Cogent
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Magdoll
Coding Genome Reconstruction using Iso-Seq data
Hi, I was trying to run the command python /get_bad_or_unmapped_hq.py hq.fasta hq.5merge and I have this error: File "/usr/local/Cogent/Cogent/helper_scripts/get_bad_or_unmapped_hq.py", line 20, in print >> sys.stderr, "Reading transcript file {0}....".format(input) TypeError:...
Hi Magdoll, I ran Cogent at the beginning of this year with no issue. I recently have recreated the environment and tried to use it and am having issues with...
Hi All steps before "Filter away 5' degraded isoforms" were good, NO Error was reported but this script generates NO OUTPUT but just these stdout: ``` filter_away_subset.py testSample.collapsed The number...
Hello All, I am receiving following error while running the Family finding step of Cogent for a large dataset. Kindly suggest. _input file:_ isoseq_flnc.fasta _command:_ python /path/to/cDNA_Cupcake/cupcake2/tofu2/run_preCluster.py --cpus=30 raise CalledProcessError(retcode,...
Since the command used to generate the unassigned.list file in the tutorial simply divides the last line of prefix.partition.txt on the commas, the first entry retains the "#unassigned:" text before...
Hi! I have four populations I have been trying to run Cogent for. Three seemed to work really well and I didn't have an issue. The other one, I have...
I am trialling Cogent on the test_human.fa data as shown on the Wiki, though I did not use the reference genome hg38 for the coding genome reconstruction as I do...
I run reconstruct using cogent 8.0 reconstruct_contig.py The results are as follows: `pulp.apis.core .PulpSolverError: PuLP: Error while executing glpsol` What's the reason? I hope we can get an answer! thank...
Hi, I am getting a errror "scipy.sparse.linalg.eigen.arpack.arpack.ArpackNoConvergence: ARPACK error -1: No convergence (77651 iterations, 66/100 eigenvectors converged)" when I rerun a one cluster after it failed in batch processing of...
Hi Liz, For about 60 clusters I have an error running reconstruct_contig.py: example error report: $ cat slurm-19441671.out 2.17-r941 /var/spool/slurm/d/job19441671/slurm_script : ligne 10 : 19632 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection...
