I can't run metaprob2

[esraagithub]

Hello I am a biologist i have a problem in running metaprob2.

I followed all instructions in this link: https://github.com/frankandreace/metaprob2

when i write this code i get "permission denied" ./METAPROB2.sh -h bash: ./METAPROB2.sh: Permission denied

also i couldn't find "METAPROB2" file in any directory so i couldn't run the program using ./METAPROB2 ...... like this example: ./METAPROB2 -s[number of expected species/genera]-c[minimum chain score] -t[number of cores to be used]-l <fasta/fastq input file>

but it run with this code ./MetaProb ..... but it gave me "Killed" at the end N. Cluster: 0 Parameter q: 30 Parameter m: 5 Parameter SeedSize: 9000 Parameter lmerfreq: 4 Parameter Kmeans iteration max: 100 Norm: D2star_All_Read_Prob_Lmer_Euclidian Graph Type: Paired Loading Sequences... Complete Loaded sequences: 23744520 Extract q-mer from Sequences... Killed

[frankandreace]

Hi, try this: go to the directory where METRAPROB2.sh is and execute 'chmod +x METRAPROB2.sh'. This should fix your problem. You can also avoid this passage by running 'sh METRAPROB2.sh' instead of './METAPROB2.sh' and it should work.

You get kill message because MetaProb is a C++ tool that does not accept arguments as the METAPROB2 pipeline does. It is not the same thing. METAPROB2 pipeline has several steps before MetaProb to increase its performance. To have a look at MetaProb manual, please visit https://bitbucket.org/samu661/metaprob/src/master/. Be aware that the source code provided there is not longer maintained and it was not working for me, so use directly the one I provide in this repo.

Let me know if it works!

[esraagithub]

Hi, try this: go to the directory where METRAPROB2.sh is and execute 'chmod +x METRAPROB2.sh'. This should fix your problem. You can also avoid this passage by running 'sh METRAPROB2.sh' instead of './METAPROB2.sh' and it should work.

You get kill message because MetaProb is a C++ tool that does not accept arguments as the METAPROB2 pipeline does. It is not the same thing. METAPROB2 pipeline has several steps before MetaProb to increase its performance. To have a look at MetaProb manual, please visit https://bitbucket.org/samu661/metaprob/src/master/. Be aware that the source code provided there is not longer maintained and it was not working for me, so use directly the one I provide in this repo.

Let me know if it works!

that really help i modified directories of MINIMAP2, MINIASM, metaprob,python and conda env to my own paths i run chmod +x METRAPROB2.sh then ./METRAPROB2.sh

note: running 'sh METRAPROB2.sh' result into the following error: METAPROB2.sh: 85: [[: not found METAPROB2.sh: 93: Bad substitution

then i run this code: ./METAPROB2.sh -t 8 ../trimmomatic_result/sample2merged.fasta ../metaprob_result metaprob_bin i got the following error at the end:

[M::main] ===> Step 4.5: aggressively cutting short overlaps <=== [M::asg_arc_del_short] removed 0 short overlaps [M::main] ===> Step 5: generating unitigs <=== [M::main] Version: 0.3-r179 [M::main] CMD: ../miniasm/miniasm -12 -m1 -g10000 -o1 -d1 -I0.00001 -s1 -i0.00001 -d10000 -F0.01 -c0 -e0 -n0 -r0.011,0.01 -f ../trimmomatic_result/sample2merged.fasta ../metaprob_result/metaprob2_tmp/metaprob_bin.paf [M::main] Real time: 1440.677 sec; CPU: 1428.775 sec ./count_reads.sh: 12: [: ./trimmomatic_result/sample2merged.fasta: unexpected operator ./count_reads.sh: 22: [: p: unexpected operator ./METAPROB2.sh: line 129: source: ../miniconda3: is a directory [METAPROB2.sh] Running COMMUNITY DETECTION Traceback (most recent call last): File "/root/esraa/metaprob2/.//community_detection_clear.py", line 14, in from sknetwork.clustering import Louvain File "/root/esraa/miniconda3/lib/python3.9/site-packages/sknetwork/init.py", line 9, in import sknetwork.topology File "/root/esraa/miniconda3/lib/python3.9/site-packages/sknetwork/topology/init.py", line 2, in from sknetwork.topology.kcliques import Cliques File "sknetwork/topology/kcliques.pyx", line 1, in init sknetwork.topology.kcliques ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. [METAPROB2.sh] Running METAPROB

Fail to open: ../metaprob_result/metaprob2_tmp/metaprob_bin.fasta