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jason-weirather / AlignQC

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.
Apache License 2.0
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Expected lines to be ordered but they appear not to be ordered #25

Open shaniAmare opened 4 years ago

shaniAmare commented 4 years ago

Hi @jason-weirather ,

Thank you for this awesome tool. I want to try it for our PacBio, Illumina, and ONT data. However, I keep on getting the error mentioned in the subject like regardless of my attempts. Can you please help me figure it out?

I used the following script:

module load anaconda2

cd /stornext/General/data/user_managed/grpu_mritchie_1/Shani/long_read_benchmark/alignqc/
source activate alignqc

module load samtools/1.7

REFERENCE="/stornext/General/data/user_managed/grpu_mritchie_1/Shani/atac-seq/20190529_MiRCL_ATAC/references/genome.fa"

mkdir "/stornext/General/data/user_managed/grpu_mritchie_1/Shani/long_read_benchmark/alignqc_output/ont"
OUT_DIR="/stornext/General/data/user_managed/grpu_mritchie_1/Shani/long_read_benchmark/alignqc_output/ont"

# full BAM files took forever - so trying on the subsample
IN_LOC_ONT="/stornext/General/data/user_managed/grpu_mritchie_1/XueyiDong/long_read_benchmark/ONT/bam_subsample"

find ${IN_LOC_ONT} -name '*.bam' -print0 | while IFS= read -r -d '' BAM
do 
OUT_P=${BAM##*/};OUT_P=${OUT_P%%.sorted*};
echo " ######## --------- processing $BAM in $OUT_P -------- #########################";
seq-tools sort --bam ${BAM} -o ${BAM}.sorted.bam;
samtools index ${BAM}.sorted.bam;
mkdir ${OUT_DIR}/${OUT_P};
echo " ######## --------- results saved in $OUT_DIR/$OUT_P -------- #########################";
alignqc analyze ${BAM}.sorted.bam -g ${REFERENCE} --no_transcriptome --threads 8 --specific_tempdir ${OUT_DIR}/${OUT_P} -o ${OUT_DIR}/${OUT_P}/${OUT_P}.ont.alignqc.xhtml
done

The error I'm getting is as follows:

 ######## --------- processing /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode05.sorted.bam in barcode05 -------- #########################
 ######## --------- results saved in /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05 -------- #########################
Using Rscript version:
R scripting front-end version 3.6.1 (2019-07-05)
WARNING: No annotation specified.  Will be unable to report feature specific outputs
Creating initial alignment mapping data
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/bam_preprocess.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode05.sorted.bam --minimum_intron_size 68 -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/temp/alndata.txt.gz --threads 8 --specific_tempdir /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/temp/
read basics
6257000
check for best set
6250000/6257982
combining results
6257982
Traverse bam for alignment analysis
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/traverse_preprocessed.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/temp/alndata.txt.gz -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/ --specific_tempdir /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/temp/ --threads 8 --min_aligned_bases 50 --max_query_overlap 10 --max_target_overlap 10 --max_target_gap 500000 --required_fractional_improvement 0.2
6257982 alignments   3844424 reads
Writing chromosome lengths from header
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/bam_to_chr_lengths.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode05.sorted.bam -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/chrlens.txt
Can we find any known read types
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/get_platform_report.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/lengths.txt.gz /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/special_report
Go through genepred best alignments and make a bed depth file
Generate the depth bed for the mapped reads
gpd_to_bed_depth.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/best.sorted.gpd.gz -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode05/data/depth.sorted.bed.gz --threads 8
Traceback (most recent call last):
  File "/home/amarasinghe.s/.conda/envs/alignqc/bin/alignqc", line 11, in <module>
    sys.exit(entry_point())
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/alignqc.py", line 47, in entry_point
    main(args,operable_argv)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/alignqc.py", line 17, in main
    analyze.external_cmd(operable_argv,version=version)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/analyze.py", line 88, in external_cmd
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/analyze.py", line 54, in main
    prepare_all_data.external(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 844, in external
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 60, in main
    make_data_bam(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 184, in make_data_bam
    gpd_to_bed_depth(cmd)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/seqtools/cli/utilities/gpd_to_bed_depth.py", line 60, in external_cmd
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/seqtools/cli/utilities/gpd_to_bed_depth.py", line 27, in main
    for covs in results:
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/multiprocessing/pool.py", line 271, in <genexpr>
    return (item for chunk in result for item in chunk)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/multiprocessing/pool.py", line 673, in next
    raise value
ValueError: Expected lines to be ordered but they appear not to be ordered on line 3362988

Then I used the seq-tools sort option to get the files sorted first as you have mentioned in this issue. However, it still doesn't seem to solve the problem as seen form below email.

 ######## --------- processing /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode01.sorted.bam in barcode01 -------- #########################
[bam_sort_core] merging from 0 files and 10 in-memory blocks...
 ######## --------- results saved in /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01 -------- #########################
Using Rscript version:
R scripting front-end version 3.6.1 (2019-07-05)
WARNING: No annotation specified.  Will be unable to report feature specific outputs
Creating initial alignment mapping data
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/bam_preprocess.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode01.sorted.bam.sorted.bam --minimum_intron_size 68 -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/temp/alndata.txt.gz --threads 8 --specific_tempdir /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/temp/
read basics
5916000
check for best set
5910000/5916804
combining results
5916804
Traverse bam for alignment analysis
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/traverse_preprocessed.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/temp/alndata.txt.gz -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/ --specific_tempdir /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/temp/ --threads 8 --min_aligned_bases 50 --max_query_overlap 10 --max_target_overlap 10 --max_target_gap 500000 --required_fractional_improvement 0.2
5916804 alignments   3720827 reads
Writing chromosome lengths from header
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/bam_to_chr_lengths.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample/bam_subsample/barcode01.sorted.bam.sorted.bam -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/chrlens.txt
Can we find any known read types
/stornext/HPCScratch/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/get_platform_report.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/lengths.txt.gz /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/special_report
Go through genepred best alignments and make a bed depth file
Generate the depth bed for the mapped reads
gpd_to_bed_depth.py /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/best.sorted.gpd.gz -o /stornext/Projects/promethion/promethion_access/lab_ritchie/transcr_bench_PacBio/short_term/alignqc/ont_bam_subsample//barcode01/data/depth.sorted.bed.gz --threads 8
Traceback (most recent call last):
  File "/home/amarasinghe.s/.conda/envs/alignqc/bin/alignqc", line 11, in <module>
    sys.exit(entry_point())
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/alignqc.py", line 47, in entry_point
    main(args,operable_argv)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/alignqc.py", line 17, in main
    analyze.external_cmd(operable_argv,version=version)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/analyze.py", line 88, in external_cmd
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/analyze.py", line 54, in main
    prepare_all_data.external(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 844, in external
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 60, in main
    make_data_bam(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/alignqc/prepare_all_data.py", line 184, in make_data_bam
    gpd_to_bed_depth(cmd)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/seqtools/cli/utilities/gpd_to_bed_depth.py", line 60, in external_cmd
    main(args)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/site-packages/seqtools/cli/utilities/gpd_to_bed_depth.py", line 27, in main
    for covs in results:
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/multiprocessing/pool.py", line 271, in <genexpr>
    return (item for chunk in result for item in chunk)
  File "/home/amarasinghe.s/.conda/envs/alignqc/lib/python2.7/multiprocessing/pool.py", line 673, in next
    raise value
ValueError: Expected lines to be ordered but they appear not to be ordered on line 3364652

I'm attaching the genome file and a small sample of the BAM file here: barcode05.sorted.bam.first_10_lines.bam.gz

The header of this .bam file is as follows:

@HD VN:1.5  SO:coordinate
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
@SQ SN:chr10    LN:133797422
@SQ SN:chr11    LN:135086622
@SQ SN:chr12    LN:133275309
@SQ SN:chr13    LN:114364328
@SQ SN:chr14    LN:107043718
@SQ SN:chr15    LN:101991189
@SQ SN:chr16    LN:90338345
@SQ SN:chr17    LN:83257441
@SQ SN:chr18    LN:80373285
@SQ SN:chr19    LN:58617616
@SQ SN:chr20    LN:64444167
@SQ SN:chr21    LN:46709983
@SQ SN:chr22    LN:50818468
@SQ SN:chrX LN:156040895
@SQ SN:chrY LN:57227415
@SQ SN:chrM LN:16569
@SQ SN:GL000008.2   LN:209709
@SQ SN:GL000009.2   LN:201709
@SQ SN:GL000194.1   LN:191469
@SQ SN:GL000195.1   LN:182896
@SQ SN:GL000205.2   LN:185591
@SQ SN:GL000208.1   LN:92689
@SQ SN:GL000213.1   LN:164239
@SQ SN:GL000214.1   LN:137718
@SQ SN:GL000216.2   LN:176608
@SQ SN:GL000218.1   LN:161147
@SQ SN:GL000219.1   LN:179198
@SQ SN:GL000220.1   LN:161802
@SQ SN:GL000221.1   LN:155397
@SQ SN:GL000224.1   LN:179693
@SQ SN:GL000225.1   LN:211173
@SQ SN:GL000226.1   LN:15008
@SQ SN:KI270302.1   LN:2274
@SQ SN:KI270303.1   LN:1942
@SQ SN:KI270304.1   LN:2165
@SQ SN:KI270305.1   LN:1472
@SQ SN:KI270310.1   LN:1201
@SQ SN:KI270311.1   LN:12399
@SQ SN:KI270312.1   LN:998
@SQ SN:KI270315.1   LN:2276
@SQ SN:KI270316.1   LN:1444
@SQ SN:KI270317.1   LN:37690
@SQ SN:KI270320.1   LN:4416
@SQ SN:KI270322.1   LN:21476
@SQ SN:KI270329.1   LN:1040
@SQ SN:KI270330.1   LN:1652
@SQ SN:KI270333.1   LN:2699
@SQ SN:KI270334.1   LN:1368
@SQ SN:KI270335.1   LN:1048
@SQ SN:KI270336.1   LN:1026
@SQ SN:KI270337.1   LN:1121
@SQ SN:KI270338.1   LN:1428
@SQ SN:KI270340.1   LN:1428
@SQ SN:KI270362.1   LN:3530
@SQ SN:KI270363.1   LN:1803
@SQ SN:KI270364.1   LN:2855
@SQ SN:KI270366.1   LN:8320
@SQ SN:KI270371.1   LN:2805
@SQ SN:KI270372.1   LN:1650
@SQ SN:KI270373.1   LN:1451
@SQ SN:KI270374.1   LN:2656
@SQ SN:KI270375.1   LN:2378
@SQ SN:KI270376.1   LN:1136
@SQ SN:KI270378.1   LN:1048
@SQ SN:KI270379.1   LN:1045
@SQ SN:KI270381.1   LN:1930
@SQ SN:KI270382.1   LN:4215
@SQ SN:KI270383.1   LN:1750
@SQ SN:KI270384.1   LN:1658
@SQ SN:KI270385.1   LN:990
@SQ SN:KI270386.1   LN:1788
@SQ SN:KI270387.1   LN:1537
@SQ SN:KI270388.1   LN:1216
@SQ SN:KI270389.1   LN:1298
@SQ SN:KI270390.1   LN:2387
@SQ SN:KI270391.1   LN:1484
@SQ SN:KI270392.1   LN:971
@SQ SN:KI270393.1   LN:1308
@SQ SN:KI270394.1   LN:970
@SQ SN:KI270395.1   LN:1143
@SQ SN:KI270396.1   LN:1880
@SQ SN:KI270411.1   LN:2646
@SQ SN:KI270412.1   LN:1179
@SQ SN:KI270414.1   LN:2489
@SQ SN:KI270417.1   LN:2043
@SQ SN:KI270418.1   LN:2145
@SQ SN:KI270419.1   LN:1029
@SQ SN:KI270420.1   LN:2321
@SQ SN:KI270422.1   LN:1445
@SQ SN:KI270423.1   LN:981
@SQ SN:KI270424.1   LN:2140
@SQ SN:KI270425.1   LN:1884
@SQ SN:KI270429.1   LN:1361
@SQ SN:KI270435.1   LN:92983
@SQ SN:KI270438.1   LN:112505
@SQ SN:KI270442.1   LN:392061
@SQ SN:KI270448.1   LN:7992
@SQ SN:KI270465.1   LN:1774
@SQ SN:KI270466.1   LN:1233
@SQ SN:KI270467.1   LN:3920
@SQ SN:KI270468.1   LN:4055
@SQ SN:KI270507.1   LN:5353
@SQ SN:KI270508.1   LN:1951
@SQ SN:KI270509.1   LN:2318
@SQ SN:KI270510.1   LN:2415
@SQ SN:KI270511.1   LN:8127
@SQ SN:KI270512.1   LN:22689
@SQ SN:KI270515.1   LN:6361
@SQ SN:KI270516.1   LN:1300
@SQ SN:KI270517.1   LN:3253
@SQ SN:KI270518.1   LN:2186
@SQ SN:KI270519.1   LN:138126
@SQ SN:KI270521.1   LN:7642
@SQ SN:KI270522.1   LN:5674
@SQ SN:KI270528.1   LN:2983
@SQ SN:KI270529.1   LN:1899
@SQ SN:KI270530.1   LN:2168
@SQ SN:KI270538.1   LN:91309
@SQ SN:KI270539.1   LN:993
@SQ SN:KI270544.1   LN:1202
@SQ SN:KI270548.1   LN:1599
@SQ SN:KI270579.1   LN:31033
@SQ SN:KI270580.1   LN:1553
@SQ SN:KI270581.1   LN:7046
@SQ SN:KI270582.1   LN:6504
@SQ SN:KI270583.1   LN:1400
@SQ SN:KI270584.1   LN:4513
@SQ SN:KI270587.1   LN:2969
@SQ SN:KI270588.1   LN:6158
@SQ SN:KI270589.1   LN:44474
@SQ SN:KI270590.1   LN:4685
@SQ SN:KI270591.1   LN:5796
@SQ SN:KI270593.1   LN:3041
@SQ SN:KI270706.1   LN:175055
@SQ SN:KI270707.1   LN:32032
@SQ SN:KI270708.1   LN:127682
@SQ SN:KI270709.1   LN:66860
@SQ SN:KI270710.1   LN:40176
@SQ SN:KI270711.1   LN:42210
@SQ SN:KI270712.1   LN:176043
@SQ SN:KI270713.1   LN:40745
@SQ SN:KI270714.1   LN:41717
@SQ SN:KI270715.1   LN:161471
@SQ SN:KI270716.1   LN:153799
@SQ SN:KI270717.1   LN:40062
@SQ SN:KI270718.1   LN:38054
@SQ SN:KI270719.1   LN:176845
@SQ SN:KI270720.1   LN:39050
@SQ SN:KI270721.1   LN:100316
@SQ SN:KI270722.1   LN:194050
@SQ SN:KI270723.1   LN:38115
@SQ SN:KI270724.1   LN:39555
@SQ SN:KI270725.1   LN:172810
@SQ SN:KI270726.1   LN:43739
@SQ SN:KI270727.1   LN:448248
@SQ SN:KI270728.1   LN:1872759
@SQ SN:KI270729.1   LN:280839
@SQ SN:KI270730.1   LN:112551
@SQ SN:KI270731.1   LN:150754
@SQ SN:KI270732.1   LN:41543
@SQ SN:KI270733.1   LN:179772
@SQ SN:KI270734.1   LN:165050
@SQ SN:KI270735.1   LN:42811
@SQ SN:KI270736.1   LN:181920
@SQ SN:KI270737.1   LN:103838
@SQ SN:KI270738.1   LN:99375
@SQ SN:KI270739.1   LN:73985
@SQ SN:KI270740.1   LN:37240
@SQ SN:KI270741.1   LN:157432
@SQ SN:KI270742.1   LN:186739
@SQ SN:KI270743.1   LN:210658
@SQ SN:KI270744.1   LN:168472
@SQ SN:KI270745.1   LN:41891
@SQ SN:KI270746.1   LN:66486
@SQ SN:KI270747.1   LN:198735
@SQ SN:KI270748.1   LN:93321
@SQ SN:KI270749.1   LN:158759
@SQ SN:KI270750.1   LN:148850
@SQ SN:KI270751.1   LN:150742
@SQ SN:KI270752.1   LN:27745
@SQ SN:KI270753.1   LN:62944
@SQ SN:KI270754.1   LN:40191
@SQ SN:KI270755.1   LN:36723
@SQ SN:KI270756.1   LN:79590
@SQ SN:KI270757.1   LN:71251
@SQ SN:chrIS    LN:10567884
@PG ID:minimap2 PN:minimap2 VN:2.17-r974-dirty  CL:minimap2 -ax splice -uf -k14 --junc-bed /wehisan/home/allstaff/d/dong.x/annotation/HumanSequins/gencode.v33.sequins.junction.bed /wehisan/home/allstaff/d/dong.x/annotation/HumanSequins/GrCh38_sequins.fa /stornext/General/data/user_managed/grpu_mritchie_1/XueyiDong/long_read_benchmark/subsample/ONT010/barcode05.fq.gz

Also, I'm attaching the full bam file and a zip file of whatever I got as an output from running the script here: https://drive.google.com/drive/folders/1HtuIZWOSCh-7PpmxLJyZNy37b8Uo9N6z?usp=sharing

Your help would be really appreciated to figure out what is going on...

Many thanks, Shani

julienlag commented 4 years ago

I'm having the same issue