Orthofinder does not run further than blast

[Estherrr1997]

(blauwe_haai) kockelmans.e@localhost:/exports/nas/kockelmans.e$ orthofinder -o orthofinder_test_2 -d -f orthofinder_files/ /home/kockelmans.e/.conda/envs/blauwe_haai/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.23.1 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-09-07 12:25:06 : Starting OrthoFinder 2.5.4 32 thread(s) for highly parallel tasks (BLAST searches etc.) 4 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "fastme -i orthofinder_test_2/Results_Sep07/WorkingDirectory/SimpleTest.phy -o orthofinder_test_2/Results_Sep07/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing

2022-09-07 13:10:59 : Creating blast_nucl database 1 of 7 2022-09-07 13:14:53 : Creating blast_nucl database 2 of 7 2022-09-07 13:20:17 : Creating blast_nucl database 3 of 7 2022-09-07 13:23:43 : Creating blast_nucl database 4 of 7 2022-09-07 13:29:14 : Creating blast_nucl database 5 of 7 2022-09-07 13:30:27 : Creating blast_nucl database 6 of 7 2022-09-07 13:35:09 : Creating blast_nucl database 7 of 7

Running blast_nucl all-versus-all

Using 32 thread(s) 2022-09-07 13:38:34 : This may take some time.... 2022-09-07 13:38:36 : Done 0 of 49

WARNING: program called by OrthoFinder produced output to stderr

Command: blastn -outfmt 6 -evalue 0.001 -query orthofinder_test_2/Results_Sep07/WorkingDirectory/Species1.fa -db orthofinder_test_2/Results_Sep07/WorkingDirectory/blast_nuclDBSpecies2 | gzip > orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast1_2.txt.gz

Command: blastn -outfmt 6 -evalue 0.001 -query orthofinder_test_2/Results_Sep07/WorkingDirectory/Species1.fa -db orthofinder_test_2/Results_Sep07/WorkingDirectory/blast_nuclDBSpecies2 | gzip > orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast1_2.txt.gz

stdout

b'' stderr

b'Killed\n'

WARNING: program called by OrthoFinder produced output to stderr

Command: blastn -outfmt 6 -evalue 0.001 -query orthofinder_test_2/Results_Sep07/WorkingDirectory/Species0.fa -db orthofinder_test_2/Results_Sep07/WorkingDirectory/blast_nuclDBSpecies0 | gzip > orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast0_0.txt.gz

stdout

b'' stderr

b'Killed\n'

WARNING: program called by OrthoFinder produced output to stderr

Command: blastn -outfmt 6 -evalue 0.001 -query orthofinder_test_2/Results_Sep07/WorkingDirectory/Species2.fa -db orthofinder_test_2/Results_Sep07/WorkingDirectory/blast_nuclDBSpecies2 | gzip > orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast2_2.txt.gz

stdout

b'' stderr

b'Killed\n'

[this WARNING repeatedly]

I am using nucleotide data, as specified in the settings. When I look into the results, this is the output: (blauwe_haai) kockelmans.e@localhost:/exports/nas/kockelmans.e/orthofinder_test_2/Results_Sep07$ ls Log.txt WorkingDirectory

It only outputs the Log.txt: 2022-09-07 12:25:06 : Started OrthoFinder version 2.5.4 Command Line: /home/kockelmans.e/.conda/envs/blauwe_haai/bin/orthofinder -o orthofinder_test_2 -d -f orthofinder_files/

WorkingDirectory_Base: orthofinder_test_2/Results_Sep07/WorkingDirectory/

Species used: 0: GCA_003427335.1_Cpunctatum_v1.0_genomic.fa 1: GCA_003427355.1_Storazame_v1.0_genomic.fa 2: GCA_021869965.1_sRhiTyp1.1_genomic.fa 3: GCF_017639515.1_sCarCar2.pri_genomic.fa 4: GCF_018977255.1_IMCB_Cmil_1.0_genomic.fa 5: GCF_902713615.1_sScyCan1.1_genomic.fa 6: Pgla_V1_contigs_mt.fa

And the Workingdirectory contains the following files: (blauwe_haai) kockelmans.e@localhost:/exports/nas/kockelmans.e/orthofinder_test_2/Results_Sep07/WorkingDirectory$ ls Blast0_0.txt.gz Blast1_6.txt.gz Blast3_5.txt.gz Blast5_4.txt.gz Species2.fa blast_nuclDBSpecies0.nto blast_nuclDBSpecies2.not blast_nuclDBSpecies4.nhr blast_nuclDBSpecies5.ntf Blast0_1.txt.gz Blast2_0.txt.gz Blast3_6.txt.gz Blast5_5.txt.gz Species3.fa blast_nuclDBSpecies1.ndb blast_nuclDBSpecies2.nsq blast_nuclDBSpecies4.nin blast_nuclDBSpecies5.nto Blast0_2.txt.gz Blast2_1.txt.gz Blast4_0.txt.gz Blast5_6.txt.gz Species4.fa blast_nuclDBSpecies1.nhr blast_nuclDBSpecies2.ntf blast_nuclDBSpecies4.njs blast_nuclDBSpecies6.ndb Blast0_3.txt.gz Blast2_2.txt.gz Blast4_1.txt.gz Blast6_0.txt.gz Species5.fa blast_nuclDBSpecies1.nin blast_nuclDBSpecies2.nto blast_nuclDBSpecies4.not blast_nuclDBSpecies6.nhr Blast0_4.txt.gz Blast2_3.txt.gz Blast4_2.txt.gz Blast6_1.txt.gz Species6.fa blast_nuclDBSpecies1.njs blast_nuclDBSpecies3.ndb blast_nuclDBSpecies4.nsq blast_nuclDBSpecies6.nin Blast0_5.txt.gz Blast2_4.txt.gz Blast4_3.txt.gz Blast6_2.txt.gz SpeciesIDs.txt blast_nuclDBSpecies1.not blast_nuclDBSpecies3.nhr blast_nuclDBSpecies4.ntf blast_nuclDBSpecies6.njs Blast0_6.txt.gz Blast2_5.txt.gz Blast4_4.txt.gz Blast6_3.txt.gz blast_nuclDBSpecies0.ndb blast_nuclDBSpecies1.nsq blast_nuclDBSpecies3.nin blast_nuclDBSpecies4.nto blast_nuclDBSpecies6.not Blast1_0.txt.gz Blast2_6.txt.gz Blast4_5.txt.gz Blast6_4.txt.gz blast_nuclDBSpecies0.nhr blast_nuclDBSpecies1.ntf blast_nuclDBSpecies3.njs blast_nuclDBSpecies5.ndb blast_nuclDBSpecies6.nsq Blast1_1.txt.gz Blast3_0.txt.gz Blast4_6.txt.gz Blast6_5.txt.gz blast_nuclDBSpecies0.nin blast_nuclDBSpecies1.nto blast_nuclDBSpecies3.not blast_nuclDBSpecies5.nhr blast_nuclDBSpecies6.ntf Blast1_2.txt.gz Blast3_1.txt.gz Blast5_0.txt.gz Blast6_6.txt.gz blast_nuclDBSpecies0.njs blast_nuclDBSpecies2.ndb blast_nuclDBSpecies3.nsq blast_nuclDBSpecies5.nin blast_nuclDBSpecies6.nto Blast1_3.txt.gz Blast3_2.txt.gz Blast5_1.txt.gz SequenceIDs.txt blast_nuclDBSpecies0.not blast_nuclDBSpecies2.nhr blast_nuclDBSpecies3.ntf blast_nuclDBSpecies5.njs Blast1_4.txt.gz Blast3_3.txt.gz Blast5_2.txt.gz Species0.fa blast_nuclDBSpecies0.nsq blast_nuclDBSpecies2.nin blast_nuclDBSpecies3.nto blast_nuclDBSpecies5.not Blast1_5.txt.gz Blast3_4.txt.gz Blast5_3.txt.gz Species1.fa blast_nuclDBSpecies0.ntf blast_nuclDBSpecies2.njs blast_nuclDBSpecies4.ndb blast_nuclDBSpecies5.nsq

It seems like Orthofinder didnt completely run, the example data output contains about 12 folders, mine only contains 1. Do you see what is going wrong here? I tried looking into the stderr file but can't read it.

Kind regards, Esther