Step3: IndexError: string index out of range

[ckiel3]

Hi I have recently moved to using a new cluster. I am using version: ipyrad [v.0.9.95] on a cluster using 20 cores

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection | a002.hpc.pomona.edu: 20 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:01:14 | dereplicating
[####################] 100% 0:34:11 | clustering/mapping
[####################] 100% 0:00:00 | building clusters
[####################] 100% 0:00:00 | chunking clusters
[####################] 100% 6:12:57 | aligning clusters

Encountered an Error.

Message: IndexError: string index out of range

I'm using a denovo assembly with 83 samples ddradseq data. I've used ipyrad a lot previously. I'm wondering is this an issue with memory allocation or version.

[isaacovercast]

Can you run it again and include the -d parameter to print debug information. Please paste the full debug output here. Also if you can include your params file that would be helpful.

[ckiel3]

CYL_1_2 ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps ./ ## [1] [project_dir]: Project dir (made in curdir if not present)

[2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files

~/ondemand/data/CYL/Barcodes_CYL_1.txt ## [3] [barcodes_path]: Location of barcodes file ~/ondemand/data/CYL/CYL_1_fastqs/*.fastq.gz ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files denovo ## [5] [assembly_method]: Assembly method (denovo, reference)

[6] [reference_sequence]: Location of reference sequence file

ddrad ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc. AATT, TAA ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2) 5 ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read 33 ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard) 6 ## [11] [mindepth_statistical]: Min depth for statistical base calling 6 ## [12] [mindepth_majrule]: Min depth for majority-rule base calling 10000 ## [13] [maxdepth]: Max cluster depth within samples 0.85 ## [14] [clust_threshold]: Clustering threshold for de novo assembly 1 ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes 0 ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter) 35 ## [17] [filter_min_trim_len]: Min length of reads after adapter trim 2 ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences 0.05 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus 0.05 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus 8 ## [21] [min_samples_locus]: Min # samples per locus for output 0.25 ## [22] [max_SNPs_locus]: Max # SNPs per locus 4 ## [23] [max_Indels_locus]: Max # of indels per locus 0.5 ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus 0, 0, 0, 0 ## [25] [trim_reads]: Trim raw read edges (R1>, <R1, R2>, <R2) (see docs) 0, 0, 0, 0 ## [26] [trim_loci]: Trim locus edges (see docs) (R1>, <R1, R2>, <R2)

• [27] [output_formats]: Output formats (see docs)

                         ## [28] [pop_assign_file]: Path to population assignment file
                         ## [29] [reference_as_filter]: Reads mapped to this reference are removed in step 3

I also reran with the -d command in the slurm script.

!/bin/bash

SBATCH -p amd

SBATCH --nodes=1

SBATCH --ntasks-per-node=20

SBATCH --mem-per-cpu=5G

SBATCH --time=10-00:15:00

SBATCH --mail-user=XXXXXXX

SBATCH --mail-type=ALL

SBATCH --job-name="CYL_1_2_1_assembly"

SBATCH --output="CYL_1_2_1_assembly"

ipyrad -p ~/ondemand/data/CYL/params_CYL1.txt -d -s 1234567 -f -c 20 --MPI

[ckiel3]

Encountered an Error. Message: IndexError: string index out of range Parallel connection closed.

IndexError Traceback (most recent call last) File ~/.conda/envs/ipyrad/lib/python3.10/site-packages/ipyrad/assemble/clustmap.py:1496, in persistent_popen_align3(clusts, maxseqs, is_gbs) 1493 lclust1 = list(chain(zip( 1494 lclust[::2], [i.split("nnnn")[0] for i in lclust[1::2]]))) 1495 lclust2 = list(chain(zip( -> 1496 lclust[::2], [i.split("nnnn")[1] for i in lclust[1::2]]))) 1498 # put back into strings

File ~/.conda/envs/ipyrad/lib/python3.10/site-packages/ipyrad/assemble/clustmap.py:1496, in (.0) 1493 lclust1 = list(chain(zip( 1494 lclust[::2], [i.split("nnnn")[0] for i in lclust[1::2]]))) 1495 lclust2 = list(chain(zip( -> 1496 lclust[::2], [i.split("nnnn")[1] for i in lclust[1::2]]))) 1498 # put back into strings

IndexError: list index out of range

During handling of the above exception, another exception occurred:

IndexError Traceback (most recent call last) File :1

File ~/.conda/envs/ipyrad/lib/python3.10/site-packages/ipyrad/assemble/clustmap.py:1405, in align_and_parse(handle, max_internal_indels, is_gbs, declone) 1402 nwodups = 0 1404 # iterate over clusters sending each to muscle, splits and aligns pairs -> 1405 aligned = persistent_popen_align3(clusts, 200, is_gbs) 1407 # store good alignments to be written to file 1408 refined = []

File ~/.conda/envs/ipyrad/lib/python3.10/site-packages/ipyrad/assemble/clustmap.py:1581, in persistent_popen_align3(clusts, maxseqs, is_gbs) 1577 lines = "".join(align1)[1:].split("\n>") 1579 ## find seed of the cluster and put it on top. 1580 #seed = [i for i in lines if i.split(";")[-1][0] == ""][0] -> 1581 seed = [i for i in lines if i.split('\n')[0][-1] == ""][0] 1582 lines.pop(lines.index(seed)) 1583 lines = [seed] + sorted( 1584 lines, key=get_derep_num, reverse=True)

File ~/.conda/envs/ipyrad/lib/python3.10/site-packages/ipyrad/assemble/clustmap.py:1581, in (.0) 1577 lines = "".join(align1)[1:].split("\n>") 1579 ## find seed of the cluster and put it on top. 1580 #seed = [i for i in lines if i.split(";")[-1][0] == ""][0] -> 1581 seed = [i for i in lines if i.split('\n')[0][-1] == ""][0] 1582 lines.pop(lines.index(seed)) 1583 lines = [seed] + sorted( 1584 lines, key=get_derep_num, reverse=True)

IndexError: string index out of range

[isaacovercast]

Can you show me the version of muscle? muscle -v. There are known issues with the latest version of muscle (v5), so we have pinned muscle to v3, but sometimes the dependency pinning doesn't work.

[ckiel3]

(ipyrad2) [ckzq2024@sagehen CYL]$ muscle -v Invalid command line option "v"

MUSCLE v3.8.1551 by Robert C. Edgar

I also wiped my old miniconda3 - reinstalled it in a clean install environment, and reran it and it failed at the same point.

[isaacovercast]

What about vsearch? vsearch -v. Sometimes vsearch updates change formatting of things that breaks ipyrad. I am running with vsearch 2.18.0 and it works fine.

If it's not this I might ask you to transfer (wetransfer/ftp/dropbox) me some/all of the raw data for the samples so I can take a look myself. The error is buried deep in the code, so I will need to take a closer look.

[ckiel3]

vsearch v2.28.1_linux_x86_64, 125.2GB RAM, 64 cores

https://github.com/torognes/vsearch

Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016)

VSEARCH: a versatile open source tool for metagenomics

PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584

Compiled with support for gzip-compressed files, and the library is loaded.

zlib version 1.2.13, compile flags a9

Compiled with support for bzip2-compressed files, and the library is loaded.

On Fri, Jul 5, 2024 at 1:18 PM Isaac Overcast @.***> wrote:

What about vsearch? vsearch -v. Sometimes vsearch updates change formatting of things that breaks ipyrad. I am running with vsearch 2.18.0 and it works fine.

If it's not this I might ask you to transfer (wetransfer/ftp/dropbox) me some/all of the raw data for the samples so I can take a look myself. The error is buried deep in the code, so I will need to take a closer look.

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2211371047, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYIPG3L7CRUSFCXVAUDZK35PPAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRGM3TCMBUG4 . You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

That is probably fine. Have you run this same data on a different cluster and it worked fine? Or you've never run this data before?

What do you think about transfering (wetransfer/ftp/dropbox) me some/all of the raw data for the samples so I can take a look myself?

[ckiel3]

Hi Issac. I'm running the data on a different cluster right now (older version of ipyrad and associated programs and miniconda). I'm currently in the process of switching clusters so I won't have access much longer. Hopefully we'll be able to figure it out.

This is the first time running this data set. It demultiplexed well. How do you prefer I sent the data to you? I have dropbox as well.

Thank you!

On Fri, Jul 5, 2024 at 2:54 PM Isaac Overcast @.***> wrote:

That is probably fine. Have you run this same data on a different cluster and it worked fine? Or you've never run this data before?

What do you think about transfering (wetransfer/ftp/dropbox) me some/all of the raw data for the samples so I can take a look myself?

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2211450991, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYKR4SDKDM2FW4FCHULZK4IYFAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRGQ2TAOJZGE . You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

Dropbox is fine.

To be sure, you have not yet run this data on the older cluster with the older ipyrad version, right?

[isaacovercast]

If u send the raw data please share the barcodes file as well

[ckiel3]

Hi Issac I’m currently running the dataset on the other cluster. It’s on step 3 at this moment - I am using the same demultiplexed fastq files as I did on the failed run. You should now have the dropbox invite. I'm also uploading the raw data file but that transfer will take a little time. Perhaps something happened in the demuliplexing process and I need to start from scratch?

thank you again.

Carrie

On Fri, Jul 5, 2024 at 4:10 PM Isaac Overcast @.***> wrote:

If u send the raw data please share the barcodes file as well

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2211494913, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYMZNYTWTLIECRBP37LZK4RXLAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRGQ4TIOJRGM . You are receiving this because you authored the thread.Message ID: @.***>

[ckiel3]

Hi Issac. it worked on a different cluster and with an older ipyrad that I installed awhile back ipyrad = - v.0.9.93, vesearch = v2.14.1, MUSCLE = v3.8.1551

I really hope to get this to work on the newer cluster that I'm on. Is it possible to install an older version of ipyrad and associated packages? maybe it's the version of python that I am using for the base environment? 3.74 is the one in my base on the older cluster vs 3.12.4 on the new cluster.

Thank you again for your time and effort.

---

ipyrad [v.0.9.93]

Interactive assembly and analysis of RAD-seq data

---

Parallel connection | c27: 20 cores

Step 1: Loading sorted fastq data to Samples

[####################] 100% 0:01:18 | loading reads

83 fastq files loaded to 83 Samples.

Step 2: Filtering and trimming reads

[####################] 100% 0:17:14 | processing reads

Step 3: Clustering/Mapping reads within samples

[####################] 100% 0:01:53 | dereplicating

[####################] 100% 1:58:12 | clustering/mapping

[####################] 100% 0:00:04 | building clusters

[####################] 100% 0:00:00 | chunking clusters

[####################] 100% 7:15:16 | aligning clusters

[####################] 100% 0:00:10 | concat clusters

[####################] 100% 0:00:20 | calc cluster stats

Step 4: Joint estimation of error rate and heterozygosity

[####################] 100% 0:01:47 | inferring [H, E]

Step 5: Consensus base/allele calling

Mean error [0.00439 sd=0.00104]

Mean hetero [0.03665 sd=0.00288]

[####################] 100% 0:00:16 | calculating depths

[####################] 100% 0:00:31 | chunking clusters

[####################] 100% 0:53:17 | consens calling

[####################] 100% 0:00:43 | indexing alleles

Step 6: Clustering/Mapping across samples

[####################] 100% 0:01:23 | concatenating inputs

[####################] 100% 1:01:01 | clustering across

[####################] 100% 0:01:11 | building clusters

[####################] 100% 0:21:02 | aligning clusters

Step 7: Filtering and formatting output files

[####################] 100% 0:00:36 | applying filters

[####################] 100% 0:02:12 | building arrays

[####################] 100% 0:01:24 | writing conversions

[####################] 100% 0:04:55 | indexing vcf depths

[####################] 100% 0:04:00 | writing vcf output

On Fri, Jul 5, 2024 at 4:43 PM Carrie Kiel @.***> wrote:

Hi Issac I’m currently running the dataset on the other cluster. It’s on step 3 at this moment - I am using the same demultiplexed fastq files as I did on the failed run. You should now have the dropbox invite. I'm also uploading the raw data file but that transfer will take a little time. Perhaps something happened in the demuliplexing process and I need to start from scratch?

thank you again.

Carrie

On Fri, Jul 5, 2024 at 4:10 PM Isaac Overcast @.***> wrote:

If u send the raw data please share the barcodes file as well

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2211494913, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYMZNYTWTLIECRBP37LZK4RXLAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRGQ4TIOJRGM . You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

Hello,

Ok, so I ran your data through step 3 and I can't reproduce the error (step 3 ran to completion).

python 3.10.12, ipyrad 0.9.95, vsearch 2.23.0, muscle 3.8.1551

One thing you could try is creating a new python env with 3.10, I have not tested ipyrad with python 3.12 (I am surprised all the dependencies installed actually), so it could be a python 3.12 issue.

conda create -n ipyrad_py310 python=3.10

I will try to test with 3.12 and simulated data. <- It runs on simulated data fine. I will try running your data on 3.12.

[isaacovercast]

I don't know what's happening on your new cluster, but I can't reproduce this error. I ran it on python 3.12.3 with a clean conda install and step 3 ran without error.

 -------------------------------------------------------------
  ipyrad [v.0.9.96]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  Parallel connection | ___: 30 cores

  Step 3: Clustering/Mapping reads within samples
  [####################] 100% 0:00:37 | dereplicating
  [####################] 100% 0:34:21 | clustering/mapping
  [####################] 100% 0:00:00 | building clusters
  [####################] 100% 0:00:00 | chunking clusters
  [####################] 100% 0:34:06 | aligning clusters
  [####################] 100% 0:00:06 | concat clusters
  [####################] 100% 0:00:06 | calc cluster stats
  Parallel connection closed.

Can you post the output of conda list inside the ipyrad environment? I really can't think of why this would be happening inside a clean install on another cluster. Perhaps there's a problem with the environment, sometimes HPC systems will put directories in your PATH that conflict or step on conda stuff.

[ckiel3]

Hi Issac attached is my clean install / I also wiped my miniconda3 and created a new environment and look how slow step one is going with python 3.10. See attached

On Mon, Jul 8, 2024 at 10:35 AM Isaac Overcast @.***> wrote:

I don't know what's happening on your new cluster, but I can't reproduce this error. I ran it on python 3.12.3 with a clean conda install and step 3 ran without error.

---

ipyrad [v.0.9.96] Interactive assembly and analysis of RAD-seq data

Parallel connection | ___: 30 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:00:37 | dereplicating [####################] 100% 0:34:21 | clustering/mapping [####################] 100% 0:00:00 | building clusters [####################] 100% 0:00:00 | chunking clusters [####################] 100% 0:34:06 | aligning clusters [####################] 100% 0:00:06 | concat clusters [####################] 100% 0:00:06 | calc cluster stats Parallel connection closed.

Can you post the output of conda list inside the ipyrad environment? I really can't think of why this would be happening inside a clean install on another cluster. Perhaps there's a problem with the environment, sometimes HPC systems will put directories in your PATH that conflict or step on conda stuff.

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2214790790, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYN46JJV7BK7FUOMKMLZLLEULAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUG44TANZZGA . You are receiving this because you authored the thread.Message ID: @.***>

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[/rhome/ckzq2024/miniconda3] >>> PREFIX=/rhome/ckzq2024/miniconda3 Unpacking payload ...

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COMMAND clean Remove unused packages and caches. compare Compare packages between conda environments. config Modify configuration values in .condarc. content-trust Signing and verification tools for Conda create Create a new conda environment from a list of specified packages. doctor Display a health report for your environment. env See conda env --help. info Display information about current conda install. init Initialize conda for shell interaction. install Install a list of packages into a specified conda environment. list List installed packages in a conda environment. notices Retrieve latest channel notifications. package Create low-level conda packages. (EXPERIMENTAL) remove (uninstall) Remove a list of packages from a specified conda environment. rename Rename an existing environment. repoquery Advanced search for repodata. run Run an executable in a conda environment. search Search for packages and display associated information using the MatchSpec format. update (upgrade) Update conda packages to the latest compatible version. @.*** ~]$ conda create -n ipyrad_py310 python=3.10 Retrieving notices: ...working... done Channels:

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environment location: /rhome/ckzq2024/.conda/envs/ipyrad_py310

added / updated specs:

• python=3.10

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.10.14-hd12c33a_0_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

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@. ~]$ conda activate ipyrad_py310 (ipyrad_py310) @. ~]$ conda install ipyrad=0.9.95 -c conda-forge -c bioconda Channels:

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• bioconda
• defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done

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environment location: /rhome/ckzq2024/.conda/envs/ipyrad_py310

added / updated specs:

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---------------------------|-----------------
libopenblas-0.3.27         |pthreads_hac2b453_1         5.3 MB  conda-forge
------------------------------------------------------------
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The following NEW packages will be INSTALLED:

anyio conda-forge/noarch::anyio-4.4.0-pyhd8ed1ab_0 argon2-cffi conda-forge/noarch::argon2-cffi-23.1.0-pyhd8ed1ab_0 argon2-cffi-bindi~ conda-forge/linux-64::argon2-cffi-bindings-21.2.0-py310h2372a71_4 arrow conda-forge/noarch::arrow-1.3.0-pyhd8ed1ab_0 asttokens conda-forge/noarch::asttokens-2.4.1-pyhd8ed1ab_0 async-lru conda-forge/noarch::async-lru-2.0.4-pyhd8ed1ab_0 attrs conda-forge/noarch::attrs-23.2.0-pyh71513ae_0 babel conda-forge/noarch::babel-2.14.0-pyhd8ed1ab_0 beautifulsoup4 conda-forge/noarch::beautifulsoup4-4.12.3-pyha770c72_0 bedtools bioconda/linux-64::bedtools-2.31.1-hf5e1c6e_1 bleach conda-forge/noarch::bleach-6.1.0-pyhd8ed1ab_0 brotli-python conda-forge/linux-64::brotli-python-1.1.0-py310hc6cd4ac_1 bwa bioconda/linux-64::bwa-0.7.18-he4a0461_0 c-ares conda-forge/linux-64::c-ares-1.28.1-hd590300_0 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 cairo conda-forge/linux-64::cairo-1.18.0-h3faef2a_0 certifi conda-forge/noarch::certifi-2024.6.2-pyhd8ed1ab_0 cffi conda-forge/linux-64::cffi-1.16.0-py310h2fee648_0 chardet conda-forge/linux-64::chardet-5.2.0-py310hff52083_1 charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0 colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 comm conda-forge/noarch::comm-0.2.2-pyhd8ed1ab_0 custom-inherit conda-forge/noarch::custom-inherit-2.4.1-pyhd8ed1ab_0 cutadapt bioconda/linux-64::cutadapt-4.9-py310h7c593f9_0 debugpy conda-forge/linux-64::debugpy-1.8.2-py310h76e45a6_0 decorator conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0 defusedxml conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0 dnaio bioconda/linux-64::dnaio-1.2.1-py310h7c593f9_1 entrypoints conda-forge/noarch::entrypoints-0.4-pyhd8ed1ab_0 exceptiongroup conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2 executing conda-forge/noarch::executing-2.0.1-pyhd8ed1ab_0 expat conda-forge/linux-64::expat-2.6.2-h59595ed_0 font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_2 fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 fonts-conda-forge conda-forge/noarch::fonts-conda-forge-1-0 fqdn conda-forge/noarch::fqdn-1.5.1-pyhd8ed1ab_0 freetype conda-forge/linux-64::freetype-2.12.1-h267a509_2 freetype-py conda-forge/noarch::freetype-py-2.3.0-pyhd8ed1ab_0 future conda-forge/noarch::future-1.0.0-pyhd8ed1ab_0 h11 conda-forge/noarch::h11-0.14.0-pyhd8ed1ab_0 h2 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_0 h5py conda-forge/linux-64::h5py-3.11.0-nompi_py310hf054cd7_102 hdf5 conda-forge/linux-64::hdf5-1.14.3-nompi_hdf9ad27_105 hpack conda-forge/noarch::hpack-4.0.0-pyh9f0ad1d_0 htslib bioconda/linux-64::htslib-1.20-h5efdd21_1 httpcore conda-forge/noarch::httpcore-1.0.5-pyhd8ed1ab_0 httpx conda-forge/noarch::httpx-0.27.0-pyhd8ed1ab_0 hyperframe conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_0 icu conda-forge/linux-64::icu-73.2-h59595ed_0 idna conda-forge/noarch::idna-3.7-pyhd8ed1ab_0 importlib-metadata conda-forge/noarch::importlib-metadata-8.0.0-pyha770c72_0 importlib_metadata conda-forge/noarch::importlib_metadata-8.0.0-hd8ed1ab_0 importlib_resourc~ conda-forge/noarch::importlib_resources-6.4.0-pyhd8ed1ab_0 ipykernel conda-forge/noarch::ipykernel-6.29.5-pyh3099207_0 ipyparallel conda-forge/noarch::ipyparallel-8.8.0-pyhd8ed1ab_0 ipyrad bioconda/noarch::ipyrad-0.9.95-pyh7cba7a3_0 ipython conda-forge/noarch::ipython-8.26.0-pyh707e725_0 isa-l conda-forge/linux-64::isa-l-2.31.0-hd590300_1 isoduration conda-forge/noarch::isoduration-20.11.0-pyhd8ed1ab_0 jedi conda-forge/noarch::jedi-0.19.1-pyhd8ed1ab_0 jinja2 conda-forge/noarch::jinja2-3.1.4-pyhd8ed1ab_0 json5 conda-forge/noarch::json5-0.9.25-pyhd8ed1ab_0 jsonpointer conda-forge/linux-64::jsonpointer-3.0.0-py310hff52083_0 jsonschema conda-forge/noarch::jsonschema-4.22.0-pyhd8ed1ab_0 jsonschema-specif~ conda-forge/noarch::jsonschema-specifications-2023.12.1-pyhd8ed1ab_0 jsonschema-with-f~ conda-forge/noarch::jsonschema-with-format-nongpl-4.22.0-pyhd8ed1ab_0 jupyter-lsp conda-forge/noarch::jupyter-lsp-2.2.5-pyhd8ed1ab_0 jupyter_client conda-forge/noarch::jupyter_client-8.6.2-pyhd8ed1ab_0 jupyter_core conda-forge/linux-64::jupyter_core-5.7.2-py310hff52083_0 jupyter_events conda-forge/noarch::jupyter_events-0.10.0-pyhd8ed1ab_0 jupyter_server conda-forge/noarch::jupyter_server-2.14.1-pyhd8ed1ab_0 jupyter_server_te~ conda-forge/noarch::jupyter_server_terminals-0.5.3-pyhd8ed1ab_0 jupyterlab conda-forge/noarch::jupyterlab-4.2.3-pyhd8ed1ab_0 jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.3.0-pyhd8ed1ab_1 jupyterlab_server conda-forge/noarch::jupyterlab_server-2.27.2-pyhd8ed1ab_0 keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0 lcms2 conda-forge/linux-64::lcms2-2.16-hb7c19ff_0 lerc conda-forge/linux-64::lerc-4.0.0-h27087fc_0 libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0 libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_1 libdeflate conda-forge/linux-64::libdeflate-1.20-hd590300_0 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-hd590300_2 libevent conda-forge/linux-64::libevent-2.1.12-hf998b51_1 libexpat conda-forge/linux-64::libexpat-2.6.2-h59595ed_0 libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 libglib conda-forge/linux-64::libglib-2.80.2-hf974151_0 libhwloc conda-forge/linux-64::libhwloc-2.10.0-default_h5622ce7_1001 libiconv conda-forge/linux-64::libiconv-1.17-hd590300_2 libjpeg-turbo conda-forge/linux-64::libjpeg-turbo-3.0.0-hd590300_1 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libllvm14 conda-forge/linux-64::libllvm14-14.0.6-hcd5def8_4 libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 libnl conda-forge/linux-64::libnl-3.9.0-hd590300_0 libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libpng conda-forge/linux-64::libpng-1.6.43-h2797004_0 libsodium conda-forge/linux-64::libsodium-1.0.18-h36c2ea0_1 libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 libtiff conda-forge/linux-64::libtiff-4.6.0-h1dd3fc0_3 libwebp-base conda-forge/linux-64::libwebp-base-1.4.0-hd590300_0 libxcb conda-forge/linux-64::libxcb-1.15-h0b41bf4_0 libxml2 conda-forge/linux-64::libxml2-2.12.7-hc051c1a_1 llvmlite conda-forge/linux-64::llvmlite-0.42.0-py310h1b8f574_1 markupsafe conda-forge/linux-64::markupsafe-2.1.5-py310h2372a71_0 matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.7-pyhd8ed1ab_0 mistune conda-forge/noarch::mistune-3.0.2-pyhd8ed1ab_0 mpi conda-forge/linux-64::mpi-1.0-openmpi mpi4py conda-forge/linux-64::mpi4py-3.1.6-py310hb2ba3f8_1 multipledispatch conda-forge/noarch::multipledispatch-0.6.0-py_0 muscle bioconda/linux-64::muscle-3.8.1551-h7d875b9_6 nbclient conda-forge/noarch::nbclient-0.10.0-pyhd8ed1ab_0 nbconvert-core conda-forge/noarch::nbconvert-core-7.16.4-pyhd8ed1ab_1 nbformat conda-forge/noarch::nbformat-5.10.4-pyhd8ed1ab_0 nest-asyncio conda-forge/noarch::nest-asyncio-1.6.0-pyhd8ed1ab_0 notebook conda-forge/noarch::notebook-7.2.1-pyhd8ed1ab_0 notebook-shim conda-forge/noarch::notebook-shim-0.2.4-pyhd8ed1ab_0 numba conda-forge/linux-64::numba-0.59.1-py310h7dc5dd1_0 numpy conda-forge/linux-64::numpy-1.26.4-py310hb13e2d6_0 openjpeg conda-forge/linux-64::openjpeg-2.5.2-h488ebb8_0 openmpi conda-forge/linux-64::openmpi-5.0.3-hfd7b305_106 overrides conda-forge/noarch::overrides-7.7.0-pyhd8ed1ab_0 packaging conda-forge/noarch::packaging-24.1-pyhd8ed1ab_0 pandas conda-forge/linux-64::pandas-2.2.2-py310hf9f9076_1 pandocfilters conda-forge/noarch::pandocfilters-1.5.0-pyhd8ed1ab_0 parso conda-forge/noarch::parso-0.8.4-pyhd8ed1ab_0 pbzip2 conda-forge/linux-64::pbzip2-1.1.13-h1fcc475_2 pcre2 conda-forge/linux-64::pcre2-10.43-hcad00b1_0 perl conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 pexpect conda-forge/noarch::pexpect-4.9.0-pyhd8ed1ab_0 pickleshare conda-forge/noarch::pickleshare-0.7.5-py_1003 pigz conda-forge/linux-64::pigz-2.8-h2797004_0 pillow conda-forge/linux-64::pillow-10.3.0-py310hf73ecf8_0 pixman conda-forge/linux-64::pixman-0.43.2-h59595ed_0 pkgutil-resolve-n~ conda-forge/noarch::pkgutil-resolve-name-1.3.10-pyhd8ed1ab_1 platformdirs conda-forge/noarch::platformdirs-4.2.2-pyhd8ed1ab_0 prometheus_client conda-forge/noarch::prometheus_client-0.20.0-pyhd8ed1ab_0 prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.47-pyha770c72_0 psutil conda-forge/linux-64::psutil-6.0.0-py310hc51659f_0 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0 pure_eval conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0 pycairo conda-forge/linux-64::pycairo-1.26.1-py310he029307_0 pycparser conda-forge/noarch::pycparser-2.22-pyhd8ed1ab_0 pygments conda-forge/noarch::pygments-2.18.0-pyhd8ed1ab_0 pypng conda-forge/noarch::pypng-0.20220715.0-pyhd8ed1ab_0 pysam bioconda/linux-64::pysam-0.22.1-py310h804392c_1 pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-fastjsonsc~ conda-forge/noarch::python-fastjsonschema-2.20.0-pyhd8ed1ab_0 python-isal conda-forge/linux-64::python-isal-1.6.1-py310h2372a71_0 python-json-logger conda-forge/noarch::python-json-logger-2.0.7-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0 python-zlib-ng conda-forge/linux-64::python-zlib-ng-0.4.3-py310hf89ee4d_1 python_abi conda-forge/linux-64::python_abi-3.10-4_cp310 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 pyyaml conda-forge/linux-64::pyyaml-6.0.1-py310h2372a71_1 pyzmq conda-forge/linux-64::pyzmq-26.0.3-py310h6883aea_0 referencing conda-forge/noarch::referencing-0.35.1-pyhd8ed1ab_0 reportlab conda-forge/linux-64::reportlab-4.2.2-py310hc51659f_0 requests conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_0 rfc3339-validator conda-forge/noarch::rfc3339-validator-0.1.4-pyhd8ed1ab_0 rfc3986-validator conda-forge/noarch::rfc3986-validator-0.1.1-pyh9f0ad1d_0 rlpycairo conda-forge/noarch::rlpycairo-0.2.0-pyhd8ed1ab_0 rpds-py conda-forge/linux-64::rpds-py-0.18.1-py310he421c4c_0 samtools bioconda/linux-64::samtools-1.20-h50ea8bc_0 scipy conda-forge/linux-64::scipy-1.14.0-py310h93e2701_1 send2trash conda-forge/noarch::send2trash-1.8.3-pyh0d859eb_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 sniffio conda-forge/noarch::sniffio-1.3.1-pyhd8ed1ab_0 soupsieve conda-forge/noarch::soupsieve-2.5-pyhd8ed1ab_1 stack_data conda-forge/noarch::stack_data-0.6.2-pyhd8ed1ab_0 terminado conda-forge/noarch::terminado-0.18.1-pyh0d859eb_0 tinycss2 conda-forge/noarch::tinycss2-1.3.0-pyhd8ed1ab_0 tomli conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0 tornado conda-forge/linux-64::tornado-6.4.1-py310hc51659f_0 toyplot conda-forge/noarch::toyplot-1.0.3-pyhd8ed1ab_0 tqdm conda-forge/noarch::tqdm-4.66.4-pyhd8ed1ab_0 traitlets conda-forge/noarch::traitlets-5.14.3-pyhd8ed1ab_0 types-python-date~ conda-forge/noarch::types-python-dateutil-2.9.0.20240316-pyhd8ed1ab_0 typing-extensions conda-forge/noarch::typing-extensions-4.12.2-hd8ed1ab_0 typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0 typing_utils conda-forge/noarch::typing_utils-0.1.0-pyhd8ed1ab_0 uri-template conda-forge/noarch::uri-template-1.3.0-pyhd8ed1ab_0 urllib3 conda-forge/noarch::urllib3-2.2.2-pyhd8ed1ab_1 vsearch bioconda/linux-64::vsearch-2.28.1-h6a68c12_0 wcwidth conda-forge/noarch::wcwidth-0.2.13-pyhd8ed1ab_0 webcolors conda-forge/noarch::webcolors-24.6.0-pyhd8ed1ab_0 webencodings conda-forge/noarch::webencodings-0.5.1-pyhd8ed1ab_2 websocket-client conda-forge/noarch::websocket-client-1.8.0-pyhd8ed1ab_0 xopen conda-forge/linux-64::xopen-2.0.1-py310hff52083_0 xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002 xorg-libice conda-forge/linux-64::xorg-libice-1.1.1-hd590300_0 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.4-h7391055_0 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.9-h8ee46fc_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0 xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2 zeromq conda-forge/linux-64::zeromq-4.3.5-h75354e8_4 zipp conda-forge/noarch::zipp-3.19.2-pyhd8ed1ab_0 zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6 zlib-ng conda-forge/linux-64::zlib-ng-2.2.1-he02047a_0 zstandard conda-forge/linux-64::zstandard-0.22.0-py310hab88d88_1 zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0

The following packages will be DOWNGRADED:

libzlib 1.3.1-h4ab18f5_1 --> 1.2.13-h4ab18f5_6

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done Verifying transaction: done Executing transaction: - On Linux, Open MPI is built with UCX support but it is disabled by default. To enable it, first install UCX (conda install -c conda-forge ucx). Afterwards, set the environment variables OMPI_MCA_pml=ucx OMPI_MCA_osc=ucx before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ...

On Linux, Open MPI is built with CUDA awareness but it is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ... Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX documentation for further details.

done (ipyrad_py310) @.*** ~]$ conda install vsearch=2.23.0 -c conda-forge -c bioconda Channels:

• conda-forge
• bioconda
• defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done

Package Plan

environment location: /rhome/ckzq2024/.conda/envs/ipyrad_py310

added / updated specs:

• vsearch=2.23.0

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
vsearch-2.23.0             |       h6a68c12_0         240 KB  bioconda
------------------------------------------------------------
                                       Total:         240 KB

The following packages will be DOWNGRADED:

vsearch 2.28.1-h6a68c12_0 --> 2.23.0-h6a68c12_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done Verifying transaction: done Executing transaction: done (ipyrad_py310) @.*** ~]$ python Python 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

[1]+ Stopped python (ipyrad_py310) @. ~]$ ls miniconda3 Miniconda3-latest-Linux-x86_64.sh ondemand R share (ipyrad_py310) @. ~]$ cd share (ipyrad_py310) @. share]$ ls CYL (ipyrad_py310) @. share]$ cd CYL (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.iqtree params_CYL1.txt CYL_1_2_1_assembly CYL_1.json Miniconda3-latest-Linux-x86_64.sh output_CYL_1_ML.log slurm_CYL_1 CYL_1_2_assembly CYL_1.phy ML_CYL.sh output_CYL_1_ML.mldist slurm_CYL_1.sh CYL_1_clust_0.85 CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.splits.nex CYL_1_demultiplex CYL_1-tmpalign output_CYL_1_ML.ckp.gz output_CYL_1_ML.treefile CYL_1_edits CYL_ML output_CYL_1_ML.contree output_CYL_1_ML.ufboot (ipyrad_py310) @. CYL]$ rm -r CYL_1-tmpalign (ipyrad_py310) @. CYL]$ rm -r CYL_1_edits (ipyrad_py310) @. CYL]$ rm -r CYL_1_clust_0.85 (ipyrad_py310) @. CYL]$ (ipyrad_py310) @. CYL]$ rm CYL_1.json (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.log params_CYL1.txt CYL_1_2_1_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.mldist slurm_CYL_1 CYL_1_2_assembly CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.splits.nex slurm_CYL_1.sh CYL_1_demultiplex CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.treefile CYL_1_fastqs Miniconda3-latest-Linux-x86_64.sh output_CYL_1_ML.iqtree output_CYL_1_ML.ufboot (ipyrad_py310) @. CYL]$ rm CYL_1_2_assembly (ipyrad_py310) @. CYL]$ rm CYL_1_2_1_assembly (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1_s1_demultiplex_stats.txt ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_demultiplex CYL_ML output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1.phy Miniconda3-latest-Linux-x86_64.sh output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 (ipyrad_py310) @. CYL]$ rm Miniconda3-latest-Linux-x86_64.sh (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh (ipyrad_py310) @. CYL]$ sbatch ML_CYL.sh Submitted batch job 12772 (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh (ipyrad_py310) @. CYL]$ squeue -u ckzq2024 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) (ipyrad_py310) @. CYL]$ sbatch slurm_CYL_1.sh Submitted batch job 12773 (ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_2_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 (ipyrad_py310) @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

(ipyrad_py310) @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_2_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 (ipyrad_py310) @. CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

(ipyrad_py310) @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

(ipyrad_py310) @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

(ipyrad_py310) @. CYL]$ client_loop: send disconnect: Broken pipe (base) @._64-apple-darwin13 ~ % ssh @. @.) Password: @.***) Duo two-factor login for ckzq2024

Enter a passcode or select one of the following options:

1. Phone call to XXX-XXX-5643
2. SMS passcodes to XXX-XXX-5643

Passcode or option (1-2): 2 @.***) New SMS passcodes sent. Duo two-factor login for ckzq2024

Enter a passcode or select one of the following options:

1. Phone call to XXX-XXX-5643
2. SMS passcodes to XXX-XXX-5643 (next code starts with: 1)

Passcode or option (1-2): 1316496 Success. Logging you in... Last login: Mon Jul 8 09:28:17 2024 from 10.116.1.43 @. ~]$ ls miniconda3 Miniconda3-latest-Linux-x86_64.sh ondemand R share @. ~]$ cd share @. share]$ lls -bash: lls: command not found @. share]$ ls CYL @. share]$ cd CYL @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_2_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:02:39 | loading reads @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_2_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 @. CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:04:35 | loading reads @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:04:49 | loading reads @. CYL]$ ls Barcodes_CYL_1.txt CYL_1.phy ML_CYL.sh output_CYL_1_ML.iqtree output_CYL_1_ML.treefile slurm_CYL_1.sh CYL_1_2_assembly CYL_1_s1_demultiplex_stats.txt output_CYL_1_ML.bionj output_CYL_1_ML.log output_CYL_1_ML.ufboot CYL_1_demultiplex CYL_ML output_CYL_1_ML.ckp.gz output_CYL_1_ML.mldist params_CYL1.txt CYL_1_fastqs CYL_pl1.txt output_CYL_1_ML.contree output_CYL_1_ML.splits.nex slurm_CYL_1 @. CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ]cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:07:29 | loading reads @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:10:21 | loading reads @.*** CYL]$ cat CYL_1_2_assembly

SLURM_JOB_ID = 12773 SLURM_JOB_NODELIST = a005

---

ipyrad [v.0.9.95] Interactive assembly and analysis of RAD-seq data

---

Parallel connection |

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. [ ] 0% 1:14:48 | loading reads @.*** CYL]$

[ckiel3]

Here are the packages in my clean conda environment in the one from the previous email. Python 3.10 -- it can barely move through step 1 as you see in the attachment in the previous email.

packages in environment at /rhome/ckzq2024/.conda/envs/ipyrad_py310:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge

_openmp_mutex 4.5 2_gnu conda-forge

anyio 4.4.0 pyhd8ed1ab_0 conda-forge

argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge

argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge

arrow 1.3.0 pyhd8ed1ab_0 conda-forge

asttokens 2.4.1 pyhd8ed1ab_0 conda-forge

async-lru 2.0.4 pyhd8ed1ab_0 conda-forge

attrs 23.2.0 pyh71513ae_0 conda-forge

babel 2.14.0 pyhd8ed1ab_0 conda-forge

beautifulsoup4 4.12.3 pyha770c72_0 conda-forge

bedtools 2.31.1 hf5e1c6e_1 bioconda

bleach 6.1.0 pyhd8ed1ab_0 conda-forge

brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge

bwa 0.7.18 he4a0461_0 bioconda

bzip2 1.0.8 hd590300_5 conda-forge

c-ares 1.28.1 hd590300_0 conda-forge

ca-certificates 2024.7.4 hbcca054_0 conda-forge

cached-property 1.5.2 hd8ed1ab_1 conda-forge

cached_property 1.5.2 pyha770c72_1 conda-forge

cairo 1.18.0 h3faef2a_0 conda-forge

certifi 2024.6.2 pyhd8ed1ab_0 conda-forge

cffi 1.16.0 py310h2fee648_0 conda-forge

chardet 5.2.0 py310hff52083_1 conda-forge

charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge

colorama 0.4.6 pyhd8ed1ab_0 conda-forge

comm 0.2.2 pyhd8ed1ab_0 conda-forge

custom-inherit 2.4.1 pyhd8ed1ab_0 conda-forge

cutadapt 4.9 py310h7c593f9_0 bioconda

debugpy 1.8.2 py310h76e45a6_0 conda-forge

decorator 5.1.1 pyhd8ed1ab_0 conda-forge

defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge

dnaio 1.2.1 py310h7c593f9_1 bioconda

entrypoints 0.4 pyhd8ed1ab_0 conda-forge

exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge

executing 2.0.1 pyhd8ed1ab_0 conda-forge

expat 2.6.2 h59595ed_0 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 h77eed37_2 conda-forge

fontconfig 2.14.2 h14ed4e7_0 conda-forge

fonts-conda-ecosystem 1 0 conda-forge

fonts-conda-forge 1 0 conda-forge

fqdn 1.5.1 pyhd8ed1ab_0 conda-forge

freetype 2.12.1 h267a509_2 conda-forge

freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge

future 1.0.0 pyhd8ed1ab_0 conda-forge

h11 0.14.0 pyhd8ed1ab_0 conda-forge

h2 4.1.0 pyhd8ed1ab_0 conda-forge

h5py 3.11.0 nompi_py310hf054cd7_102 conda-forge

hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge

hpack 4.0.0 pyh9f0ad1d_0 conda-forge

htslib 1.20 h5efdd21_1 bioconda

httpcore 1.0.5 pyhd8ed1ab_0 conda-forge

httpx 0.27.0 pyhd8ed1ab_0 conda-forge

hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge

icu 73.2 h59595ed_0 conda-forge

idna 3.7 pyhd8ed1ab_0 conda-forge

importlib-metadata 8.0.0 pyha770c72_0 conda-forge

importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge

importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge

ipykernel 6.29.5 pyh3099207_0 conda-forge

ipyparallel 8.8.0 pyhd8ed1ab_0 conda-forge

ipyrad 0.9.95 pyh7cba7a3_0 bioconda

ipython 8.26.0 pyh707e725_0 conda-forge

isa-l 2.31.0 hd590300_1 conda-forge

isoduration 20.11.0 pyhd8ed1ab_0 conda-forge

jedi 0.19.1 pyhd8ed1ab_0 conda-forge

jinja2 3.1.4 pyhd8ed1ab_0 conda-forge

json5 0.9.25 pyhd8ed1ab_0 conda-forge

jsonpointer 3.0.0 py310hff52083_0 conda-forge

jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge

jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge

jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge

jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge

jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge

jupyter_core 5.7.2 py310hff52083_0 conda-forge

jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge

jupyter_server 2.14.1 pyhd8ed1ab_0 conda-forge

jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge

jupyterlab 4.2.3 pyhd8ed1ab_0 conda-forge

jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge

jupyterlab_server 2.27.2 pyhd8ed1ab_0 conda-forge

keyutils 1.6.1 h166bdaf_0 conda-forge

krb5 1.21.3 h659f571_0 conda-forge

lcms2 2.16 hb7c19ff_0 conda-forge

ld_impl_linux-64 2.40 hf3520f5_7 conda-forge

lerc 4.0.0 h27087fc_0 conda-forge

libaec 1.1.3 h59595ed_0 conda-forge

libblas 3.9.0 22_linux64_openblas conda-forge

libcblas 3.9.0 22_linux64_openblas conda-forge

libcurl 8.8.0 hca28451_1 conda-forge

libdeflate 1.20 hd590300_0 conda-forge

libedit 3.1.20191231 he28a2e2_2 conda-forge

libev 4.33 hd590300_2 conda-forge

libevent 2.1.12 hf998b51_1 conda-forge

libexpat 2.6.2 h59595ed_0 conda-forge

libffi 3.4.2 h7f98852_5 conda-forge

libgcc-ng 14.1.0 h77fa898_0 conda-forge

libgfortran-ng 14.1.0 h69a702a_0 conda-forge

libgfortran5 14.1.0 hc5f4f2c_0 conda-forge

libglib 2.80.2 hf974151_0 conda-forge

libgomp 14.1.0 h77fa898_0 conda-forge

libhwloc 2.10.0 default_h5622ce7_1001 conda-forge

libiconv 1.17 hd590300_2 conda-forge

libjpeg-turbo 3.0.0 hd590300_1 conda-forge

liblapack 3.9.0 22_linux64_openblas conda-forge

libllvm14 14.0.6 hcd5def8_4 conda-forge

libnghttp2 1.58.0 h47da74e_1 conda-forge

libnl 3.9.0 hd590300_0 conda-forge

libnsl 2.0.1 hd590300_0 conda-forge

libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge

libpng 1.6.43 h2797004_0 conda-forge

libsodium 1.0.18 h36c2ea0_1 conda-forge

libsqlite 3.46.0 hde9e2c9_0 conda-forge

libssh2 1.11.0 h0841786_0 conda-forge

libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge

libtiff 4.6.0 h1dd3fc0_3 conda-forge

libuuid 2.38.1 h0b41bf4_0 conda-forge

libwebp-base 1.4.0 hd590300_0 conda-forge

libxcb 1.15 h0b41bf4_0 conda-forge

libxcrypt 4.4.36 hd590300_1 conda-forge

libxml2 2.12.7 hc051c1a_1 conda-forge

libzlib 1.2.13 h4ab18f5_6 conda-forge

llvmlite 0.42.0 py310h1b8f574_1 conda-forge

markupsafe 2.1.5 py310h2372a71_0 conda-forge

matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge

mistune 3.0.2 pyhd8ed1ab_0 conda-forge

mpi 1.0 openmpi conda-forge

mpi4py 3.1.6 py310hb2ba3f8_1 conda-forge

multipledispatch 0.6.0 py_0 conda-forge

muscle 3.8.1551 h7d875b9_6 bioconda

nbclient 0.10.0 pyhd8ed1ab_0 conda-forge

nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge

nbformat 5.10.4 pyhd8ed1ab_0 conda-forge

ncurses 6.5 h59595ed_0 conda-forge

nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge

notebook 7.2.1 pyhd8ed1ab_0 conda-forge

notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge

numba 0.59.1 py310h7dc5dd1_0 conda-forge

numpy 1.26.4 py310hb13e2d6_0 conda-forge

openjpeg 2.5.2 h488ebb8_0 conda-forge

openmpi 5.0.3 hfd7b305_106 conda-forge

openssl 3.3.1 h4ab18f5_1 conda-forge

overrides 7.7.0 pyhd8ed1ab_0 conda-forge

packaging 24.1 pyhd8ed1ab_0 conda-forge

pandas 2.2.2 py310hf9f9076_1 conda-forge

pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge

parso 0.8.4 pyhd8ed1ab_0 conda-forge

pbzip2 1.1.13 h1fcc475_2 conda-forge

pcre2 10.43 hcad00b1_0 conda-forge

perl 5.32.1 7_hd590300_perl5 conda-forge

pexpect 4.9.0 pyhd8ed1ab_0 conda-forge

pickleshare 0.7.5 py_1003 conda-forge

pigz 2.8 h2797004_0 conda-forge

pillow 10.3.0 py310hf73ecf8_0 conda-forge

pip 24.0 pyhd8ed1ab_0 conda-forge

pixman 0.43.2 h59595ed_0 conda-forge

pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge

platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge

prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge

prompt-toolkit 3.0.47 pyha770c72_0 conda-forge

psutil 6.0.0 py310hc51659f_0 conda-forge

pthread-stubs 0.4 h36c2ea0_1001 conda-forge

ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge

pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge

pycairo 1.26.1 py310he029307_0 conda-forge

pycparser 2.22 pyhd8ed1ab_0 conda-forge

pygments 2.18.0 pyhd8ed1ab_0 conda-forge

pypng 0.20220715.0 pyhd8ed1ab_0 conda-forge

pysam 0.22.1 py310h804392c_1 bioconda

pysocks 1.7.1 pyha2e5f31_6 conda-forge

python 3.10.14 hd12c33a_0_cpython conda-forge

python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge

python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge

python-isal 1.6.1 py310h2372a71_0 conda-forge

python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge

python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge

python-zlib-ng 0.4.3 py310hf89ee4d_1 conda-forge

python_abi 3.10 4_cp310 conda-forge

pytz 2024.1 pyhd8ed1ab_0 conda-forge

pyyaml 6.0.1 py310h2372a71_1 conda-forge

pyzmq 26.0.3 py310h6883aea_0 conda-forge

readline 8.2 h8228510_1 conda-forge

referencing 0.35.1 pyhd8ed1ab_0 conda-forge

reportlab 4.2.2 py310hc51659f_0 conda-forge

requests 2.32.3 pyhd8ed1ab_0 conda-forge

rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge

rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge

rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge

rpds-py 0.18.1 py310he421c4c_0 conda-forge

samtools 1.20 h50ea8bc_0 bioconda

scipy 1.14.0 py310h93e2701_1 conda-forge

send2trash 1.8.3 pyh0d859eb_0 conda-forge

setuptools 70.1.1 pyhd8ed1ab_0 conda-forge

six 1.16.0 pyh6c4a22f_0 conda-forge

sniffio 1.3.1 pyhd8ed1ab_0 conda-forge

soupsieve 2.5 pyhd8ed1ab_1 conda-forge

stack_data 0.6.2 pyhd8ed1ab_0 conda-forge

terminado 0.18.1 pyh0d859eb_0 conda-forge

tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge

tk 8.6.13 noxft_h4845f30_101 conda-forge

tomli 2.0.1 pyhd8ed1ab_0 conda-forge

tornado 6.4.1 py310hc51659f_0 conda-forge

toyplot 1.0.3 pyhd8ed1ab_0 conda-forge

tqdm 4.66.4 pyhd8ed1ab_0 conda-forge

traitlets 5.14.3 pyhd8ed1ab_0 conda-forge

types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge

typing-extensions 4.12.2 hd8ed1ab_0 conda-forge

typing_extensions 4.12.2 pyha770c72_0 conda-forge

typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge

tzdata 2024a h0c530f3_0 conda-forge

uri-template 1.3.0 pyhd8ed1ab_0 conda-forge

urllib3 2.2.2 pyhd8ed1ab_1 conda-forge

vsearch 2.23.0 h6a68c12_0 bioconda

wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge

webcolors 24.6.0 pyhd8ed1ab_0 conda-forge

webencodings 0.5.1 pyhd8ed1ab_2 conda-forge

websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge

wheel 0.43.0 pyhd8ed1ab_1 conda-forge

xopen 2.0.1 py310hff52083_0 conda-forge

xorg-kbproto 1.0.7 h7f98852_1002 conda-forge

xorg-libice 1.1.1 hd590300_0 conda-forge

xorg-libsm 1.2.4 h7391055_0 conda-forge

xorg-libx11 1.8.9 h8ee46fc_0 conda-forge

xorg-libxau 1.0.11 hd590300_0 conda-forge

xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge

xorg-libxext 1.3.4 h0b41bf4_2 conda-forge

xorg-libxrender 0.9.11 hd590300_0 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

zeromq 4.3.5 h75354e8_4 conda-forge

zipp 3.19.2 pyhd8ed1ab_0 conda-forge

zlib 1.2.13 h4ab18f5_6 conda-forge

zlib-ng 2.2.1 he02047a_0 conda-forge

zstandard 0.22.0 py310hab88d88_1 conda-forge

zstd 1.5.6 ha6fb4c9_0 conda-forge

-----------AND here is the conda list in a different environment with running the python 3.12 where it always fails in step 3

packages in environment at /rhome/ckzq2024/.conda/envs/ipyrad2:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge

_openmp_mutex 4.5 2_gnu conda-forge

anyio 4.4.0 pyhd8ed1ab_0 conda-forge

argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge

argon2-cffi-bindings 21.2.0 py312h98912ed_4 conda-forge

arrow 1.3.0 pyhd8ed1ab_0 conda-forge

asttokens 2.4.1 pyhd8ed1ab_0 conda-forge

async-lru 2.0.4 pyhd8ed1ab_0 conda-forge

attrs 23.2.0 pyh71513ae_0 conda-forge

babel 2.14.0 pyhd8ed1ab_0 conda-forge

beautifulsoup4 4.12.3 pyha770c72_0 conda-forge

bedtools 2.31.1 hf5e1c6e_1 bioconda

bleach 6.1.0 pyhd8ed1ab_0 conda-forge

brotli-python 1.1.0 py312h30efb56_1 conda-forge

bwa 0.7.18 he4a0461_0 bioconda

bzip2 1.0.8 hd590300_5 conda-forge

c-ares 1.28.1 hd590300_0 conda-forge

ca-certificates 2024.7.4 hbcca054_0 conda-forge

cached-property 1.5.2 hd8ed1ab_1 conda-forge

cached_property 1.5.2 pyha770c72_1 conda-forge

cairo 1.18.0 h3faef2a_0 conda-forge

certifi 2024.6.2 pyhd8ed1ab_0 conda-forge

cffi 1.16.0 py312hf06ca03_0 conda-forge

chardet 5.2.0 py312h7900ff3_1 conda-forge

charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge

colorama 0.4.6 pyhd8ed1ab_0 conda-forge

comm 0.2.2 pyhd8ed1ab_0 conda-forge

custom-inherit 2.4.1 pyhd8ed1ab_0 conda-forge

cutadapt 4.9 py312hf67a6ed_0 bioconda

debugpy 1.8.2 py312h7070661_0 conda-forge

decorator 5.1.1 pyhd8ed1ab_0 conda-forge

defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge

dnaio 1.2.1 py312hf67a6ed_1 bioconda

entrypoints 0.4 pyhd8ed1ab_0 conda-forge

exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge

executing 2.0.1 pyhd8ed1ab_0 conda-forge

expat 2.6.2 h59595ed_0 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 h77eed37_2 conda-forge

fontconfig 2.14.2 h14ed4e7_0 conda-forge

fonts-conda-ecosystem 1 0 conda-forge

fonts-conda-forge 1 0 conda-forge

fqdn 1.5.1 pyhd8ed1ab_0 conda-forge

freetype 2.12.1 h267a509_2 conda-forge

freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge

future 1.0.0 pyhd8ed1ab_0 conda-forge

h11 0.14.0 pyhd8ed1ab_0 conda-forge

h2 4.1.0 pyhd8ed1ab_0 conda-forge

h5py 3.11.0 nompi_py312hb7ab980_102 conda-forge

hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge

hpack 4.0.0 pyh9f0ad1d_0 conda-forge

htslib 1.20 h5efdd21_1 bioconda

httpcore 1.0.5 pyhd8ed1ab_0 conda-forge

httpx 0.27.0 pyhd8ed1ab_0 conda-forge

hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge

icu 73.2 h59595ed_0 conda-forge

idna 3.7 pyhd8ed1ab_0 conda-forge

impi_rt 2021.12.0 ha770c72_536 conda-forge

importlib-metadata 8.0.0 pyha770c72_0 conda-forge

importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge

importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge

ipykernel 6.29.5 pyh3099207_0 conda-forge

ipyparallel 8.8.0 pyhd8ed1ab_0 conda-forge

ipyrad 0.9.93 pyh7cba7a3_0 bioconda

ipython 8.26.0 pyh707e725_0 conda-forge

isa-l 2.31.0 hd590300_1 conda-forge

isoduration 20.11.0 pyhd8ed1ab_0 conda-forge

jedi 0.19.1 pyhd8ed1ab_0 conda-forge

jinja2 3.1.4 pyhd8ed1ab_0 conda-forge

json5 0.9.25 pyhd8ed1ab_0 conda-forge

jsonpointer 3.0.0 py312h7900ff3_0 conda-forge

jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge

jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge

jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge

jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge

jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge

jupyter_core 5.7.2 py312h7900ff3_0 conda-forge

jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge

jupyter_server 2.14.1 pyhd8ed1ab_0 conda-forge

jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge

jupyterlab 4.2.3 pyhd8ed1ab_0 conda-forge

jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge

jupyterlab_server 2.27.2 pyhd8ed1ab_0 conda-forge

keyutils 1.6.1 h166bdaf_0 conda-forge

krb5 1.21.3 h659f571_0 conda-forge

lcms2 2.16 hb7c19ff_0 conda-forge

ld_impl_linux-64 2.40 hf3520f5_7 conda-forge

lerc 4.0.0 h27087fc_0 conda-forge

libaec 1.1.3 h59595ed_0 conda-forge

libblas 3.9.0 22_linux64_openblas conda-forge

libcblas 3.9.0 22_linux64_openblas conda-forge

libcurl 8.8.0 hca28451_1 conda-forge

libdeflate 1.20 hd590300_0 conda-forge

libedit 3.1.20191231 he28a2e2_2 conda-forge

libev 4.33 hd590300_2 conda-forge

libexpat 2.6.2 h59595ed_0 conda-forge

libffi 3.4.2 h7f98852_5 conda-forge

libgcc-ng 14.1.0 h77fa898_0 conda-forge

libgfortran-ng 14.1.0 h69a702a_0 conda-forge

libgfortran5 14.1.0 hc5f4f2c_0 conda-forge

libglib 2.80.2 hf974151_0 conda-forge

libgomp 14.1.0 h77fa898_0 conda-forge

libiconv 1.17 hd590300_2 conda-forge

libjpeg-turbo 3.0.0 hd590300_1 conda-forge

liblapack 3.9.0 22_linux64_openblas conda-forge

libllvm14 14.0.6 hcd5def8_4 conda-forge

libnghttp2 1.58.0 h47da74e_1 conda-forge

libnsl 2.0.1 hd590300_0 conda-forge

libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge

libpng 1.6.43 h2797004_0 conda-forge

libsodium 1.0.18 h36c2ea0_1 conda-forge

libsqlite 3.46.0 hde9e2c9_0 conda-forge

libssh2 1.11.0 h0841786_0 conda-forge

libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge

libtiff 4.6.0 h1dd3fc0_3 conda-forge

libuuid 2.38.1 h0b41bf4_0 conda-forge

libwebp-base 1.4.0 hd590300_0 conda-forge

libxcb 1.15 h0b41bf4_0 conda-forge

libxcrypt 4.4.36 hd590300_1 conda-forge

libzlib 1.2.13 h4ab18f5_6 conda-forge

llvmlite 0.42.0 py312hb06c811_1 conda-forge

markupsafe 2.1.5 py312h98912ed_0 conda-forge

matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge

mistune 3.0.2 pyhd8ed1ab_0 conda-forge

mpi 1.0 impi conda-forge

mpi4py 3.1.6 py312h61186ca_1 conda-forge

multipledispatch 0.6.0 py_0 conda-forge

muscle 3.8.1551 h7d875b9_6 bioconda

nbclient 0.10.0 pyhd8ed1ab_0 conda-forge

nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge

nbformat 5.10.4 pyhd8ed1ab_0 conda-forge

ncurses 6.5 h59595ed_0 conda-forge

nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge

notebook 7.2.1 pyhd8ed1ab_0 conda-forge

notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge

numba 0.59.1 py312hacefee8_0 conda-forge

numpy 1.26.4 py312heda63a1_0 conda-forge

openjpeg 2.5.2 h488ebb8_0 conda-forge

openssl 3.3.1 h4ab18f5_1 conda-forge

overrides 7.7.0 pyhd8ed1ab_0 conda-forge

packaging 24.1 pyhd8ed1ab_0 conda-forge

pandas 2.2.2 py312h1d6d2e6_1 conda-forge

pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge

parso 0.8.4 pyhd8ed1ab_0 conda-forge

pbzip2 1.1.13 h1fcc475_2 conda-forge

pcre2 10.43 hcad00b1_0 conda-forge

perl 5.32.1 7_hd590300_perl5 conda-forge

pexpect 4.9.0 pyhd8ed1ab_0 conda-forge

pickleshare 0.7.5 py_1003 conda-forge

pigz 2.8 h2797004_0 conda-forge

pillow 10.3.0 py312hdcec9eb_0 conda-forge

pip 24.0 pyhd8ed1ab_0 conda-forge

pixman 0.43.2 h59595ed_0 conda-forge

pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge

platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge

prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge

prompt-toolkit 3.0.47 pyha770c72_0 conda-forge

psutil 6.0.0 py312h9a8786e_0 conda-forge

pthread-stubs 0.4 h36c2ea0_1001 conda-forge

ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge

pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge

pycairo 1.26.1 py312h3bc4990_0 conda-forge

pycparser 2.22 pyhd8ed1ab_0 conda-forge

pygments 2.18.0 pyhd8ed1ab_0 conda-forge

pypng 0.20220715.0 pyhd8ed1ab_0 conda-forge

pysam 0.22.1 py312hcfdcdd7_1 bioconda

pysocks 1.7.1 pyha2e5f31_6 conda-forge

python 3.12.3 hab00c5b_0_cpython conda-forge

python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge

python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge

python-isal 1.6.1 py312h98912ed_0 conda-forge

python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge

python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge

python-zlib-ng 0.4.3 py312hdfe76eb_1 conda-forge

python_abi 3.12 4_cp312 conda-forge

pytz 2024.1 pyhd8ed1ab_0 conda-forge

pyyaml 6.0.1 py312h98912ed_1 conda-forge

pyzmq 26.0.3 py312h8fd38d8_0 conda-forge

readline 8.2 h8228510_1 conda-forge

referencing 0.35.1 pyhd8ed1ab_0 conda-forge

reportlab 4.2.2 py312h9a8786e_0 conda-forge

requests 2.32.3 pyhd8ed1ab_0 conda-forge

rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge

rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge

rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge

rpds-py 0.18.1 py312h4413252_0 conda-forge

samtools 1.20 h50ea8bc_0 bioconda

scipy 1.14.0 py312hc2bc53b_0 conda-forge

send2trash 1.8.3 pyh0d859eb_0 conda-forge

setuptools 70.1.1 pyhd8ed1ab_0 conda-forge

six 1.16.0 pyh6c4a22f_0 conda-forge

sniffio 1.3.1 pyhd8ed1ab_0 conda-forge

soupsieve 2.5 pyhd8ed1ab_1 conda-forge

stack_data 0.6.2 pyhd8ed1ab_0 conda-forge

terminado 0.18.1 pyh0d859eb_0 conda-forge

tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge

tk 8.6.13 noxft_h4845f30_101 conda-forge

tomli 2.0.1 pyhd8ed1ab_0 conda-forge

tornado 6.4.1 py312h9a8786e_0 conda-forge

toyplot 1.0.3 pyhd8ed1ab_0 conda-forge

tqdm 4.66.4 pyhd8ed1ab_0 conda-forge

traitlets 5.14.3 pyhd8ed1ab_0 conda-forge

types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge

typing-extensions 4.12.2 hd8ed1ab_0 conda-forge

typing_extensions 4.12.2 pyha770c72_0 conda-forge

typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge

tzdata 2024a h0c530f3_0 conda-forge

uri-template 1.3.0 pyhd8ed1ab_0 conda-forge

urllib3 2.2.2 pyhd8ed1ab_1 conda-forge

vsearch 2.14.1 h2d02072_0 bioconda

wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge

webcolors 24.6.0 pyhd8ed1ab_0 conda-forge

webencodings 0.5.1 pyhd8ed1ab_2 conda-forge

websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge

wheel 0.43.0 pyhd8ed1ab_1 conda-forge

xopen 2.0.1 py312h7900ff3_0 conda-forge

xorg-kbproto 1.0.7 h7f98852_1002 conda-forge

xorg-libice 1.1.1 hd590300_0 conda-forge

xorg-libsm 1.2.4 h7391055_0 conda-forge

xorg-libx11 1.8.9 h8ee46fc_0 conda-forge

xorg-libxau 1.0.11 hd590300_0 conda-forge

xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge

xorg-libxext 1.3.4 h0b41bf4_2 conda-forge

xorg-libxrender 0.9.11 hd590300_0 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

zeromq 4.3.5 h75354e8_4 conda-forge

zipp 3.19.2 pyhd8ed1ab_0 conda-forge

zlib 1.2.13 h4ab18f5_6 conda-forge

zlib-ng 2.2.1 he02047a_0 conda-forge

zstandard 0.22.0 py312h5b18bf6_1 conda-forge

zstd 1.5.6 ha6fb4c9_0 conda-forge

On Mon, Jul 8, 2024 at 11:26 AM Carrie Kiel @.***> wrote:

Hi Issac attached is my clean install / I also wiped my miniconda3 and created a new environment and look how slow step one is going with python 3.10. See attached

On Mon, Jul 8, 2024 at 10:35 AM Isaac Overcast @.***> wrote:

I don't know what's happening on your new cluster, but I can't reproduce this error. I ran it on python 3.12.3 with a clean conda install and step 3 ran without error.

---

ipyrad [v.0.9.96] Interactive assembly and analysis of RAD-seq data

Parallel connection | ___: 30 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:00:37 | dereplicating [####################] 100% 0:34:21 | clustering/mapping [####################] 100% 0:00:00 | building clusters [####################] 100% 0:00:00 | chunking clusters [####################] 100% 0:34:06 | aligning clusters [####################] 100% 0:00:06 | concat clusters [####################] 100% 0:00:06 | calc cluster stats Parallel connection closed.

Can you post the output of conda list inside the ipyrad environment? I really can't think of why this would be happening inside a clean install on another cluster. Perhaps there's a problem with the environment, sometimes HPC systems will put directories in your PATH that conflict or step on conda stuff.

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2214790790, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYN46JJV7BK7FUOMKMLZLLEULAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUG44TANZZGA . You are receiving this because you authored the thread.Message ID: @.***>

[ckiel3]

Hi Issac. Update: I tried nearly everything in my ability and so did our HPC admins - different environments and different versions and different pythons and the same error. I even tried to copy my env that worked on my old cluster. One thing is that it did work on Jupyter hub connected to Pomona College - feeling hopeful they copied that env. to my HPC account but it failed at the same place. They are trying one more thing for me that involves Docker. Otherwise, I'm afraid that I won't be able to use ipyrad for the foreseeable future unless you have any more ideas.

thank you,

Carrie

On Tue, Jul 9, 2024 at 9:32 AM Carrie Kiel @.***> wrote:

Issac, Still no luck. I am working with our Systems Administrator to troubleshoot a few things.

thank you.

On Mon, Jul 8, 2024 at 1:05 PM Carrie Kiel @.***> wrote:

Here are the packages in my clean conda environment in the one from the previous email. Python 3.10 -- it can barely move through step 1 as you see in the attachment in the previous email.

packages in environment at /rhome/ckzq2024/.conda/envs/ipyrad_py310:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge

_openmp_mutex 4.5 2_gnu conda-forge

anyio 4.4.0 pyhd8ed1ab_0 conda-forge

argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge

argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge

arrow 1.3.0 pyhd8ed1ab_0 conda-forge

asttokens 2.4.1 pyhd8ed1ab_0 conda-forge

async-lru 2.0.4 pyhd8ed1ab_0 conda-forge

attrs 23.2.0 pyh71513ae_0 conda-forge

babel 2.14.0 pyhd8ed1ab_0 conda-forge

beautifulsoup4 4.12.3 pyha770c72_0 conda-forge

bedtools 2.31.1 hf5e1c6e_1 bioconda

bleach 6.1.0 pyhd8ed1ab_0 conda-forge

brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge

bwa 0.7.18 he4a0461_0 bioconda

bzip2 1.0.8 hd590300_5 conda-forge

c-ares 1.28.1 hd590300_0 conda-forge

ca-certificates 2024.7.4 hbcca054_0 conda-forge

cached-property 1.5.2 hd8ed1ab_1 conda-forge

cached_property 1.5.2 pyha770c72_1 conda-forge

cairo 1.18.0 h3faef2a_0 conda-forge

certifi 2024.6.2 pyhd8ed1ab_0 conda-forge

cffi 1.16.0 py310h2fee648_0 conda-forge

chardet 5.2.0 py310hff52083_1 conda-forge

charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge

colorama 0.4.6 pyhd8ed1ab_0 conda-forge

comm 0.2.2 pyhd8ed1ab_0 conda-forge

custom-inherit 2.4.1 pyhd8ed1ab_0 conda-forge

cutadapt 4.9 py310h7c593f9_0 bioconda

debugpy 1.8.2 py310h76e45a6_0 conda-forge

decorator 5.1.1 pyhd8ed1ab_0 conda-forge

defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge

dnaio 1.2.1 py310h7c593f9_1 bioconda

entrypoints 0.4 pyhd8ed1ab_0 conda-forge

exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge

executing 2.0.1 pyhd8ed1ab_0 conda-forge

expat 2.6.2 h59595ed_0 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 h77eed37_2 conda-forge

fontconfig 2.14.2 h14ed4e7_0 conda-forge

fonts-conda-ecosystem 1 0 conda-forge

fonts-conda-forge 1 0 conda-forge

fqdn 1.5.1 pyhd8ed1ab_0 conda-forge

freetype 2.12.1 h267a509_2 conda-forge

freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge

future 1.0.0 pyhd8ed1ab_0 conda-forge

h11 0.14.0 pyhd8ed1ab_0 conda-forge

h2 4.1.0 pyhd8ed1ab_0 conda-forge

h5py 3.11.0 nompi_py310hf054cd7_102 conda-forge

hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge

hpack 4.0.0 pyh9f0ad1d_0 conda-forge

htslib 1.20 h5efdd21_1 bioconda

httpcore 1.0.5 pyhd8ed1ab_0 conda-forge

httpx 0.27.0 pyhd8ed1ab_0 conda-forge

hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge

icu 73.2 h59595ed_0 conda-forge

idna 3.7 pyhd8ed1ab_0 conda-forge

importlib-metadata 8.0.0 pyha770c72_0 conda-forge

importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge

importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge

ipykernel 6.29.5 pyh3099207_0 conda-forge

ipyparallel 8.8.0 pyhd8ed1ab_0 conda-forge

ipyrad 0.9.95 pyh7cba7a3_0 bioconda

ipython 8.26.0 pyh707e725_0 conda-forge

isa-l 2.31.0 hd590300_1 conda-forge

isoduration 20.11.0 pyhd8ed1ab_0 conda-forge

jedi 0.19.1 pyhd8ed1ab_0 conda-forge

jinja2 3.1.4 pyhd8ed1ab_0 conda-forge

json5 0.9.25 pyhd8ed1ab_0 conda-forge

jsonpointer 3.0.0 py310hff52083_0 conda-forge

jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge

jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge

jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge

jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge

jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge

jupyter_core 5.7.2 py310hff52083_0 conda-forge

jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge

jupyter_server 2.14.1 pyhd8ed1ab_0 conda-forge

jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge

jupyterlab 4.2.3 pyhd8ed1ab_0 conda-forge

jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge

jupyterlab_server 2.27.2 pyhd8ed1ab_0 conda-forge

keyutils 1.6.1 h166bdaf_0 conda-forge

krb5 1.21.3 h659f571_0 conda-forge

lcms2 2.16 hb7c19ff_0 conda-forge

ld_impl_linux-64 2.40 hf3520f5_7 conda-forge

lerc 4.0.0 h27087fc_0 conda-forge

libaec 1.1.3 h59595ed_0 conda-forge

libblas 3.9.0 22_linux64_openblas conda-forge

libcblas 3.9.0 22_linux64_openblas conda-forge

libcurl 8.8.0 hca28451_1 conda-forge

libdeflate 1.20 hd590300_0 conda-forge

libedit 3.1.20191231 he28a2e2_2 conda-forge

libev 4.33 hd590300_2 conda-forge

libevent 2.1.12 hf998b51_1 conda-forge

libexpat 2.6.2 h59595ed_0 conda-forge

libffi 3.4.2 h7f98852_5 conda-forge

libgcc-ng 14.1.0 h77fa898_0 conda-forge

libgfortran-ng 14.1.0 h69a702a_0 conda-forge

libgfortran5 14.1.0 hc5f4f2c_0 conda-forge

libglib 2.80.2 hf974151_0 conda-forge

libgomp 14.1.0 h77fa898_0 conda-forge

libhwloc 2.10.0 default_h5622ce7_1001 conda-forge

libiconv 1.17 hd590300_2 conda-forge

libjpeg-turbo 3.0.0 hd590300_1 conda-forge

liblapack 3.9.0 22_linux64_openblas conda-forge

libllvm14 14.0.6 hcd5def8_4 conda-forge

libnghttp2 1.58.0 h47da74e_1 conda-forge

libnl 3.9.0 hd590300_0 conda-forge

libnsl 2.0.1 hd590300_0 conda-forge

libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge

libpng 1.6.43 h2797004_0 conda-forge

libsodium 1.0.18 h36c2ea0_1 conda-forge

libsqlite 3.46.0 hde9e2c9_0 conda-forge

libssh2 1.11.0 h0841786_0 conda-forge

libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge

libtiff 4.6.0 h1dd3fc0_3 conda-forge

libuuid 2.38.1 h0b41bf4_0 conda-forge

libwebp-base 1.4.0 hd590300_0 conda-forge

libxcb 1.15 h0b41bf4_0 conda-forge

libxcrypt 4.4.36 hd590300_1 conda-forge

libxml2 2.12.7 hc051c1a_1 conda-forge

libzlib 1.2.13 h4ab18f5_6 conda-forge

llvmlite 0.42.0 py310h1b8f574_1 conda-forge

markupsafe 2.1.5 py310h2372a71_0 conda-forge

matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge

mistune 3.0.2 pyhd8ed1ab_0 conda-forge

mpi 1.0 openmpi conda-forge

mpi4py 3.1.6 py310hb2ba3f8_1 conda-forge

multipledispatch 0.6.0 py_0 conda-forge

muscle 3.8.1551 h7d875b9_6 bioconda

nbclient 0.10.0 pyhd8ed1ab_0 conda-forge

nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge

nbformat 5.10.4 pyhd8ed1ab_0 conda-forge

ncurses 6.5 h59595ed_0 conda-forge

nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge

notebook 7.2.1 pyhd8ed1ab_0 conda-forge

notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge

numba 0.59.1 py310h7dc5dd1_0 conda-forge

numpy 1.26.4 py310hb13e2d6_0 conda-forge

openjpeg 2.5.2 h488ebb8_0 conda-forge

openmpi 5.0.3 hfd7b305_106 conda-forge

openssl 3.3.1 h4ab18f5_1 conda-forge

overrides 7.7.0 pyhd8ed1ab_0 conda-forge

packaging 24.1 pyhd8ed1ab_0 conda-forge

pandas 2.2.2 py310hf9f9076_1 conda-forge

pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge

parso 0.8.4 pyhd8ed1ab_0 conda-forge

pbzip2 1.1.13 h1fcc475_2 conda-forge

pcre2 10.43 hcad00b1_0 conda-forge

perl 5.32.1 7_hd590300_perl5 conda-forge

pexpect 4.9.0 pyhd8ed1ab_0 conda-forge

pickleshare 0.7.5 py_1003 conda-forge

pigz 2.8 h2797004_0 conda-forge

pillow 10.3.0 py310hf73ecf8_0 conda-forge

pip 24.0 pyhd8ed1ab_0 conda-forge

pixman 0.43.2 h59595ed_0 conda-forge

pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge

platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge

prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge

prompt-toolkit 3.0.47 pyha770c72_0 conda-forge

psutil 6.0.0 py310hc51659f_0 conda-forge

pthread-stubs 0.4 h36c2ea0_1001 conda-forge

ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge

pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge

pycairo 1.26.1 py310he029307_0 conda-forge

pycparser 2.22 pyhd8ed1ab_0 conda-forge

pygments 2.18.0 pyhd8ed1ab_0 conda-forge

pypng 0.20220715.0 pyhd8ed1ab_0 conda-forge

pysam 0.22.1 py310h804392c_1 bioconda

pysocks 1.7.1 pyha2e5f31_6 conda-forge

python 3.10.14 hd12c33a_0_cpython conda-forge

python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge

python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge

python-isal 1.6.1 py310h2372a71_0 conda-forge

python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge

python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge

python-zlib-ng 0.4.3 py310hf89ee4d_1 conda-forge

python_abi 3.10 4_cp310 conda-forge

pytz 2024.1 pyhd8ed1ab_0 conda-forge

pyyaml 6.0.1 py310h2372a71_1 conda-forge

pyzmq 26.0.3 py310h6883aea_0 conda-forge

readline 8.2 h8228510_1 conda-forge

referencing 0.35.1 pyhd8ed1ab_0 conda-forge

reportlab 4.2.2 py310hc51659f_0 conda-forge

requests 2.32.3 pyhd8ed1ab_0 conda-forge

rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge

rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge

rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge

rpds-py 0.18.1 py310he421c4c_0 conda-forge

samtools 1.20 h50ea8bc_0 bioconda

scipy 1.14.0 py310h93e2701_1 conda-forge

send2trash 1.8.3 pyh0d859eb_0 conda-forge

setuptools 70.1.1 pyhd8ed1ab_0 conda-forge

six 1.16.0 pyh6c4a22f_0 conda-forge

sniffio 1.3.1 pyhd8ed1ab_0 conda-forge

soupsieve 2.5 pyhd8ed1ab_1 conda-forge

stack_data 0.6.2 pyhd8ed1ab_0 conda-forge

terminado 0.18.1 pyh0d859eb_0 conda-forge

tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge

tk 8.6.13 noxft_h4845f30_101 conda-forge

tomli 2.0.1 pyhd8ed1ab_0 conda-forge

tornado 6.4.1 py310hc51659f_0 conda-forge

toyplot 1.0.3 pyhd8ed1ab_0 conda-forge

tqdm 4.66.4 pyhd8ed1ab_0 conda-forge

traitlets 5.14.3 pyhd8ed1ab_0 conda-forge

types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge

typing-extensions 4.12.2 hd8ed1ab_0 conda-forge

typing_extensions 4.12.2 pyha770c72_0 conda-forge

typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge

tzdata 2024a h0c530f3_0 conda-forge

uri-template 1.3.0 pyhd8ed1ab_0 conda-forge

urllib3 2.2.2 pyhd8ed1ab_1 conda-forge

vsearch 2.23.0 h6a68c12_0 bioconda

wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge

webcolors 24.6.0 pyhd8ed1ab_0 conda-forge

webencodings 0.5.1 pyhd8ed1ab_2 conda-forge

websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge

wheel 0.43.0 pyhd8ed1ab_1 conda-forge

xopen 2.0.1 py310hff52083_0 conda-forge

xorg-kbproto 1.0.7 h7f98852_1002 conda-forge

xorg-libice 1.1.1 hd590300_0 conda-forge

xorg-libsm 1.2.4 h7391055_0 conda-forge

xorg-libx11 1.8.9 h8ee46fc_0 conda-forge

xorg-libxau 1.0.11 hd590300_0 conda-forge

xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge

xorg-libxext 1.3.4 h0b41bf4_2 conda-forge

xorg-libxrender 0.9.11 hd590300_0 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

zeromq 4.3.5 h75354e8_4 conda-forge

zipp 3.19.2 pyhd8ed1ab_0 conda-forge

zlib 1.2.13 h4ab18f5_6 conda-forge

zlib-ng 2.2.1 he02047a_0 conda-forge

zstandard 0.22.0 py310hab88d88_1 conda-forge

zstd 1.5.6 ha6fb4c9_0 conda-forge

-----------AND here is the conda list in a different environment with running the python 3.12 where it always fails in step 3

packages in environment at /rhome/ckzq2024/.conda/envs/ipyrad2:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge

_openmp_mutex 4.5 2_gnu conda-forge

anyio 4.4.0 pyhd8ed1ab_0 conda-forge

argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge

argon2-cffi-bindings 21.2.0 py312h98912ed_4 conda-forge

arrow 1.3.0 pyhd8ed1ab_0 conda-forge

asttokens 2.4.1 pyhd8ed1ab_0 conda-forge

async-lru 2.0.4 pyhd8ed1ab_0 conda-forge

attrs 23.2.0 pyh71513ae_0 conda-forge

babel 2.14.0 pyhd8ed1ab_0 conda-forge

beautifulsoup4 4.12.3 pyha770c72_0 conda-forge

bedtools 2.31.1 hf5e1c6e_1 bioconda

bleach 6.1.0 pyhd8ed1ab_0 conda-forge

brotli-python 1.1.0 py312h30efb56_1 conda-forge

bwa 0.7.18 he4a0461_0 bioconda

bzip2 1.0.8 hd590300_5 conda-forge

c-ares 1.28.1 hd590300_0 conda-forge

ca-certificates 2024.7.4 hbcca054_0 conda-forge

cached-property 1.5.2 hd8ed1ab_1 conda-forge

cached_property 1.5.2 pyha770c72_1 conda-forge

cairo 1.18.0 h3faef2a_0 conda-forge

certifi 2024.6.2 pyhd8ed1ab_0 conda-forge

cffi 1.16.0 py312hf06ca03_0 conda-forge

chardet 5.2.0 py312h7900ff3_1 conda-forge

charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge

colorama 0.4.6 pyhd8ed1ab_0 conda-forge

comm 0.2.2 pyhd8ed1ab_0 conda-forge

custom-inherit 2.4.1 pyhd8ed1ab_0 conda-forge

cutadapt 4.9 py312hf67a6ed_0 bioconda

debugpy 1.8.2 py312h7070661_0 conda-forge

decorator 5.1.1 pyhd8ed1ab_0 conda-forge

defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge

dnaio 1.2.1 py312hf67a6ed_1 bioconda

entrypoints 0.4 pyhd8ed1ab_0 conda-forge

exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge

executing 2.0.1 pyhd8ed1ab_0 conda-forge

expat 2.6.2 h59595ed_0 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 h77eed37_2 conda-forge

fontconfig 2.14.2 h14ed4e7_0 conda-forge

fonts-conda-ecosystem 1 0 conda-forge

fonts-conda-forge 1 0 conda-forge

fqdn 1.5.1 pyhd8ed1ab_0 conda-forge

freetype 2.12.1 h267a509_2 conda-forge

freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge

future 1.0.0 pyhd8ed1ab_0 conda-forge

h11 0.14.0 pyhd8ed1ab_0 conda-forge

h2 4.1.0 pyhd8ed1ab_0 conda-forge

h5py 3.11.0 nompi_py312hb7ab980_102 conda-forge

hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge

hpack 4.0.0 pyh9f0ad1d_0 conda-forge

htslib 1.20 h5efdd21_1 bioconda

httpcore 1.0.5 pyhd8ed1ab_0 conda-forge

httpx 0.27.0 pyhd8ed1ab_0 conda-forge

hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge

icu 73.2 h59595ed_0 conda-forge

idna 3.7 pyhd8ed1ab_0 conda-forge

impi_rt 2021.12.0 ha770c72_536 conda-forge

importlib-metadata 8.0.0 pyha770c72_0 conda-forge

importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge

importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge

ipykernel 6.29.5 pyh3099207_0 conda-forge

ipyparallel 8.8.0 pyhd8ed1ab_0 conda-forge

ipyrad 0.9.93 pyh7cba7a3_0 bioconda

ipython 8.26.0 pyh707e725_0 conda-forge

isa-l 2.31.0 hd590300_1 conda-forge

isoduration 20.11.0 pyhd8ed1ab_0 conda-forge

jedi 0.19.1 pyhd8ed1ab_0 conda-forge

jinja2 3.1.4 pyhd8ed1ab_0 conda-forge

json5 0.9.25 pyhd8ed1ab_0 conda-forge

jsonpointer 3.0.0 py312h7900ff3_0 conda-forge

jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge

jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge

jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge

jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge

jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge

jupyter_core 5.7.2 py312h7900ff3_0 conda-forge

jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge

jupyter_server 2.14.1 pyhd8ed1ab_0 conda-forge

jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge

jupyterlab 4.2.3 pyhd8ed1ab_0 conda-forge

jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge

jupyterlab_server 2.27.2 pyhd8ed1ab_0 conda-forge

keyutils 1.6.1 h166bdaf_0 conda-forge

krb5 1.21.3 h659f571_0 conda-forge

lcms2 2.16 hb7c19ff_0 conda-forge

ld_impl_linux-64 2.40 hf3520f5_7 conda-forge

lerc 4.0.0 h27087fc_0 conda-forge

libaec 1.1.3 h59595ed_0 conda-forge

libblas 3.9.0 22_linux64_openblas conda-forge

libcblas 3.9.0 22_linux64_openblas conda-forge

libcurl 8.8.0 hca28451_1 conda-forge

libdeflate 1.20 hd590300_0 conda-forge

libedit 3.1.20191231 he28a2e2_2 conda-forge

libev 4.33 hd590300_2 conda-forge

libexpat 2.6.2 h59595ed_0 conda-forge

libffi 3.4.2 h7f98852_5 conda-forge

libgcc-ng 14.1.0 h77fa898_0 conda-forge

libgfortran-ng 14.1.0 h69a702a_0 conda-forge

libgfortran5 14.1.0 hc5f4f2c_0 conda-forge

libglib 2.80.2 hf974151_0 conda-forge

libgomp 14.1.0 h77fa898_0 conda-forge

libiconv 1.17 hd590300_2 conda-forge

libjpeg-turbo 3.0.0 hd590300_1 conda-forge

liblapack 3.9.0 22_linux64_openblas conda-forge

libllvm14 14.0.6 hcd5def8_4 conda-forge

libnghttp2 1.58.0 h47da74e_1 conda-forge

libnsl 2.0.1 hd590300_0 conda-forge

libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge

libpng 1.6.43 h2797004_0 conda-forge

libsodium 1.0.18 h36c2ea0_1 conda-forge

libsqlite 3.46.0 hde9e2c9_0 conda-forge

libssh2 1.11.0 h0841786_0 conda-forge

libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge

libtiff 4.6.0 h1dd3fc0_3 conda-forge

libuuid 2.38.1 h0b41bf4_0 conda-forge

libwebp-base 1.4.0 hd590300_0 conda-forge

libxcb 1.15 h0b41bf4_0 conda-forge

libxcrypt 4.4.36 hd590300_1 conda-forge

libzlib 1.2.13 h4ab18f5_6 conda-forge

llvmlite 0.42.0 py312hb06c811_1 conda-forge

markupsafe 2.1.5 py312h98912ed_0 conda-forge

matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge

mistune 3.0.2 pyhd8ed1ab_0 conda-forge

mpi 1.0 impi conda-forge

mpi4py 3.1.6 py312h61186ca_1 conda-forge

multipledispatch 0.6.0 py_0 conda-forge

muscle 3.8.1551 h7d875b9_6 bioconda

nbclient 0.10.0 pyhd8ed1ab_0 conda-forge

nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge

nbformat 5.10.4 pyhd8ed1ab_0 conda-forge

ncurses 6.5 h59595ed_0 conda-forge

nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge

notebook 7.2.1 pyhd8ed1ab_0 conda-forge

notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge

numba 0.59.1 py312hacefee8_0 conda-forge

numpy 1.26.4 py312heda63a1_0 conda-forge

openjpeg 2.5.2 h488ebb8_0 conda-forge

openssl 3.3.1 h4ab18f5_1 conda-forge

overrides 7.7.0 pyhd8ed1ab_0 conda-forge

packaging 24.1 pyhd8ed1ab_0 conda-forge

pandas 2.2.2 py312h1d6d2e6_1 conda-forge

pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge

parso 0.8.4 pyhd8ed1ab_0 conda-forge

pbzip2 1.1.13 h1fcc475_2 conda-forge

pcre2 10.43 hcad00b1_0 conda-forge

perl 5.32.1 7_hd590300_perl5 conda-forge

pexpect 4.9.0 pyhd8ed1ab_0 conda-forge

pickleshare 0.7.5 py_1003 conda-forge

pigz 2.8 h2797004_0 conda-forge

pillow 10.3.0 py312hdcec9eb_0 conda-forge

pip 24.0 pyhd8ed1ab_0 conda-forge

pixman 0.43.2 h59595ed_0 conda-forge

pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge

platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge

prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge

prompt-toolkit 3.0.47 pyha770c72_0 conda-forge

psutil 6.0.0 py312h9a8786e_0 conda-forge

pthread-stubs 0.4 h36c2ea0_1001 conda-forge

ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge

pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge

pycairo 1.26.1 py312h3bc4990_0 conda-forge

pycparser 2.22 pyhd8ed1ab_0 conda-forge

pygments 2.18.0 pyhd8ed1ab_0 conda-forge

pypng 0.20220715.0 pyhd8ed1ab_0 conda-forge

pysam 0.22.1 py312hcfdcdd7_1 bioconda

pysocks 1.7.1 pyha2e5f31_6 conda-forge

python 3.12.3 hab00c5b_0_cpython conda-forge

python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge

python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge

python-isal 1.6.1 py312h98912ed_0 conda-forge

python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge

python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge

python-zlib-ng 0.4.3 py312hdfe76eb_1 conda-forge

python_abi 3.12 4_cp312 conda-forge

pytz 2024.1 pyhd8ed1ab_0 conda-forge

pyyaml 6.0.1 py312h98912ed_1 conda-forge

pyzmq 26.0.3 py312h8fd38d8_0 conda-forge

readline 8.2 h8228510_1 conda-forge

referencing 0.35.1 pyhd8ed1ab_0 conda-forge

reportlab 4.2.2 py312h9a8786e_0 conda-forge

requests 2.32.3 pyhd8ed1ab_0 conda-forge

rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge

rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge

rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge

rpds-py 0.18.1 py312h4413252_0 conda-forge

samtools 1.20 h50ea8bc_0 bioconda

scipy 1.14.0 py312hc2bc53b_0 conda-forge

send2trash 1.8.3 pyh0d859eb_0 conda-forge

setuptools 70.1.1 pyhd8ed1ab_0 conda-forge

six 1.16.0 pyh6c4a22f_0 conda-forge

sniffio 1.3.1 pyhd8ed1ab_0 conda-forge

soupsieve 2.5 pyhd8ed1ab_1 conda-forge

stack_data 0.6.2 pyhd8ed1ab_0 conda-forge

terminado 0.18.1 pyh0d859eb_0 conda-forge

tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge

tk 8.6.13 noxft_h4845f30_101 conda-forge

tomli 2.0.1 pyhd8ed1ab_0 conda-forge

tornado 6.4.1 py312h9a8786e_0 conda-forge

toyplot 1.0.3 pyhd8ed1ab_0 conda-forge

tqdm 4.66.4 pyhd8ed1ab_0 conda-forge

traitlets 5.14.3 pyhd8ed1ab_0 conda-forge

types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge

typing-extensions 4.12.2 hd8ed1ab_0 conda-forge

typing_extensions 4.12.2 pyha770c72_0 conda-forge

typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge

tzdata 2024a h0c530f3_0 conda-forge

uri-template 1.3.0 pyhd8ed1ab_0 conda-forge

urllib3 2.2.2 pyhd8ed1ab_1 conda-forge

vsearch 2.14.1 h2d02072_0 bioconda

wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge

webcolors 24.6.0 pyhd8ed1ab_0 conda-forge

webencodings 0.5.1 pyhd8ed1ab_2 conda-forge

websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge

wheel 0.43.0 pyhd8ed1ab_1 conda-forge

xopen 2.0.1 py312h7900ff3_0 conda-forge

xorg-kbproto 1.0.7 h7f98852_1002 conda-forge

xorg-libice 1.1.1 hd590300_0 conda-forge

xorg-libsm 1.2.4 h7391055_0 conda-forge

xorg-libx11 1.8.9 h8ee46fc_0 conda-forge

xorg-libxau 1.0.11 hd590300_0 conda-forge

xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge

xorg-libxext 1.3.4 h0b41bf4_2 conda-forge

xorg-libxrender 0.9.11 hd590300_0 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

zeromq 4.3.5 h75354e8_4 conda-forge

zipp 3.19.2 pyhd8ed1ab_0 conda-forge

zlib 1.2.13 h4ab18f5_6 conda-forge

zlib-ng 2.2.1 he02047a_0 conda-forge

zstandard 0.22.0 py312h5b18bf6_1 conda-forge

zstd 1.5.6 ha6fb4c9_0 conda-forge

On Mon, Jul 8, 2024 at 11:26 AM Carrie Kiel @.***> wrote:

Hi Issac attached is my clean install / I also wiped my miniconda3 and created a new environment and look how slow step one is going with python 3.10. See attached

On Mon, Jul 8, 2024 at 10:35 AM Isaac Overcast @.***> wrote:

I don't know what's happening on your new cluster, but I can't reproduce this error. I ran it on python 3.12.3 with a clean conda install and step 3 ran without error.

---

ipyrad [v.0.9.96] Interactive assembly and analysis of RAD-seq data

Parallel connection | ___: 30 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:00:37 | dereplicating [####################] 100% 0:34:21 | clustering/mapping [####################] 100% 0:00:00 | building clusters [####################] 100% 0:00:00 | chunking clusters [####################] 100% 0:34:06 | aligning clusters [####################] 100% 0:00:06 | concat clusters [####################] 100% 0:00:06 | calc cluster stats Parallel connection closed.

Can you post the output of conda list inside the ipyrad environment? I really can't think of why this would be happening inside a clean install on another cluster. Perhaps there's a problem with the environment, sometimes HPC systems will put directories in your PATH that conflict or step on conda stuff.

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2214790790, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYN46JJV7BK7FUOMKMLZLLEULAVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUG44TANZZGA . You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

From gitter:

It seems like it randomly crashes on step 3 on all of our 3rd gen epyc system.
ckiel3 was able to get it run a few time on our AMD system.

I tested the same slurm script and conda environment on an Intel system and it finishes every time.

This makes me think it is either something about piping all the data or muscle is crashing on this hw.

[isaacovercast]

Hi Carrie, Any updates on this? Hopefully the HPC admin was able to figure out a solution. Let me know. Hope you're doing well, -isaac

[ckiel3]

Hi Issac hope you are well! Yes, just got back from vacation. I will post this solution on GitHub and Gitter. Viet installed download an older version of Muscle from the source and replaced it in the environment. It seems that the new version of Muscle was not compatible with the chip on our HPC.

From Viet: “Since I saw it segfault/crashed in the system log that you don’t have access to. So I went on here https://drive5.com/muscle/downloads_v3.htm to download the 3.8 version (https://drive5.com/muscle/muscle_src_3.8.1551.tar.gz) to replace the one muscle that was in the virtual environment."

It works great now! I tested it on larger datasets and all have run to completion. I really want to thank you both for your commitment and tenacity for solving this problem.

On Mon, Aug 12, 2024 at 1:21 PM Isaac Overcast @.***> wrote:

Hi Carrie, Any updates on this? Hopefully the HPC admin was able to figure out a solution. Let me know. Hope you're doing well, -isaac

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/562#issuecomment-2284839455, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXZYM43XKMYG4JHACGOBTZREKN3AVCNFSM6AAAAABKICT3VWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBUHAZTSNBVGU . You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

Hi Carrie,

Wow, that is a very crazy bug, and I'm happy to hear that Viet found a solution. Thank you for posting the follow-up fix for downloading and installing the older version of muscle. Hopefully if anybody in the future runs into this problem they will find this and it'll make it easier for them to figure it out faster. Wonderful that we found a solution!