Comments (25)
leepc12
commented on June 27, 2024
Remove any FASTQ definition ("atac.fastqs*") from your input JSON and add
"atac.nodup_bams" : [ "rep1.bam", "rep2.bam" ],
from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
I'm getting an error:
[error] WorkflowManagerActor Workflow a7b66b90-77f3-47b9-afa6-d874bd8e21ab failed (during ExecutingWorkflowState): Job atac.spr:2:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
{
"atac.pipeline_type" : "atac",
"atac.genome_tsv" : "test_genome_database/hg38_local.tsv",
"atac.nodup_bams" : [ "test_sample/induced/rep1/KJ064_R1_TRIM.trim.nodup.bam", "test_sample/induced/rep2/KJ065_R1_TRIM.trim.nodup.bam", "test_sample/induced/rep3/KJ066_R1_TRIM.trim.nodup.bam"],
"atac.paired_end" : true,
"atac.multimapping" : 4,
"atac.auto_detect_adapter" : true,
"atac.smooth_win" : 73,
"atac.enable_idr" : true,
"atac.idr_thresh" : 0.05,
"atac.enable_xcor" : true,
"atac.title" : "induced",
"atac.description" : "ATAC-seq on induced RPEs",
"atac.trim_adapter.cpu" : 1,
"atac.trim_adapter.mem_mb" : 4000,
"atac.trim_adapter.time_hr" : 1,
"atac.bowtie2_cpu" : 1,
"atac.bowtie2_mem_mb" : 4000,
"atac.bowtie2_time_hr" : 1,
"atac.filter_cpu" : 1,
"atac.filter_mem_mb" : 4000,
"atac.filter_time_hr" : 1,
"atac.macs2_mem_mb" : 4000,
"atac.macs2_time_hr" : 1,
"atac.ataqc.mem_mb" : 4000,
"atac.ataqc.time_hr" : 1
}
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leepc12
commented on June 27, 2024
test_genome_database/hg38_local.tsv doesn't exist
Did you download genome database for test samples?
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kirstyjamieson
commented on June 27, 2024
Sorry, that was the wrong output. This is my current one:
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
We will look into this problem. Please do not enable_xcor until this problem is fixed.
Remove "atac.enable_xcor" : true, from your input JSON.
from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
Thanks. I also realized I sent the old run.sh. This is the current one.
#!/bin/bash
#$ -l arch=linux-x64
#$ -l h_rt=48:0:0
#$ -l mem_free=8G
#$ -S /bin/bash
#$ -cwd
#$ -j y
#$ -r y
export _JAVA_OPTIONS="-Xms256M -Xmx16384M -XX:ParallelGCThreads=1"
export PATH="/netapp/home/kirsty.jamieson/miniconda3/bin:$PATH"
LIB=/scrapp/kirsty.jamieson/atac-seq-pipeline
source activate encode-atac-seq-pipeline
INPUT=$LIB/examples/local/ENCSR356KRQ_subsampled.json
java -jar -Dconfig.file=$LIB/backends/backend.conf
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
Please attach a tar ball of all logs for debugging. When you created this issue, you should see an instruction to make a tar ball.
Is there a particular reason that two memory settings differ (mem_free=8G and -Xmx16384M)?
from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
No good reason, I'll remove -Xmx16384M in the future.
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
Your TAG-ALIGN looks trivially small.
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 51 Nov 27 15:31 KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 4060 Nov 27 15:15 script
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 405 Nov 27 15:15 script.background
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 163 Nov 27 15:15 script.submit
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 0 Nov 27 15:15 stderr
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 0 Nov 27 15:15 stderr.background
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 2102 Nov 27 15:31 stdout
PID=10830: -rw-r--r-- 1 kirsty.jamieson shen 5 Nov 27 15:15 stdout.background
Something is wrong with your BAM inputs?
from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
I don't think the bam file is the issue. It was generated from your previous pipeline and gave a reasonable-sized tag-align.
-rw-r--r-- 1 kirsty.jamieson shen 7026944483 Sep 22 12:51 KJ064_R1_TRIM.trim.bam
-rw-r--r-- 1 kirsty.jamieson shen 2793488 Sep 22 12:54 KJ064_R1_TRIM.trim.bam.bai
-rw-r--r-- 1 kirsty.jamieson shen 2319815474 Sep 22 11:37 KJ064_R1_TRIM.trim.fastq.gz
-rw-r--r-- 1 kirsty.jamieson shen 1504625562 Sep 22 13:49 KJ064_R1_TRIM.trim.nodup.bam
-rw-r--r-- 1 kirsty.jamieson shen 6809488 Sep 22 13:50 KJ064_R1_TRIM.trim.nodup.bam.bai
-rw-r--r-- 1 kirsty.jamieson shen 254422820 Sep 22 14:05 KJ064_R1_TRIM.trim.nodup.tagAlign.gz
-rw-r--r-- 1 kirsty.jamieson shen 237655009 Sep 22 14:10 KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.25M.tagAlign.gz
-rw-r--r-- 1 kirsty.jamieson shen 254694043 Sep 22 14:07 KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
Can you upload an input JSON for that previous pipeline run (which starts from FASTQs)?
Is this sample paired end?
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kirstyjamieson
commented on June 27, 2024
I used the json you provided. Yes, it's paired end.
debug_[nodup_#55_sample_fastq].tar.gz
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kirstyjamieson
commented on June 27, 2024
Could you send me a json file that you used for a successful run starting from bam?
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leepc12
commented on June 27, 2024
@kirstyjamieson: Here is an example input JSON file which starts from nodup_bams.
{
"atac.pipeline_type" : "atac",
"atac.genome_tsv" : "/mnt/data/pipeline_genome_data/hg38_chr19_chrM/hg38_chr19_chrM_klab.tsv",
"atac.nodup_bams" : [
"./cromwell-executions/atac/c33c7037-5873-4772-aef2-e748a27b6fd4/call-filter/shard-0/execution/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam",
"./cromwell-executions/atac/c33c7037-5873-4772-aef2-e748a27b6fd4/call-filter/shard-1/execution/ENCFF641SFZ.subsampled.400.trim.merged.nodup.bam"
],
"atac.paired_end" : true,
"atac.multimapping" : 4,
"atac.auto_detect_adapter" : true,
"atac.smooth_win" : 73,
"atac.enable_idr" : true,
"atac.idr_thresh" : 0.05,
"atac.enable_xcor" : true,
"atac.title" : "ENCSR356KRQ",
"atac.description" : "ATAC-seq on primary keratinocytes in day 0.0 of differentiation"
}
I tested pipelines starting from FASTQs and NODUP_BAMs. Both worked fine. Got the same BED outputs (*.tagAlign.gz).
$ find -name *.tagAlign.gz | grep -v inputs | grep -v glob | xargs ls -l
-rw-r--r-- 2 leepc12 users 175596 Nov 29 13:02 ./cromwell-executions/atac/c33c7037-5873-4772-aef2-e748a27b6fd4/call-bam2ta/shard-0/execution/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
-rw-r--r-- 2 leepc12 users 225168 Nov 29 13:02 ./cromwell-executions/atac/c33c7037-5873-4772-aef2-e748a27b6fd4/call-bam2ta/shard-1/execution/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
-rw-r--r-- 2 leepc12 users 175596 Nov 29 13:37 ./cromwell-executions/atac/e8d64aa0-6394-409c-a171-1d3e64d6dffa/call-bam2ta/shard-0/execution/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
-rw-r--r-- 2 leepc12 users 225168 Nov 29 13:37 ./cromwell-executions/atac/e8d64aa0-6394-409c-a171-1d3e64d6dffa/call-bam2ta/shard-1/execution/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
I took the nodup bams generated from the successful run when I started at your subsampled fastq and that worked. I get mixed results when I start with my own tag-align files. For one pair, it succeeded and for another pair it failed at the very end with:
"SingleWorkflowRunnerActor received Failure message: connection exception: closed java.sql.SQLNonTransientConnectionException: connection exception: closed."
I did manage to get idr peaks before it failed.
I also tried 3 replicates with tag-aligns and got a different failure, much earlier on:
"WorkflowManagerActor Workflow 72c2bf95-1c83-49e4-9e6f-e48151ac76bb failed (during ExecutingWorkflowState): cromwell.backend.standard.StandardAsyncExecutionActor$$anon$2: Failed to evaluate job outputs"
So the pipeline seems to work well with subsampled files but fails with my much larger files.
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leepc12
commented on June 27, 2024
Let's stick to a single failure case (starting from your own large nodup_bam files).
You got this good-sized NODUP_BAM and TAG-ALIGN when you started a pipeline from FASTQ
-rw-r--r-- 1 kirsty.jamieson shen 1504625562 Sep 22 13:49 KJ064_R1_TRIM.trim.nodup.bam
-rw-r--r-- 1 kirsty.jamieson shen 254422820 Sep 22 14:05 KJ064_R1_TRIM.trim.nodup.tagAlign.gz
But you failed to get the same TAG-ALIGN when you started from NODUP_BAM.
Please upload your input JSON files for those two cases.
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kirstyjamieson
commented on June 27, 2024
Those files were generated with the previous pipeline.
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leepc12
commented on June 27, 2024
I have processed >100 large samples from ENCODE and they all worked fine.
It looks like bam2ta task failed due to resource limit.
Please increase memory in your job submission shell script first.
#$ -l mem_free=24G
Also remove all resource settings from your input JSON file. Those resources are too small for your large samples.
"atac.trim_adapter.cpu" : 1,
"atac.trim_adapter.mem_mb" : 4000,
"atac.trim_adapter.time_hr" : 1,
"atac.bowtie2_cpu" : 1,
"atac.bowtie2_mem_mb" : 4000,
"atac.bowtie2_time_hr" : 1,
"atac.filter_cpu" : 1,
"atac.filter_mem_mb" : 4000,
"atac.filter_time_hr" : 1,
"atac.macs2_mem_mb" : 4000,
"atac.macs2_time_hr" : 1,
"atac.ataqc.mem_mb" : 4000,
"atac.ataqc.time_hr" : 1
Next time please use a template examples/template_pe.json (https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/examples/template_pe.json). This template has all default parameters.
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kirstyjamieson
commented on June 27, 2024
I tried increasing memory and used the default parameters from the template. I am still getting mixed results.
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
@kirstyjamieson: Please pick one failed sample and upload an error log, tar ball and input JSON for it.
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kirstyjamieson
commented on June 27, 2024
run_induced_nodupbam.sh.txt
run_induced_nodupbam.sh.o525095.txt
debug_[#59_12_5_18].tar.gz
induced_nodupbam.json
{
"atac.nodup_bams" : [
"test_sample/induced/rep1/KJ064_R1_TRIM.trim.nodup.bam",
"test_sample/induced/rep2/KJ065_R1_TRIM.trim.nodup.bam",
"test_sample/induced/rep3/KJ066_R1_TRIM.trim.nodup.bam"
],
"atac.title" : "Induced RPEs",
"atac.description" : "3 replicates for induced RPEs starting from nodup bam.",
"atac.pipeline_type" : "atac",
"atac.genome_tsv" : "genome/hg38/hg38.tsv",
"atac.paired_end" : true,
"atac.align_only" : false,
"atac.true_rep_only" : false,
"atac.cutadapt_min_trim_len" : 5,
"atac.cutadapt_err_rate" : 0.1,
"atac.multimapping" : 0,
"atac.bowtie2_score_min" : "",
"atac.dup_marker" : "picard",
"atac.mapq_thresh" : 30,
"atac.no_dup_removal" : false,
"atac.regex_filter_reads" : "chrM",
"atac.subsample_reads" : 0,
"atac.enable_xcor" : false,
"atac.xcor_subsample_reads" : 25000000,
"atac.keep_irregular_chr_in_bfilt_peak" : false,
"atac.cap_num_peak" : 300000,
"atac.pval_thresh" : 0.01,
"atac.smooth_win" : 150,
"atac.enable_idr" : true,
"atac.idr_thresh" : 0.1,
"atac.disable_ataqc" : false,
"atac.trim_adapter_cpu" : 2,
"atac.trim_adapter_mem_mb" : 12000,
"atac.trim_adapter_time_hr" : 24,
"atac.trim_adapter_disks" : "local-disk 100 HDD",
"atac.bowtie2_cpu" : 4,
"atac.bowtie2_mem_mb" : 20000,
"atac.bowtie2_time_hr" : 48,
"atac.bowtie2_disks" : "local-disk 100 HDD",
"atac.filter_cpu" : 2,
"atac.filter_mem_mb" : 20000,
"atac.filter_time_hr" : 24,
"atac.filter_disks" : "local-disk 100 HDD",
"atac.bam2ta_cpu" : 2,
"atac.bam2ta_mem_mb" : 10000,
"atac.bam2ta_time_hr" : 6,
"atac.bam2ta_disks" : "local-disk 100 HDD",
"atac.spr_mem_mb" : 16000,
"atac.xcor_cpu" : 2,
"atac.xcor_mem_mb" : 16000,
"atac.xcor_time_hr" : 6,
"atac.xcor_disks" : "local-disk 100 HDD",
"atac.macs2_mem_mb" : 16000,
"atac.macs2_time_hr" : 24,
"atac.macs2_disks" : "local-disk 100 HDD",
"atac.ataqc_mem_mb" : 16000,
"atac.ataqc_mem_java_mb" : 16000,
"atac.ataqc_time_hr" : 24,
"atac.ataqc_disks" : "local-disk 100 HDD"
}
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
Pipeline failed to convert your BAMs into BEDs.
Let's do some line-by-line debugging.
YOUR_WORK_DIR=~/temp_dir
mkdir -p $YOUR_WORK_DIR && cd $YOUR_WORK_DIR
source activate encode-atac-seq-pipeline
sambamba sort -n /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-0/inputs/-1239304996/KJ064_R1_TRIM.trim.nodup.bam -o KJ064_R1_TRIM.trim.nodup.nmsrt.bam -t 2
LC_COLLATE=C bedtools bamtobed -bedpe -mate1 -i KJ064_R1_TRIM.trim.nodup.nmsrt.bam | gzip -nc > KJ064_R1_TRIM.trim.nodup.bedpe.gz
zcat -f KJ064_R1_TRIM.trim.nodup.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | grep -P -v 'chrM' | gzip -nc > KJ064_R1_TRIM.trim.nodup.tagAlign.gz
zcat -f KJ064_R1_TRIM.trim.nodup.tagAlign.gz | awk 'BEGIN {OFS = "\t"}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -nc > KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
ls -l
Can you also share your BAM files (test_sample/induced/rep1/KJ064_R1_TRIM.trim.nodup.bam, ...) with me via Dropbox (leepc12 at gmail dot com) or Google Drive (leepc12 at gmail dot com)? I would like to replicate this error on my computer.
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kirstyjamieson
commented on June 27, 2024
Yeah, I can't get to the beds. I shared the files on google drive.
#!/bin/bash
#$ -l arch=linux-x64
#$ -l h_rt=48:0:0
#$ -l mem_free=24G
#$ -S /bin/bash
#$ -cwd
#$ -j y
#$ -r y
export TMPDIR="/scrapp/kirsty.jamieson/tmp/"
export PATH="/netapp/home/kirsty.jamieson/miniconda3/bin:$PATH"
LIB=/scrapp/kirsty.jamieson/atac-seq-pipeline
source activate encode-atac-seq-pipeline
sambamba sort -n /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-0/inputs/-1239304996/KJ064_R1_TRIM.trim.nodup.bam -o KJ064_R1_TRIM.trim.nodup.nmsrt.bam -t 2
LC_COLLATE=C bedtools bamtobed -bedpe -mate1 -i KJ064_R1_TRIM.trim.nodup.nmsrt.bam | gzip -nc > KJ064_R1_TRIM.trim.nodup.bedpe.gz
zcat -f KJ064_R1_TRIM.trim.nodup.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | grep -P -v 'chrM' | gzip -nc > KJ064_R1_TRIM.trim.nodup.tagAlign.gz
zcat -f KJ064_R1_TRIM.trim.nodup.tagAlign.gz | awk 'BEGIN {OFS = "\t"}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -nc > KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
ls -l
Output
-rw-r--r-- 1 kirsty.jamieson shen 1103 Dec 5 13:07 debug.sh
-rw-r--r-- 1 kirsty.jamieson shen 89 Dec 5 13:10 debug.sh.o525406
-rw-r--r-- 1 kirsty.jamieson shen 86 Dec 5 13:28 KJ064_R1_TRIM.trim.nodup.bedpe.gz
-rw-r--r-- 1 kirsty.jamieson shen 1719191526 Dec 5 13:24 KJ064_R1_TRIM.trim.nodup.nmsrt.bam
-rw-r--r-- 1 kirsty.jamieson shen 51 Dec 5 13:28 KJ064_R1_TRIM.trim.nodup.tagAlign.gz
-rw-r--r-- 1 kirsty.jamieson shen 51 Dec 5 13:28 KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
from atac-seq-pipeline.
leepc12
commented on June 27, 2024
I replicated this error. It turns out that your BAM file does not have any paired-ended reads.
(encode-atac-seq-pipeline) leepc12@kadru:/srv/scratch/leepc12/debug_atac_59_4_run$ ll
total 3148308
drwxr-xr-x 2 leepc12 users 4096 Dec 5 15:23 ./
drwxr-xr-x 67 leepc12 users 20480 Dec 5 14:54 ../
-rw-r--r-- 1 leepc12 users 1504625562 Dec 5 14:59 KJ064_R1_TRIM.trim.nodup.bam
-rw-r--r-- 1 leepc12 users 86 Dec 5 15:23 KJ064_R1_TRIM.trim.nodup.bedpe.gz
-rw-r--r-- 1 leepc12 users 1719191526 Dec 5 15:21 KJ064_R1_TRIM.trim.nodup.nmsrt.bam
-rw-r--r-- 1 leepc12 users 51 Dec 5 15:23 KJ064_R1_TRIM.trim.nodup.tagAlign.gz
-rw-r--r-- 1 leepc12 users 51 Dec 5 15:23 KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz
(encode-atac-seq-pipeline) leepc12@kadru:/srv/scratch/leepc12/debug_atac_59_4_run$ samtools view KJ064_R1_TRIM.trim.nodup.nmsrt.bam | head
A00351:44:H5W3YDSXX:1:1101:10004:13651 0 chr15 34808208 255 51M * 0 0 CAGTGAGGCAGTATGAGTCAGCACTCCCTTTTTGCCAGGATGGTGTCAGGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:15154 0 chr14 68816824 255 51M * 0 0 CCTCGGAGGCAGCACGATGGACGTGGCCACACTGCCCTCCAGTGGCCAGCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:15812 0 chr2 34664477 255 35M * 0 0 TTCTTTCGGAGAAACAAGCCAAGCCTCCCTACAGCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:35 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:70 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:19194 0 chr7 83446287 255 44M * 0 0 GTATATAGGCTCATCTGAATAACAGTGAAGGCATCTTACAATTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:44 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:88 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:19695 16 chr5 112146436 40 51M * 0 0 AGGAGCAGAGGATCTTCCAACGCTGTTTGCGCTCCCCAAAGACTCTTGCAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 XS:i:40 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:23109 16 chr3 57692747 40 51M * 0 0 GAGGAGCGCCGAGAAAGGGCGGGGCCGGGCCTCACCTCCACGGCCTGGCCC ,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:F:FFFFFFF: MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 XS:i:42 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:23766 0 chr19 39098460 255 51M * 0 0 GAGCCAGGCTCCATGACTGTAACTTGGACCACATGGGTCCCAACCCGCTCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:24111 0 chr11 45286298 40 51M * 0 0 AGCCAGCAGCTCTCCCGCCGCCAGAGGGGCGGGGACGGAGGGAGGGAGGAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 XS:i:40 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:26553 16 chr9 133371276 255 51M * 0 0 CACATCCTAGAAACAAGCACCTGCGGCCCAGCGGCTTCCCTCACATCAGCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:102 YT:Z:UU
A00351:44:H5W3YDSXX:1:1101:10004:28526 0 chr7 70866137 255 48M * 0 0 CTACAGCTTCATCCTTTGAGACCTGGAGTGCCAGGACACCCAGGCTCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:48 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:96 YT:Z:UU
(encode-atac-seq-pipeline) leepc12@kadru:/srv/scratch/leepc12/debug_atac_59_4_run$ samtools view -c -f 1 KJ064_R1_TRIM.trim.nodup.nmsrt.bam | head
0
Please try with single-ended settings.
{
...
"atac.paired_end" : false,
...
}from atac-seq-pipeline.
kirstyjamieson
commented on June 27, 2024
Yes, you are right! I had a typo in my script from the original pipeline where I generated the bam, so it only recognized the first read of the pair. Thank you for your help!
from atac-seq-pipeline.
Related Issues (20)
- Unable to run the pipeline. invalid jar file error HOT 3
- 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
- More than 10 replicates HOT 3
- Encode-atac-seq-pipeline environment can't be found?
- [Question]: Do reads need to be deduped before FRiP calculation HOT 6
- Invalid MEMLIMIT unit value with LSF jobs on Linux
- two replicates and the combined have different signal
- --read-len selection
- Memory Saving: too many large files?
- The pipeline stalled at "chip.read_genome_tsv" for local backend HOT 2
- Differences in qc when validating installation HOT 3
- Failed on fastqs having identical filename but different path HOT 3
- Confirming that separate conditions/treatments should be analyzed by separate pipelines HOT 2
- Don't need to trim adapters
- Add --ntasks-per-node or --exclusive option for your multi-process jobs.
- bam files with replicates HOT 1
- If the pipeline can be used when data is from other platforms (eg: DNBSEQ-G400). HOT 1
- Discrepancy between signal p-value and fold change bigwig tracks around the open regions
- build_genome_sh did not finish running
- How to set the seed when subsampling reads HOT 1
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