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erro #149

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jwli-code opened this issue Dec 19, 2024 · 1 comment
Open

erro #149

jwli-code opened this issue Dec 19, 2024 · 1 comment

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@jwli-code
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What caused it?

Found 1 command tree.

Found 1 command tree.
--
-- Estimating memory usage for 'Bna_GH06_v1.0.0.meryl/'.
--

Failed with 'Segmentation fault'; backtrace (libbacktrace):

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.gt2.meryl
    output to Bna_GH06_v1.0.solid.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.
--
-- Estimating memory usage for 'Bna_GH06_v1.0.0.meryl'.
--

Failed with 'Segmentation fault'; backtrace (libbacktrace):
/public/home/jwli1/micromamba/envs/merqury/share/merqury/eval/spectra-cn.sh: line 58: 24090 Segmentation fault      meryl-lookup -bed -sequence $asm_fa -mers ${asm}.0.meryl > ${asm}_only.bed
--
-- Estimating memory usage for 'Bna_GH06_v1.0.0.meryl'.
--

Failed with 'Segmentation fault'; backtrace (libbacktrace):
/public/home/jwli1/micromamba/envs/merqury/share/merqury/eval/spectra-cn.sh: line 58: 24091 Segmentation fault      meryl-lookup -wig-depth -sequence $asm_fa -mers ${asm}.0.meryl > ${asm}_only.wig

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

Found 1 command tree.
Loading required package: argparse
Loading required package: ggplot2
Loading required package: scales
Warning messages:
1: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
2: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
3.5.0.
ℹ Please use the `legend.position.inside` argument of `theme()` instead.
3: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

cat Bna_GH06_v1.0.qv
Bna_GH06_v1.0   0       5095693304      +inf    0
@jwli-code
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Author

meryl=1.4.1

Usage: spectra-cn.sh [-c] <read.meryl> <asm1.fasta> [asm2.fasta] out-prefix
        -c              : [OPTIONAL] input meryl databases are homopolymer compressed, while asm.fasta isn't
        <read.meryl>    : Generated with meryl count from i.e. illumina wgs reads
        <asm1.fasta>    : haplotype 1 assembly. gzipped or not
        [asm2.fasta]    : haplotype 2 assembly. gzipped or not
        <out-prefix>: output prefix. Required.
                When only <asm1.fasta> is given, results will be generated in haploid mode.
                When <asm2.fasta> is given, results will be generated for each asm1 asm2 haploid assembly and asm1+asm2 diploid assembly.


Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opLessThan
    Bna_GH06_v1.0.meryl
    print to (stdout)
Detected k-mer size 20

No modules available..
# Get solid k-mers
Generate Bna_GH06_v1.0.hist

Found 1 command tree.

java -jar -Xmx1g /share/home/yangqingyong/software/merqury/eval/kmerHistToPloidyDepth.jar Bna_GH06_v1.0.hist > Bna_GH06_v1.0.hist.ploidy
Processing file Bna_GH06_v1.0.hist
Start sampling here: 2, 4.9678483E7
Next max here: 4, 5.233136E7
Stop sampling here: 5, 4.8058686E7
Running time : 0 h 0 m 0 sec

ploidy  depth   boundary
0       0       2
1       4       5

Filter out kmers <= 2

meryl greater-than 2 output Bna_GH06_v1.0.gt2.meryl Bna_GH06_v1.0.meryl

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opGreaterThan
    threshold=2
    Bna_GH06_v1.0.meryl
    output to Bna_GH06_v1.0.gt2.meryl

Cleaning up.

Bye.

Done: Bna_GH06_v1.0.gt2.meryl
=== Generate spectra-cn plots per assemblies and get QV, k-mer completeness ===

# Collect read counts per asm copies
# Read only

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opDifference
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.0.meryl

Cleaning up.

Bye.

Found 1 command tree.
# Copy 1 ~ 4
Copy = 1 ..

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    opEqualTo
      threshold=1
      Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.1.meryl

Cleaning up.

Bye.

Found 1 command tree.

Copy = 2 ..

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    opEqualTo
      threshold=2
      Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.2.meryl

Cleaning up.

Bye.

Found 1 command tree.

Copy = 3 ..

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    opEqualTo
      threshold=3
      Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.3.meryl

Cleaning up.

Bye.

Found 1 command tree.

Copy = 4 ..

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    opEqualTo
      threshold=4
      Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.4.meryl

Cleaning up.

Bye.

Found 1 command tree.

Copy >4 ..

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    opGreaterThan
      threshold=4
      Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.gt4.meryl

Cleaning up.

Bye.

Found 1 command tree.

# Copy numbers in k-mers found only in asm

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opDifference
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.meryl
    output to Bna_GH06_v1.0.0.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

# Plot Bna_GH06_v1.0.Bna_GH06_v1.0.spectra-cn.hist
  Rscript /share/home/yangqingyong/software/merqury/plot/plot_spectra_cn.R -f Bna_GH06_v1.0.Bna_GH06_v1.0.spectra-cn.hist -o Bna_GH06_v1.0.Bna_GH06_v1.0.spectra-cn -z Bna_GH06_v1.0.Bna_GH06_v1.0.only.hist
/share/home/yangqingyong/software/merqury/eval/spectra-cn.sh: line 126: Rscript: command not found

# QV statistics

Found 1 command tree.

Found 1 command tree.

# Per seq QV statistics

Estimating memory usage for 'Bna_GH06_v1.0.0.meryl/'.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Memory required:  32.000 GB
Memory limit:     2015.040 GB

Loading kmers from 'Bna_GH06_v1.0.0.meryl/' into lookup table.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Counting size of buckets.


Summing bucket sizes.
  block indices are 14 bits wide -- sum lengths 16128 (including 16128 empty pointers)
  block lengths are 0 bits wide -- max length  0

Setting pointers.

Will load 0 kmers.  Skipping 0 (too low) and 0 (too high) kmers.

Allocating space for 16128 kmer positions.
  suffixes of  34 bits each ->       548352 bits (  0.000 GB) in blocks of  32.000 MB
  values   of   6 bits each ->        96768 bits (  0.000 GB) in blocks of  32.000 MB

Filling buckets.


Loaded 0 kmers.  Skipped 0 (too low) and 0 (too high) kmers.

Opening inputs:
  'Bna_GH06_v1.0.fasta'

Opening outputs:
  '-'

Bye!  (0 seconds to initialize and 8 seconds to compute)

# k-mer completeness (recoveray rate) with solid k-mers for Bna_GH06_v1.0 with > 2 counts

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.gt2.meryl
    output to Bna_GH06_v1.0.solid.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

# Generate Bna_GH06_v1.0_only.wig

Estimating memory usage for 'Bna_GH06_v1.0.0.meryl'.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Memory required:  32.000 GB
Memory limit:     2015.040 GB

Loading kmers from 'Bna_GH06_v1.0.0.meryl' into lookup table.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Counting size of buckets.


Summing bucket sizes.
  block indices are 14 bits wide -- sum lengths 16128 (including 16128 empty pointers)
  block lengths are 0 bits wide -- max length  0

Setting pointers.

Will load 0 kmers.  Skipping 0 (too low) and 0 (too high) kmers.

Allocating space for 16128 kmer positions.
  suffixes of  34 bits each ->       548352 bits (  0.000 GB) in blocks of  32.000 MB
  values   of   6 bits each ->        96768 bits (  0.000 GB) in blocks of  32.000 MB

Filling buckets.


Loaded 0 kmers.  Skipped 0 (too low) and 0 (too high) kmers.

Opening inputs:
  'Bna_GH06_v1.0.fasta'

Opening outputs:
  '-'

Bye!  (0 seconds to initialize and 8 seconds to compute)

Estimating memory usage for 'Bna_GH06_v1.0.0.meryl'.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Memory required:  32.000 GB
Memory limit:     2015.040 GB

Loading kmers from 'Bna_GH06_v1.0.0.meryl' into lookup table.

 p         blocks   ent/blk             bits gigabytes (allowed: 2015 GB)
-- -------------- --------- ---------------- ---------
 6             64         0     274877909952    32.000  (smallest)
 7            128         0     274877912960    32.000
 8            256         0     274877918976    32.000
 9            512         0     274877931008    32.000
10           1024         0     274877955072    32.000
-- -------------- --------- ---------------- ---------
                0 total kmers

For 0 distinct 20-mers (with 6 bits used for indexing and 34 bits for tags):
    0.000 GB memory for block indices -           64 elements 15 bits wide)
    0.000 GB memory for block lengths -           64 elements  0 bits wide)
    0.000 GB memory for kmer tags     -            0 elements 34 bits wide)
    0.000 GB memory for kmer values   -            0 elements  6 bits wide)
   32.000 GB memory for buffers
   32.000 GB memory

Counting size of buckets.


Summing bucket sizes.
  block indices are 14 bits wide -- sum lengths 16128 (including 16128 empty pointers)
  block lengths are 0 bits wide -- max length  0

Setting pointers.

Will load 0 kmers.  Skipping 0 (too low) and 0 (too high) kmers.

Allocating space for 16128 kmer positions.
  suffixes of  34 bits each ->       548352 bits (  0.000 GB) in blocks of  32.000 MB
  values   of   6 bits each ->        96768 bits (  0.000 GB) in blocks of  32.000 MB

Filling buckets.


Loaded 0 kmers.  Skipped 0 (too low) and 0 (too high) kmers.

Opening inputs:
  'Bna_GH06_v1.0.fasta'

Opening outputs:
  '-'

Bye!  (0 seconds to initialize and 8 seconds to compute)
Bna_GH06_v1.0_only.wig generated.

No asm2_fa given. Done.
# Bna_GH06_v1.0 only

Found 1 command tree.

PROCESSING TREE #1 using 64 threads.
  opIntersect
    Bna_GH06_v1.0.meryl
    Bna_GH06_v1.0.meryl
    output to read.k20.Bna_GH06_v1.0.meryl

Cleaning up.

Bye.
# Write output

Found 1 command tree.

Found 1 command tree.
# Get asm only for spectra-asm

Found 1 command tree.
#       Plot Bna_GH06_v1.0.spectra-asm.hist
  Rscript /share/home/yangqingyong/software/merqury/plot/plot_spectra_cn.R -f Bna_GH06_v1.0.spectra-asm.hist -o Bna_GH06_v1.0.spectra-asm -z Bna_GH06_v1.0.dist_only.hist
/share/home/yangqingyong/software/merqury/eval/spectra-cn.sh: line 189: Rscript: command not found

# Clean up
Done!

cat Bna_GH06_v1.0.Bna_GH06_v1.0.qv
chrA01  0       29147546        inf     0
chrA02  0       33047894        inf     0
chrA03  0       37399238        inf     0
chrA04  0       22103731        inf     0
chrA05  0       24907059        inf     0
chrA06  0       29800754        inf     0
chrA07  0       27054433        inf     0
chrA08  0       23149729        inf     0
chrA09  0       47733660        inf     0
chrA10  0       22090406        inf     0
chrC01  0       42472332        inf     0
chrC02  0       51267068        inf     0
chrC03  0       73834858        inf     0
chrC04  0       63559254        inf     0
chrC05  0       55510541        inf     0
chrC06  0       47310606        inf     0
chrC07  0       61208939        inf     0
chrC08  0       50207797        inf     0
chrC09  0       53196269        inf     0
scaffold20      0       1080816 inf     0
scaffold22      0       839079  inf     0
scaffold25      0       764981  inf     0
scaffold30      0       571905  inf     0
scaffold31      0       533924  inf     0
scaffold32      0       499943  inf     0
scaffold33      0       485962  inf     0

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