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RVanDamme / MUFFIN

hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis
https://rvandamme.github.io/MUFFIN_Documentation/#introduction
GNU General Public License v3.0
65 stars 11 forks source link

ImportError: this version of pandas is incompatible with numpy < 1.12.0 #16

Closed CeciliaDeng closed 4 months ago

CeciliaDeng commented 3 years ago

Hi @RVanDamme, I'm keen to try MUFFIN and ran the test with command

git clone https://github.com/RVanDamme/MUFFIN.git nextflow run RVanDamme/MUFFIN --output /workspace/18_MUFFIN/01_TEST --rna --cpus 8 --memory 32g -profile local,singularity,test

A README_output.txt and subset/ directory were created under the output folder. However, the process failed with

Command executed: mkdir concoct_out cut_up_fasta.py assembly.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa samtools index -@ 8 ont_sorted.bam samtools index -@ 8 illumina_sorted.bam concoct_coverage_table.py contigs_10K.bed *.bam > coverage_table.tsv concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_out --thread 8 merge_cutup_clustering.py concoct_out/clustering_gt1000.csv > concoct_out/clustering_merged.csv mkdir fasta_bins extract_fasta_bins.py assembly.fasta concoct_out/clustering_merged.csv --output_path fasta_bins Command exit status: 1 Command output: (empty)

Command error: Traceback (most recent call last): File "/opt/conda/bin/concoct_coverage_table.py", line 18, in import pandas as pd File "/opt/conda/lib/python2.7/site-packages/pandas/init.py", line 23, in from pandas.compat.numpy import * File "/opt/conda/lib/python2.7/site-packages/pandas/compat/numpy/init.py", line 24, in 'this pandas version'.format(_np_version)) ImportError: this version of pandas is incompatible with numpy < 1.12.0 your numpy version is 1.8.1. Please upgrade numpy to >= 1.12.0 to use this pandas version Work dir: /workspace/Other/work/d7/9a3c7a714f6185250a30a77d58d70d Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh

How to fix this, please? Thought numpy/panda versions were packed in the singularity image. Where is the .command.sh file? I can't find it under the current dir, the output dir, or the Work dir. Thanks.

replikation commented 3 years ago

hi

replikation commented 3 years ago

Hi,

i was not able to reproduce the error. would you please manually remove the concoct image and retry it? I tested the most recent master from git and let it rebuild (singularity images) and download everything ("clean slate").

these are the images created and used during the test run (located in ./work/singularity), please check also the sizes. singularity images sometimes have issues

533M Nov 17 18:22 nanozoo-checkm-1.1.3--c79a047.img
458M Nov 17 10:39 nanozoo-concoct-1.1.0--03a3888.img
213M Nov 17 10:17 nanozoo-eggnog-mapper-2.0.1--d5e0c8c.img
203M Nov 17 10:21 nanozoo-fastp-0.20.0--78a7c63.img
515M Nov 17 10:36 nanozoo-maxbin2-2.2.7--b643a6b.img
228M Nov 17 10:38 nanozoo-metabat2-2.13--0e2577e.img
1.3G Nov 17 17:45 nanozoo-metawrap-v1.3--a7eb9af.img
208M Nov 17 10:36 nanozoo-minimap2-2.17--caba7af.img
386M Nov 17 10:36 nanozoo-pilon-1.23--b21026d.img
368M Nov 17 18:21 nanozoo-sourmash-2.0.1--6970ddc.img
200M Nov 17 10:29 nanozoo-spades-3.13.1--2c2a4c0.img
222M Nov 17 10:17 nanozoo-template-3.8--ccd0653.img
CeciliaDeng commented 3 years ago

Thank you, @replikation. The test run has been pulling images and I haven't got the numpy error yet. Will try on real data if the test run finishes ok.