4/1’: No such file or directory gawk: cmd. line:28: (FILENAME=- FNR=53) fatal: can't redirect to/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job4/1/umi11765bins.fastq' (No such file or directory) mkdir: cannot create directory ‘.//var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job5/1’: No such file or directory gawk: cmd. line:28: (FILENAME=- FNR=113) fatal: can't redirect to `/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins/job5/1/umi9722bins.fastq' (No such file or directory) find: ‘/var/lib/minknow/data/UMI_trial_3/UMI_trial_3_comb/fastq/longread-umi_analysis_round3/umi_binning/read_binning/bins///’: No such file or directoryI'm so close to getting this to work, so any help would be greatly appreciated. Thank you!