Error in ASSIGN_UMIS

[Zaf4]

Got this error message.

INFO:    Converting SIF file to temporary sandbox...
WARNING: underlay of /etc/localtime required more than 50 (86) bind mounts
[Parallel(n_jobs=2)]: Using backend LokyBackend with 2 concurrent workers.
Traceback (most recent call last):
  File "/home/zafer.kosar/nextflow-gpseq/bin/umis2cutsite.py", line 197, in <module>
    umi_final = pd.concat(pd_list)  #list with umis assigned to cutsite and distances
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py", line 372, in concat
    op = _Concatenator(
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py", line 429, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
INFO:    Cleaning up image...

.command.sh

#!/bin/bash -ue
umis2cutsite.py sample_1.clean_umis.txt.gz hg38_DpnII_GATC_sites.bed.gz "sample_1_umi_atcs.txt.gz" \
--compress --threads 2

.nextflow.log

log file

[Zaf4]

most components ran without error.

[34/a749d6] process > FASTQC (FASTQC on sample_1)    [100%] 1 of 1 ✔
[2e/949328] process > GET_CUTSITES (Getting cutsi... [100%] 1 of 1 ✔
[f9/ff4653] process > EXTRACT (fbarber extract on... [100%] 1 of 1 ✔
[eb/d4cf00] process > FILTER (fbarber filter on s... [100%] 1 of 1 ✔
[46/8b1364] process > ALIGN (bowtie2 on sample_1)    [100%] 1 of 1 ✔
[41/ee0019] process > FILTER_BAM (filtering bam o... [100%] 1 of 1 ✔
[59/b3dc75] process > CORRECT_POS (Correcting for... [100%] 1 of 1 ✔
[88/cf7f89] process > GROUP_UMIS (Grouping UMIs o... [100%] 1 of 1 ✔
[32/8c1f97] process > ASSIGN_UMIS (Assigning UMIs... [100%] 1 of 1, failed: 1 ✘
[-        ] process > DEDUPLICATE                    -
[-        ] process > GENERATE_BED                   -
[6e/7d68fb] process > MULTIQC (MultiQC on all sam... [100%] 1 of 1 ✔
[-        ] process > COUNT_FILTERS                  -
[-        ] process > GENERATE_SUMMARY_PLOTS         -
[-        ] process > GENERATE_GPSEQ_METADATA        -
[35/4950fc] process > GET_CHROMSIZES (getting chr... [100%] 1 of 1 ✔
[-        ] process > CALCULATE_GPSEQ_SCORE     

[ljwharbers]

Most likely it's already due to a step earlier. If I remember correctly this error results from empty UMI files. You can try two thing, go to the work directories of the previous steps and see where you're losing (if this is the case) all your reads. The work directories are written in the log file and also before each step like here: [41/ee0019] process > FILTER_BAM (filtering bam o... [100%] 1 of 1 ✔ This shows that the work directory is in work/41/ee0019.....

The second thing you can do is run it on the test data using the provided reference files. Simply run `nextflow run main.nf -profile test,ht_hpc'

Finally, as a little note, if you specify -profile ht_hpc (like you correctly did) and --genome hg38 it will automatically take the correct reference and blacklists files, so you won't have to specify them seperately like you did here.

Let me know if this works.

[Zaf4]

I also ran things with --genome hg38. Still got the same error.

                             sample_1_umi_atcs.txt.log                          
                    INFO     Reading RSs                     umis2cutsite.py:155
[02/09/24 13:16:25] INFO     Reading UMIs                    umis2cutsite.py:167
                    INFO     Found 0 chromosomes             umis2cutsite.py:178
                    INFO     Assigning UMIs to RSs           umis2cutsite.py:189

[Zaf4]

I sent another job with another data MS28_S4_LALL_R1_001.fastq.gz from Wenjing. Trying now...

[ljwharbers]

Clearly it didn't find any chromosomes. I'll need to look at the exact command line and log files to have a better idea where it's going wrong. Just message me on slack.

[Zaf4]

Fixed by using correct barcodes.