search

bergmanlab / mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data
93 stars 30 forks source link

Failed to solve conda environment for mcc_relocate2 #113

Closed s-andrews closed 1 year ago

s-andrews commented 1 year ago

I've installed mcclintock and am trying to run the test suite but am getting a failure from trying to build the mcc_relocate2 conda environment.

[andrewss@headstone mcclintock]$ conda activate mcclintock
(mcclintock) [andrewss@headstone mcclintock]$ python3 mcclintock.py \
>     -r test/sacCer2.fasta \
>     -c test/sac_cer_TE_seqs.fasta \
>     -g test/reference_TE_locations.gff \
>     -t test/sac_cer_te_families.tsv \
>     -1 test/SRR800842_1.fastq.gz \
>     -2 test/SRR800842_2.fastq.gz \
>     -p 4 \
>     -o ../test_results/
SETUP            checking fasta: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/sacCer2.fasta
SETUP            checking fastq: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/SRR800842_1.fastq.gz
SETUP            checking fastq: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/SRR800842_2.fastq.gz
SETUP            checking fasta: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/sac_cer_TE_seqs.fasta
SETUP            checking locations gff: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/reference_TE_locations.gff
SETUP            checking taxonomy TSV: /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/test/sac_cer_te_families.tsv
SETUP            McClintock Version: 3ffe2f36cf32e846caab417307a301abd784a9b0
CreateCondaEnvironmentException:
Could not create conda environment from /bi/group/bioinf/Jon_Houseley/McClintock/mcclintock/install/envs/mcc_relocate2.yml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
Building graph of deps:   0%|          | 0/13 [00:00<?, ?it/s]
Examining @/linux-64::__archspec==1=x86_64:   0%|          | 0/13 [00:00<?, ?it/s]
Examining bedtools==2.26.0-0:   8%|▊         | 1/13 [00:00<00:00, 5683.34it/s]
Examining perl[version='>=5.26.2,<5.26.3.0a0']:  15%|█▌        | 2/13 [00:00<00:00, 1219.45it/s]
Examining blat==35:  23%|██▎       | 3/13 [00:00<00:00, 56.19it/s]
Examining pysam==0.9.0:  31%|███       | 4/13 [00:00<00:00, 67.75it/s]
Examining samtools==1.3-0:  38%|███▊      | 5/13 [00:00<00:00, 20.45it/s]
Examining samtools==1.3-0:  46%|████▌     | 6/13 [00:00<00:00, 24.53it/s]
Examining @/linux-64::__glibc==2.17=0:  46%|████▌     | 6/13 [00:00<00:00, 24.53it/s]
Examining seqtk==1.2-0:  54%|█████▍    | 7/13 [00:00<00:00, 24.53it/s]
Examining @/linux-64::__unix==0=0:  62%|██████▏   | 8/13 [00:00<00:00, 24.53it/s]
Examining bowtie2==2.2.8:  69%|██████▉   | 9/13 [00:00<00:00, 24.53it/s]
Examining @/linux-64::__linux==3.10.0=0:  77%|███████▋  | 10/13 [00:00<00:00, 24.53it/s]
Examining @/linux-64::__linux==3.10.0=0:  85%|████████▍ | 11/13 [00:00<00:00, 30.06it/s]
Examining python==2.7.12:  85%|████████▍ | 11/13 [00:00<00:00, 30.06it/s]
Examining bwa==0.6.2-0:  92%|█████████▏| 12/13 [00:00<00:00, 30.06it/s]

Determining conflicts:   0%|          | 0/13 [00:00<?, ?it/s]
Examining conflict for bedtools samtools pysam blat seqtk python bwa:   0%|          | 0/13 [00:00<?, ?it/s]
Examining conflict for bowtie2 bedtools pysam bwa:   8%|▊         | 1/13 [00:00<00:01,  6.10it/s]
Examining conflict for bowtie2 bedtools pysam bwa:  15%|█▌        | 2/13 [00:00<00:00, 12.18it/s]
Examining conflict for bedtools pysam perl blat samtools seqtk bowtie2 python bwa:  15%|█▌        | 2/13 [00:00<00:00, 12.18it/s]
Examining conflict for bedtools samtools pysam bowtie2 bwa:  23%|██▎       | 3/13 [00:00<00:00, 12.18it/s]
Examining conflict for bedtools samtools pysam bowtie2 bwa:  31%|███       | 4/13 [00:00<00:01,  6.91it/s]
Examining conflict for bedtools samtools pysam blat seqtk bowtie2 python bwa:  31%|███       | 4/13 [00:00<00:01,  6.91it/s]
Examining conflict for bedtools samtools pysam blat seqtk bowtie2 python bwa:  38%|███▊      | 5/13 [00:00<00:01,  6.52it/s]
Examining conflict for pysam bowtie2 perl:  38%|███▊      | 5/13 [00:00<00:01,  6.52it/s]
Examining conflict for pysam bowtie2 perl:  46%|████▌     | 6/13 [00:00<00:01,  6.21it/s]
Examining conflict for samtools perl bwa:  46%|████▌     | 6/13 [00:00<00:01,  6.21it/s]
Examining conflict for samtools perl bwa:  54%|█████▍    | 7/13 [00:00<00:00,  6.99it/s]
Examining conflict for samtools perl bwa __glibc:  54%|█████▍    | 7/13 [00:01<00:00,  6.99it/s]
Examining conflict for samtools perl bwa __glibc:  62%|██████▏   | 8/13 [00:01<00:00,  6.99it/s]
Examining conflict for bowtie2 python pysam:  62%|██████▏   | 8/13 [00:01<00:00,  6.99it/s]
Examining conflict for samtools pysam:  69%|██████▉   | 9/13 [00:01<00:00,  6.99it/s]
Examining conflict for samtools pysam:  77%|███████▋  | 10/13 [00:01<00:00,  8.51it/s]
Examining conflict for samtools bowtie2 pysam python:  77%|███████▋  | 10/13 [00:01<00:00,  8.51it/s]
Examining conflict for bowtie2 pysam:  85%|████████▍ | 11/13 [00:01<00:00,  8.51it/s]
Examining conflict for bowtie2 pysam:  92%|█████████▏| 12/13 [00:01<00:00,  7.42it/s]

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed
Solving environment: ...working...

Building graph of deps:   0%|          | 0/13 [00:00<?, ?it/s]
Examining @/linux-64::__archspec==1=x86_64:   0%|          | 0/13 [00:00<?, ?it/s]
Examining bedtools==2.26.0-0:   8%|▊         | 1/13 [00:00<00:00, 6955.73it/s]
Examining perl[version='>=5.26.2,<5.26.3.0a0']:  15%|█▌        | 2/13 [00:00<00:00, 1558.35it/s]
Examining blat==35:  23%|██▎       | 3/13 [00:00<00:00, 56.66it/s]
Examining pysam==0.9.0:  31%|███       | 4/13 [00:00<00:00, 68.13it/s]
Examining samtools==1.3-0:  38%|███▊      | 5/13 [00:00<00:00, 20.58it/s]
Examining samtools==1.3-0:  46%|████▌     | 6/13 [00:00<00:00, 24.69it/s]
Examining @/linux-64::__glibc==2.17=0:  46%|████▌     | 6/13 [00:00<00:00, 24.69it/s]
Examining seqtk==1.2-0:  54%|█████▍    | 7/13 [00:00<00:00, 24.69it/s]
Examining @/linux-64::__unix==0=0:  62%|██████▏   | 8/13 [00:00<00:00, 24.69it/s]
Examining bowtie2==2.2.8:  69%|██████▉   | 9/13 [00:00<00:00, 24.69it/s]
Examining @/linux-64::__linux==3.10.0=0:  77%|███████▋  | 10/13 [00:00<00:00, 24.69it/s]
Examining @/linux-64::__linux==3.10.0=0:  85%|████████▍ | 11/13 [00:00<00:00, 30.07it/s]
Examining python==2.7.12:  85%|████████▍ | 11/13 [00:00<00:00, 30.07it/s]
Examining bwa==0.6.2-0:  92%|█████████▏| 12/13 [00:00<00:00, 30.07it/s]

Determining conflicts:   0%|          | 0/13 [00:00<?, ?it/s]
Examining conflict for bedtools samtools pysam blat seqtk python bwa:   0%|          | 0/13 [00:00<?, ?it/s]
Examining conflict for bowtie2 bedtools pysam bwa:   8%|▊         | 1/13 [00:00<00:02,  5.90it/s]
Examining conflict for bowtie2 bedtools pysam bwa:  15%|█▌        | 2/13 [00:00<00:00, 11.79it/s]
Examining conflict for bedtools pysam perl blat samtools seqtk bowtie2 python bwa:  15%|█▌        | 2/13 [00:00<00:00, 11.79it/s]
Examining conflict for bedtools samtools pysam bowtie2 bwa:  23%|██▎       | 3/13 [00:00<00:00, 11.79it/s]
Examining conflict for bedtools samtools pysam bowtie2 bwa:  31%|███       | 4/13 [00:00<00:01,  6.73it/s]
Examining conflict for bedtools samtools pysam blat seqtk bowtie2 python bwa:  31%|███       | 4/13 [00:00<00:01,  6.73it/s]
Examining conflict for bedtools samtools pysam blat seqtk bowtie2 python bwa:  38%|███▊      | 5/13 [00:00<00:01,  6.33it/s]
Examining conflict for pysam bowtie2 perl:  38%|███▊      | 5/13 [00:00<00:01,  6.33it/s]
Examining conflict for pysam bowtie2 perl:  46%|████▌     | 6/13 [00:00<00:01,  6.01it/s]
Examining conflict for samtools perl bwa:  46%|████▌     | 6/13 [00:01<00:01,  6.01it/s]
Examining conflict for samtools perl bwa:  54%|█████▍    | 7/13 [00:01<00:00,  6.75it/s]
Examining conflict for samtools perl bwa __glibc:  54%|█████▍    | 7/13 [00:01<00:00,  6.75it/s]
Examining conflict for samtools perl bwa __glibc:  62%|██████▏   | 8/13 [00:01<00:00,  6.76it/s]
Examining conflict for bowtie2 python pysam:  62%|██████▏   | 8/13 [00:01<00:00,  6.76it/s]
Examining conflict for samtools pysam:  69%|██████▉   | 9/13 [00:01<00:00,  6.76it/s]
Examining conflict for samtools pysam:  77%|███████▋  | 10/13 [00:01<00:00,  8.26it/s]
Examining conflict for samtools bowtie2 pysam python:  77%|███████▋  | 10/13 [00:01<00:00,  8.26it/s]
Examining conflict for bowtie2 pysam:  85%|████████▍ | 11/13 [00:01<00:00,  8.26it/s]
Examining conflict for bowtie2 pysam:  92%|█████████▏| 12/13 [00:01<00:00,  7.23it/s]

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package isl conflicts for:
bedtools==2.26.0-0 -> libgcc -> isl
bowtie2==2.2.8 -> libgcc -> isl
bwa==0.6.2-0 -> libgcc -> isl
pysam==0.9.0 -> libgcc -> isl

Package zlib conflicts for:
python==2.7.12 -> zlib=1.2
blat==35 -> libpng -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|1.2.8|>=1.2.13,<1.3.0a0']
bowtie2==2.2.8 -> python=3.5 -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|1.2.11.*|1.2.8']
blat==35 -> zlib=1.2.11
bedtools==2.26.0-0 -> zlib
pysam==0.9.0 -> bcftools==1.3 -> zlib[version='1.2.*|1.2.11|1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0|1.2.8.*']
bwa==0.6.2-0 -> zlib[version='1.2.8.*|>=1.2.11,<1.3.0a0']
seqtk==1.2-0 -> zlib=1.2.11
samtools==1.3-0 -> zlib[version='>=1.2.11,<1.3.0a0']

Package _libgcc_mutex conflicts for:
samtools==1.3-0 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge|main']
bwa==0.6.2-0 -> libgcc-ng[version='>=4.9'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge|main']
perl[version='>=5.26.2,<5.26.3.0a0'] -> libgcc-ng[version='>=7.2.0'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge|main']

Package libzlib conflicts for:
blat==35 -> libpng -> libzlib[version='1.2.11|1.2.11|1.2.11|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|1.2.13|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12',build='h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_4']
bedtools==2.26.0-0 -> zlib -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_1|h166bdaf_3|h166bdaf_4|h166bdaf_2|h166bdaf_0']
seqtk==1.2-0 -> zlib=1.2.11 -> libzlib[version='1.2.11|1.2.13|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12',build='h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_4']
bwa==0.6.2-0 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_1|h166bdaf_3|h166bdaf_4|h166bdaf_2|h166bdaf_0']
samtools==1.3-0 -> libzlib[version='>=1.2.11,<1.3.0a0']
python==2.7.12 -> zlib=1.2 -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_1|h166bdaf_3|h166bdaf_4|h166bdaf_2|h166bdaf_0']
samtools==1.3-0 -> curl[version='>=7.81.0,<8.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h36c2ea0_1012|h36c2ea0_1013|h166bdaf_1014|h166bdaf_1|h166bdaf_3|h166bdaf_4|h166bdaf_2|h166bdaf_0']
pysam==0.9.0 -> bcftools==1.3 -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']

Package samtools conflicts for:
pysam==0.9.0 -> samtools==1.3
samtools==1.3-0

Package openssl conflicts for:
samtools==1.3-0 -> curl[version='>=7.81.0,<8.0a0'] -> openssl[version='>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.0.8,<4.0a0|>=3.1.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0']
samtools==1.3-0 -> openssl[version='>=1.1.0,<=1.1.1|>=1.1.1l,<1.1.2a']

Package libffi conflicts for:
pysam==0.9.0 -> python=3.5 -> libffi[version='3.2.*|>=3.2.1,<4.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.4,<3.5|>=3.4,<4.0a0']
bowtie2==2.2.8 -> python=3.5 -> libffi[version='3.2.*|>=3.2.1,<4.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.4,<3.5|>=3.4,<4.0a0']

Package libgcc-ng conflicts for:
bwa==0.6.2-0 -> libgcc-ng[version='>=4.9']
bwa==0.6.2-0 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0|>=12|>=10.3.0']
samtools==1.3-0 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0|>=7.3.0']
pysam==0.9.0 -> bcftools==1.3 -> libgcc-ng[version='7.2.0.*|>=10.3.0|>=9.3.0|>=7.3.0|>=4.9|>=7.2.0|>=7.5.0|>=11.2.0|>=12|>=9.4.0']
bowtie2==2.2.8 -> libgcc -> libgcc-ng[version='7.2.0.*|>=7.2.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0']
python==2.7.12 -> openssl=1.0 -> libgcc-ng[version='7.2.0.*|>=7.2.0|>=7.3.0|>=4.9|>=11.2.0|>=7.5.0|>=12|>=10.3.0']
blat==35 -> libpng -> libgcc-ng[version='7.2.0.*|>=7.2.0|>=7.3.0|>=12|>=7.5.0|>=4.9|>=11.2.0|>=10.3.0']
perl[version='>=5.26.2,<5.26.3.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.5.0|>=7.3.0']
bedtools==2.26.0-0 -> libgcc -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=7.2.0|>=7.5.0|>=7.3.0|>=12|>=10.3.0|>=4.9']
samtools==1.3-0 -> curl[version='>=7.81.0,<8.0a0'] -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=12|>=9.4.0|>=7.2.0|>=4.9']
seqtk==1.2-0 -> zlib=1.2.11 -> libgcc-ng[version='7.2.0.*|>=7.3.0|>=7.5.0|>=7.2.0|>=10.3.0|>=4.9|>=11.2.0|>=12']

Package libstdcxx-ng conflicts for:
samtools==1.3-0 -> ncurses -> libstdcxx-ng[version='7.2.0.*|>=7.2.0|>=7.3.0|>=7.5.0|>=4.9']
bedtools==2.26.0-0 -> libgcc -> libstdcxx-ng[version='>=7.2.0']
bwa==0.6.2-0 -> libgcc -> libstdcxx-ng[version='>=7.2.0']
bowtie2==2.2.8 -> libgcc -> libstdcxx-ng[version='7.2.0.*|>=7.2.0|>=7.5.0|>=7.3.0|>=4.9']
pysam==0.9.0 -> libgcc -> libstdcxx-ng[version='7.2.0.*|>=7.2.0|>=7.5.0|>=7.3.0|>=4.9']

Package perl conflicts for:
perl[version='>=5.26.2,<5.26.3.0a0']
pysam==0.9.0 -> bcftools -> perl
bowtie2==2.2.8 -> perl-threaded -> perl[version='5.22.0.*|>=5.22.0,<5.23.0']

Package ncurses conflicts for:
bowtie2==2.2.8 -> python=3.5 -> ncurses[version='5.9.*|5.9|6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0.0a0|>=6.3,<7.0a0']
python==2.7.12 -> ncurses=5.9
pysam==0.9.0 -> python=3.5 -> ncurses[version='5.9.*|5.9|6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0.0a0|>=6.3,<7.0a0|>=6.2,<6.3.0a0|>=6.1,<6.2.0a0|>=5.9,<5.10.0a0']
samtools==1.3-0 -> ncursesThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0
  - bwa==0.6.2-0 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
  - perl[version='>=5.26.2,<5.26.3.0a0'] -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
  - samtools==1.3-0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

  File "/bi/home/andrewss/mambaforge/envs/mcclintock/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create

Any suggestions would be very welcome - thanks.

s-andrews commented 1 year ago

This is with a fresh install of mamba:

$ mamba --version
mamba 1.4.1
conda 23.1.0

I'm running on CentOS7. The set of installed packages in the environment is:

$ conda list
# packages in environment at /bi/home/andrewss/mambaforge/envs/mcclintock:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aioeasywebdav             2.4.0           py38h578d9bd_1001    conda-forge
aiohttp                   3.7.4.post0      py38h497a2fe_1    conda-forge
amply                     0.1.5              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
art                       2016.06.05           h589041f_9    bioconda
async-timeout             3.0.1                   py_1000    conda-forge
atk                       2.36.0               ha770c72_4    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attmap                    0.13.2             pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bcrypt                    3.2.2            py38h0a891b7_1    conda-forge
bedtools                  2.30.0               h468198e_3    bioconda
biopython                 1.77             py38h1e0a361_1    conda-forge
boto3                     1.26.126           pyhd8ed1ab_0    conda-forge
botocore                  1.29.126           pyhd8ed1ab_0    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cachetools                5.3.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.14.4           py38ha312104_0    conda-forge
chardet                   4.0.0            py38h578d9bd_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
coin-or-cbc               2.10.10              h9002f0b_0    conda-forge
coin-or-cgl               0.60.7               h516709c_0    conda-forge
coin-or-clp               1.17.8               h1ee7a9c_0    conda-forge
coin-or-osi               0.108.8              ha2443b9_0    conda-forge
coin-or-utils             2.11.9               hee58242_0    conda-forge
coincbc                   2.10.10           0_metapackage    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     4.12.0           py38h578d9bd_0    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
configargparse            1.5.3              pyhd8ed1ab_0    conda-forge
cryptography              39.0.0           py38h1724139_0    conda-forge
curl                      7.87.0               h6312ad2_0    conda-forge
datrie                    0.8.2            py38h0a891b7_6    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.19             py38h578d9bd_1    conda-forge
dropbox                   11.36.0            pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fftw                      3.3.10          nompi_hc118613_107    conda-forge
filechunkio               1.8                        py_2    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
ftputil                   5.0.4              pyhd8ed1ab_0    conda-forge
gdk-pixbuf                2.42.2               h19a9c64_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
ghostscript               9.18                          1    bioconda
giflib                    5.2.1                h0b41bf4_3    conda-forge
git                       2.23.0          pl526hce37bd2_2    conda-forge
gitdb                     4.0.10             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.31             pyhd8ed1ab_0    conda-forge
glib                      2.66.3               h58526e2_0    conda-forge
gobject-introspection     1.66.1           py38h4eacb9c_3    conda-forge
google-api-core           2.11.0             pyhd8ed1ab_0    conda-forge
google-api-python-client  2.86.0             pyhd8ed1ab_0    conda-forge
google-auth               2.17.3             pyh1a96a4e_0    conda-forge
google-auth-httplib2      0.1.0              pyhd8ed1ab_1    conda-forge
google-cloud-core         2.3.2              pyhd8ed1ab_0    conda-forge
google-cloud-storage      2.8.0              pyh1a96a4e_0    conda-forge
google-crc32c             1.1.2            py38h57c428a_4    conda-forge
google-resumable-media    2.5.0              pyhd8ed1ab_0    conda-forge
googleapis-common-protos  1.57.1             pyhd8ed1ab_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  2.42.3               h6939c30_2    conda-forge
grpcio                    1.51.1           py38h7dc2bf5_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gtk2                      2.24.32              h90f3771_0    conda-forge
gts                       0.7.6                h1fc3fae_2    conda-forge
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
htslib                    1.17                 h6bc39ce_0    bioconda
httplib2                  0.22.0             pyhd8ed1ab_0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagemagick               7.0.10_28       pl5262hd815ba0_2    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0            py38h578d9bd_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.20.1               hf9c8cef_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libabseil                 20220623.0      cxx17_h05df665_6    conda-forge
libarchive                3.5.2                hb890918_3    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.87.0               h6312ad2_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.66.3               hbe7bbb4_0    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libgrpc                   1.51.1               h05bd8bd_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
liblapacke                3.9.0           16_linux64_openblas    conda-forge
libmamba                  0.21.2               h3985d26_0    conda-forge
libmambapy                0.21.2           py38h908000c_0    conda-forge
libnghttp2                1.51.0               hdcd2b5c_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libprotobuf               3.21.12              h3eb15da_0    conda-forge
librsvg                   2.50.2               h3442318_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.23               h3eb15da_0    conda-forge
libsqlite                 3.40.0               h753d276_1    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.2.0                hf544144_3    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.2.0                h3452ae3_0    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.9.14               h74e7548_0
libzlib                   1.2.13               h166bdaf_4    conda-forge
logmuse                   0.2.6              pyh8c360ce_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     0.21.2           py38h1abaa86_0    conda-forge
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2            py38h1de0b5d_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
multidict                 6.0.4            py38h1de0b5d_0    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
numpy                     1.24.3           py38h59b608b_0    conda-forge
oauth2client              4.1.3                      py_0    conda-forge
openjpeg                  2.3.1                hf7af979_3    conda-forge
openssl                   1.1.1t               h0b41bf4_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    2.0.1            py38h01efb38_0    conda-forge
pango                     1.42.4               h7062337_4    conda-forge
paramiko                  3.1.0              pyhd8ed1ab_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
peppy                     0.35.5             pyhd8ed1ab_0    conda-forge
perl                      5.26.2            h36c2ea0_1008    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.5.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
prettytable               3.7.0              pyhd8ed1ab_0    conda-forge
protobuf                  4.21.12          py38h8dc9893_0    conda-forge
psutil                    5.9.5            py38h1de0b5d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pulp                      2.7.0            py38h578d9bd_0    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4            py38h0a891b7_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.15.1             pyhd8ed1ab_0    conda-forge
pygraphviz                1.7              py38h0d738da_0    conda-forge
pynacl                    1.5.0            py38h0a891b7_2    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py38h1de0b5d_0    conda-forge
pysftp                    0.2.9                      py_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.3.1              pyhd8ed1ab_0    conda-forge
python                    3.8.2           he5300dc_7_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-irodsclient        1.1.6              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_5    conda-forge
ratelimiter               1.2.0           pyhd8ed1ab_1003    conda-forge
re2                       2022.06.01           h27087fc_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
reproc                    14.2.4               h0b41bf4_0    conda-forge
reproc-cpp                14.2.4               hcb278e6_0    conda-forge
requests                  2.29.0             pyhd8ed1ab_0    conda-forge
rich                      13.3.5             pyhd8ed1ab_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
ruamel_yaml               0.15.80         py38h0a891b7_1008    conda-forge
s3transfer                0.6.0              pyhd8ed1ab_0    conda-forge
samtools                  1.17                 h00cdaf9_0    bioconda
seqtk                     1.3                  h7132678_4    bioconda
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
slacker                   0.14.0                     py_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snakemake                 5.32.0                        0    bioconda
snakemake-minimal         5.32.0                     py_0    bioconda
sqlite                    3.40.0               h4ff8645_1    conda-forge
stone                     3.3.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toposort                  1.10               pyhd8ed1ab_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
ubiquerg                  0.6.2              pyhd8ed1ab_0    conda-forge
unzip                     6.0                  h7f98852_3    conda-forge
uritemplate               4.1.1              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
veracitools               0.1.3                      py_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
wgsim                     1.0                  h7132678_5    bioconda
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.15.0           py38h1de0b5d_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxpm               3.5.13               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.6.3                he1b5a44_4    conda-forge
yarl                      1.9.1            py38h01eb140_0    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstandard                 0.19.0           py38h5945529_1    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge
cbergman commented 1 year ago

Hi @s-andrews

We just recently identified this bug (or a related one) and are currently working on a fix to this in the install_fixes branch. If what we have identified is what is causing your issue, the problem is related to a python2.7 version dependency in conda caused by McClintock relying on a bioconda recipe to install Relocate2. For all other component TE detectors McClintock creates its own custom conda environment and installs the component source code directly. We are now changing our installation procedure to install Relocate2 using a custom conda environment so we are less dependent on the Relocate2 bioconda recipe being maintained. We need to do one more set of tests, but should have this solved in the next day or so. I'll update when we have completed our tests and merge the install_fixes branch into the master branch.

One thing I did notice in your logs above: did you run the McClintock component installation command before trying to run McClintock on the test data? https://github.com/bergmanlab/mcclintock/#install-mcclintock-component-methods. In general, there are 3 parts to the installation procedure: 1. install conda/mamba; 2. clone the McClintock repository, create/activate the McClintock conda environment; and 3. install the component methods. Building the component method environments happens at step 3, and is assumed to have been done prior to running McClintock itself.

Hope this helps and more soon.

Best regards, Casey

cbergman commented 1 year ago

Hi @s-andrews

We have completed testing our fixes for the Relocate2 installation error we identified. Can you please try re-installing the entire McClintock 2 system following the instructions here: https://github.com/bergmanlab/mcclintock#-installing-mcclintock? We have not made any changes to the McClintock conda environment, so in principle you should be able to do a clean install using the updated code as follows:

cd mcclintock
git pull
conda activate mcclintock
python3 mcclintock.py --install

Please let us know if this solves your installation problem for Relocate2.

Many thanks, Casey

cbergman commented 1 year ago

Hi @s-andrews

Could you let us know if this issue is resolved on your side? Otherwise, we'll assume it is solved and close at the end of the month.

Best regards, Casey

s-andrews commented 1 year ago

The fix for the relocate package worked and we were able to get that to run. I still couldn't get the entire test set to work as there was a separate issue with the TEMP2 program where it would just hang indefinitely, but if I excluded that then I could get the rest to run. I never went back to debug that as we'd got what we needed from our data by that stage.

I've got the logs from an isolated failed run of TEMP2 and have put them up at http://ftp1.babraham.ac.uk/ftpusr50/ (for the next 2 weeks) if you want to take a look.

Thanks for your help with this.

cbergman commented 1 year ago

Thanks Simon. I'll go ahead and close this issue then and look into the TEMP2 logs you posted.

Best regards, Casey