Open Rafaelsoler13 opened 1 year ago
Hi there,
The error message says STDERR=/bin/bash: line 1: -1: command not found
so I wonder if this is just an issue of you not installing dependencies. Can you double-check what line 1
is referring to here?
Your tsv file looks fine; maybe try using absolute paths (so replace ~ with the full path), and double check if all the files are where they are?
I used absolute paths to run it but it still does not work. The error is with Bowtie2:
***
Error: Must specify at least one read input with -U/-1/-2
(ERR): bowtie2-align exited with value 1
STDOUT=
But I am putting corretly the fastq files:
"atac.fastqs_rep1_R1" : [ "/media/analysis/ATAC_non_canonical_species/raw_data/SRR19213758_1.fastq.gz" ],
"atac.fastqs_rep1_R2" : [ "/media/analysis/ATAC_non_canonical_species/raw_data/SRR19213758_2.fastq.gz" ],
"atac.fastqs_rep2_R1" : [ "/media/analysis/ATAC_non_canonical_species/raw_data/SRR19213759_1.fastq.gz" ],
"atac.fastqs_rep2_R2" : [ "/media/analysis/ATAC_non_canonical_species/raw_data/SRR19213759_2.fastq.gz" ],
I tried to align the samples using Bowtie2 from my PC, and actually it works
bowtie2 --very-sensitive -p 8 -X 2000 -x chicken_bowtie -1 raw_data/SRR19213758_1.fastq.gz -2 raw_data/SRR19213758_2.fastq.gz -S SRR19213758.sam
11553902 (100.00%) were paired; of these:
2217557 (19.19%) aligned concordantly 0 times
8884460 (76.90%) aligned concordantly exactly 1 time
451885 (3.91%) aligned concordantly >1 times
----
2217557 pairs aligned concordantly 0 times; of these:
820611 (37.01%) aligned discordantly 1 time
----
1396946 pairs aligned 0 times concordantly or discordantly; of these:
2793892 mates make up the pairs; of these:
2499890 (89.48%) aligned 0 times
215809 (7.72%) aligned exactly 1 time
78193 (2.80%) aligned >1 times
89.18% overall alignment rate
What could be happening?
Interesting. As I am not a developer I don't think I can help beyond this. There must be something else wrong either during the building of the custom genome, or your installation. Have you tried running a test sample using the default human genome? You should consider trying that first to rule out bad installation.
Yes! Actually the tutorial run without a problem!
Sorry for late response, You don't those files tss file, reg2map.. They are extra data for some additional analyses in the pipeline. Disable analysis using those data. Add the following to your input JSON.
{
"atac.enable_tss_enrich" : false,
"atac.enable_annot_enrich" : false,
"atac.enable_compare_to_roadmap" : false,
"atac.enable_gc_bias" : false
}
How did u run Caper? It looks like it ran inside a docker container. What is the exact command line used for running Caper? e.g. `caper run atac.wdl -i input.json --docker"?
Hello,
I am trying to run the pipeline for chicken samples and have tried to create a custom genome reference for the pipeline. However, after finishing the steps here [https://github.com/ENCODE-described DCC/atac-seq-pipeline/blob/master/docs/build_genome_database.md] (build_genome_database.md), the tsv file I get it fails to create the tss file, reg2map... Are these files needed to run the pipeline? If so, what can I do to get them (it doesn't say anything here [https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/build_genome_database.md])
Also, I am trying to run the pipeline with the json file generated, and it gives me this errors in the alignment:
This is the json file:
And this one the tsv file.
Best,
Rafael