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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
451 stars 149 forks source link

Trim Galore frozen at adapter trimming step #190

Open faye-romero opened 2 months ago

faye-romero commented 2 months ago

Hello @FelixKrueger ,

Trim Galore seems to freeze at the adapter trimming step. The job continues to run, but the files have not been updated in a long time. Here is my command:

/path/to/trim_galore L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz L10_FKDN230346750-1A_HW7YWDSX5_L3_2.fq.gz --cores 8 --quality 20 --fastqc --length 20 --paired --retain_unpaired --output_dir ./trimgalore_out

And here is the error log:

Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 2.10
Could not detect version of Python used by Cutadapt from the first line of Cutadapt (but found this: >>>#!/bin/bash<<<)
Letting the (modified) Cutadapt deal with the Python version instead
Parallel gzip (pigz) detected. Proceeding with multicore (de)compression using 8 cores

Proceeding with 'pigz -p 4' for decompression
To decrease CPU usage of decompression, please install 'igzip' and run again

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Output will be written into the directory: /ocean/projects/bio230049p/shared/FSJ_BioInf/L10/trimgalore_out/

AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /ocean/projects/bio230049p/shared/rawData/L10/L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type    Count   Sequence    Sequences analysed  Percentage
Illumina    940 AGATCGGAAGAGC   1000000 0.09
smallRNA    16  TGGAATTCTCGG    1000000 0.00
Nextera 8   CTGTCTCTTATA    1000000 0.00
Using Illumina adapter for trimming (count: 940). Second best hit was smallRNA (count: 16)

Writing report to '/ocean/projects/bio230049p/shared/FSJ_BioInf/L10/trimgalore_out/L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /ocean/projects/bio230049p/shared/rawData/L10/L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 2.10
Python version: could not detect
Number of cores used for trimming: 8
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bb (default)
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 2.10). Setting -j 8
Writing final adapter and quality trimmed output to L10_FKDN230346750-1A_HW7YWDSX5_L3_1_trimmed.fq.gz

  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /ocean/projects/bio230049p/shared/rawData/L10/L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz <<<

The log ends there. The only output files are L10_FKDN230346750-1A_HW7YWDSX5_L3_1.fq.gz_trimming_report.txt and L10_FKDN230346750-1A_HW7YWDSX5_L3_1_trimmed.fq.gz, which again, haven't been updated for a long time. The trimming report only displays the summary of the run parameters and nothing else.

Any help would be much appreciated.

FelixKrueger commented 2 months ago

Hmm, this is odd. I saw the following line: Python version: could not detect. Maybe this has something to do with it? Could you try to run e.g. cutadapt --help, or try to start cutadapt for the fille L10_FKDN230346750-1A_HW7YWDSX5_L3_1_trimmed.fq.gz on its own?

tyxdavid commented 2 months ago

Same problem here when processing paired sequencing data. Strangely, (1) it happened on some files but not the others; (2) when I move the same sequencing data to another machine for processing, it ran smoothly. The difference between the machine (machine A) that could not process and the one that could (machine B), was the OS system and the conda environment. However, the version of TrimGalore on A and B are same (0.6.10).

On machine A, the OS is CentOS 8, and the conda env. is: 

_libgc_libgcc_mutex             0.1                 conda_forge    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blas                      1.0                    openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
bottleneck                1.3.2            py36heb32a55_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
brotli                    1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
brotli-bin                1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
bzip2                     1.0.8                h5eee18b_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
c-ares                    1.19.1               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ca-certificates           2024.3.11            h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
certifi                   2021.5.30        py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cffi                      1.14.6           py36h400218f_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
curl                      8.2.1                h37d81fd_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cutadapt                  3.5              py36h91eb985_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
cycler                    0.11.0             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dataclasses               0.8                pyh4f3eec9_6    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dbus                      1.13.18              hb2f20db_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dnaio                     0.6.0            py36hc5360cc_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
expat                     2.5.0                h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fastqc                    0.12.1               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono 2.37                 hd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fontconfig                2.14.1               h4c34cd2_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fonttools                 4.25.0             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
freetype                  2.12.1               h4a9f257_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gdbm                      1.18                 hd4cb3f1_4    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gettext                   0.21.0               h39681ba_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
glib                      2.68.4               h9c3ff4c_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
glib-tools                2.68.4               h9c3ff4c_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
htseq                     0.13.5           py36h7d1f7ee_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
icu                       58.2                 he6710b0_3    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
importlib_resources       5.2.0              pyhd3eb1b0_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
isa-l                     2.30.0               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jpeg                      9e                   h5eee18b_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
kiwisolver                1.3.1            py36h2531618_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
krb5                      1.20.1               h568e23c_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
lcms2                     2.12                 h3be6417_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ld_impl_linux-64          2.38                 h1181459_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libblas                   3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libbrotlicommon           1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libbrotlidec              1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libbrotlienc              1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libcblas                  3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcurl                   8.2.1                h91b91d3_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libdeflate                1.0                  h14c3975_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
libedit                   3.1.20230828         h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libev                     4.33                 h7f8727e_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libffi                    3.3                  he6710b0_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgcc-ng                 13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            11.2.0               h00389a5_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgfortran5              11.2.0               h1234567_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libglib                   2.68.4               h3e27bee_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.16                 h7f8727e_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
liblapack                 3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.52.0               ha637b67_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libopenblas               0.3.21               h043d6bf_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libpng                    1.6.39               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libssh2                   1.10.0               h37d81fd_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libstdcxx-ng              13.2.0               h7e041cc_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.2.0                hecacb30_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libuuid                   1.41.5               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libwebp-base              1.3.2                h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxcb                    1.15                 h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxml2                   2.10.3               hcbfbd50_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libzlib                   1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lz4-c                     1.9.4                h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
matplotlib-base           3.3.4            py36h62a2d02_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
munkres                   1.1.4                      py_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ncurses                   6.4                  h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numexpr                   2.7.3            py36h4be448d_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy                     1.19.2           py36h6163131_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy-base                1.19.2           py36h75fe3a5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
olefile                   0.46               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openjdk                   8.0.152              h7b6447c_3    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openjpeg                  2.4.0                h3ad879b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openssl                   1.1.1w               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
packaging                 21.3               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pandas                    1.1.5            py36ha9443f7_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pbzip2                    1.1.13                        0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre                      8.45                 h295c915_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pcre2                     10.42                hebb0a14_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
perl                      5.26.2               h14c3975_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pigz                      2.6                  h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pillow                    8.3.1            py36h2c7a002_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pip                       21.2.2           py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pycparser                 2.21               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pyparsing                 3.0.4              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pysam                     0.15.3           py36hda2845c_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
python                    3.6.13               h12debd9_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-dateutil           2.8.2              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-isal               0.11.1           py36h8f6f2f9_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-tzdata             2023.3             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python_abi                3.6                     2_cp36m    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytz                      2021.3             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
readline                  8.2                  h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
scipy                     1.5.3            py36h81d768a_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools                58.0.4           py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
six                       1.16.0             pyhd3eb1b0_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sqlite                    3.41.2               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tk                        8.6.12               h1ccaba5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tornado                   6.1              py36h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
trim-galore               0.6.10               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
tzdata                    2024a                h04d1e81_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
wheel                     0.37.1             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xopen                     1.2.0            py36h5fab9bb_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.10               h5eee18b_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zipp                      3.6.0              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zlib                      1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib-ng                   2.0.7                h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zstandard                 0.15.2           py36h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zstd                      1.5.5                hc292b87_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
c_mutex             0.1                 conda_forge    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blas                      1.0                    openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
bottleneck                1.3.2            py36heb32a55_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
brotli                    1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
brotli-bin                1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
bzip2                     1.0.8                h5eee18b_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
c-ares                    1.19.1               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ca-certificates           2024.3.11            h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
certifi                   2021.5.30        py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cffi                      1.14.6           py36h400218f_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
curl                      8.2.1                h37d81fd_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cutadapt                  3.5              py36h91eb985_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
cycler                    0.11.0             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dataclasses               0.8                pyh4f3eec9_6    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dbus                      1.13.18              hb2f20db_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dnaio                     0.6.0            py36hc5360cc_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
expat                     2.5.0                h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fastqc                    0.12.1               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono 2.37                 hd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fontconfig                2.14.1               h4c34cd2_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fonttools                 4.25.0             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
freetype                  2.12.1               h4a9f257_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gdbm                      1.18                 hd4cb3f1_4    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gettext                   0.21.0               h39681ba_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
glib                      2.68.4               h9c3ff4c_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
glib-tools                2.68.4               h9c3ff4c_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
htseq                     0.13.5           py36h7d1f7ee_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
icu                       58.2                 he6710b0_3    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
importlib_resources       5.2.0              pyhd3eb1b0_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
isa-l                     2.30.0               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jpeg                      9e                   h5eee18b_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
kiwisolver                1.3.1            py36h2531618_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
krb5                      1.20.1               h568e23c_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
lcms2                     2.12                 h3be6417_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ld_impl_linux-64          2.38                 h1181459_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libblas                   3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libbrotlicommon           1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libbrotlidec              1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libbrotlienc              1.0.9                h5eee18b_7    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libcblas                  3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcurl                   8.2.1                h91b91d3_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libdeflate                1.0                  h14c3975_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
libedit                   3.1.20230828         h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libev                     4.33                 h7f8727e_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libffi                    3.3                  he6710b0_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgcc-ng                 13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            11.2.0               h00389a5_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgfortran5              11.2.0               h1234567_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libglib                   2.68.4               h3e27bee_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.16                 h7f8727e_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
liblapack                 3.9.0           16_linux64_openblas    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.52.0               ha637b67_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libopenblas               0.3.21               h043d6bf_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libpng                    1.6.39               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libssh2                   1.10.0               h37d81fd_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libstdcxx-ng              13.2.0               h7e041cc_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.2.0                hecacb30_2    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libuuid                   1.41.5               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libwebp-base              1.3.2                h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxcb                    1.15                 h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxml2                   2.10.3               hcbfbd50_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libzlib                   1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lz4-c                     1.9.4                h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
matplotlib-base           3.3.4            py36h62a2d02_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
munkres                   1.1.4                      py_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ncurses                   6.4                  h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numexpr                   2.7.3            py36h4be448d_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy                     1.19.2           py36h6163131_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy-base                1.19.2           py36h75fe3a5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
olefile                   0.46               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openjdk                   8.0.152              h7b6447c_3    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openjpeg                  2.4.0                h3ad879b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openssl                   1.1.1w               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
packaging                 21.3               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pandas                    1.1.5            py36ha9443f7_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pbzip2                    1.1.13                        0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre                      8.45                 h295c915_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pcre2                     10.42                hebb0a14_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
perl                      5.26.2               h14c3975_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pigz                      2.6                  h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pillow                    8.3.1            py36h2c7a002_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pip                       21.2.2           py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pycparser                 2.21               pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pyparsing                 3.0.4              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pysam                     0.15.3           py36hda2845c_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
python                    3.6.13               h12debd9_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-dateutil           2.8.2              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-isal               0.11.1           py36h8f6f2f9_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-tzdata             2023.3             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python_abi                3.6                     2_cp36m    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytz                      2021.3             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
readline                  8.2                  h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
scipy                     1.5.3            py36h81d768a_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools                58.0.4           py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
six                       1.16.0             pyhd3eb1b0_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sqlite                    3.41.2               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tk                        8.6.12               h1ccaba5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tornado                   6.1              py36h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
trim-galore               0.6.10               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
tzdata                    2024a                h04d1e81_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
wheel                     0.37.1             pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xopen                     1.2.0            py36h5fab9bb_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.10               h5eee18b_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zipp                      3.6.0              pyhd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zlib                      1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib-ng                   2.0.7                h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zstandard                 0.15.2           py36h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zstd                      1.5.5                hc292b87_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

On machine B, the OS is CentOS 7, and the conda env. is: 

_libgcc_mutex             0.1                 conda_forge    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bowtie                    1.3.1            py36h89b54cb_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bwa                       0.7.17              he4a0461_11    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
ca-certificates           2024.3.11            h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
certifi                   2021.5.30        py36h06a4308_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cutadapt                  3.5              py36h91eb985_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
dataclasses               0.8                pyh4f3eec9_6    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dbus                      1.13.18              hb2f20db_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
dnaio                     0.6.0            py36hc5360cc_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
expat                     2.5.0                h6a678d5_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fastqc                    0.12.1               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono 2.37                 hd3eb1b0_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fontconfig                2.14.1               h52c9d5c_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
freetype                  2.12.1               h4a9f257_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
glib                      2.69.1               h4ff587b_1    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
icu                       58.2                 he6710b0_3    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
isa-l                     2.30.0               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ld_impl_linux-64          2.38                 h1181459_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libffi                    3.3                  he6710b0_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgcc-ng                 13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.2.0               h807b86a_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng                    1.6.39               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libstdcxx-ng              11.2.0               h1234567_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libuuid                   1.41.5               h5eee18b_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxcb                    1.15                 h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxml2                   2.9.14               h74e7548_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libzlib                   1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses                   6.3                  h5eee18b_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openjdk                   11.0.13              h87a67e3_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openssl                   1.1.1w               h7f8727e_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pbzip2                    1.1.13                        0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre                      8.45                 h295c915_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
perl                      5.26.2               h14c3975_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pigz                      2.6                  h27cfd23_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pip                       21.2.2           py36h06a4308_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python                    3.6.13               h12debd9_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-isal               0.11.1           py36h8f6f2f9_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi                3.6                     2_cp36m    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline                  8.1.2                h7f8727e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
setuptools                49.6.0           py36h5fab9bb_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sqlite                    3.38.5               hc218d9a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tbb                       2020.2               h4bd325d_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk                        8.6.12               h1ccaba5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
trim-galore               0.6.10               hdfd78af_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
wheel                     0.37.1             pyhd3eb1b0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xopen                     1.2.0            py36h5fab9bb_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.5                h7f8727e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zlib                      1.2.13               hd590300_5    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
FelixKrueger commented 2 months ago

Thanks for the comment. This is arguably really difficult to spot (or debug...). So try to update Conda or switch machines, and hope for the better?