[E::fai_read] Could not understand FASTA index and RepeatLandscape

[enriquepola1996]

Hello, thank you very much for this nice tool, I am running a fungal genome for the first time but it seems that there was a problem at the end, "Could not understand FASTA index", how could I solve this? At the exit, only a pdf returned to me.

I will greatly appreciate the help.

My installation:

conda create -n earlgrey -c conda-forge -c bioconda earlgrey=4.2.4

My commands:

earlGrey -g fungal_T9_kmer.fasta -s fungal_T9_kmer -t 8 -r Fungi -d yes -o ./earlGreyOutputs

My output fyles:

(earlgrey) enrique@DESKTOP-62E8R2K:~/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_summaryFiles$ ls -l
total 41444
-rw-r--r-- 1 enrique enrique 96364 Jul 9 05:16 fungal _T9_kmer-families.fa.strained
-rw-r--r-- 1 enrique enrique 78467 Jul 9 05:13 fungal _T9_kmer.familyLevelCount.txt
-rw-r--r-- 1 enrique enrique 493491 Jul 9 05:16 fungal _T9_kmer.filteredRepeats.bed
-rw-r--r-- 1 enrique enrique 1110064 Jul 9 05:16 fungal _T9_kmer.filteredRepeats.gff
-rw-r--r-- 1 enrique enrique 350 Jul 9 05:13 fungal _T9_kmer.highLevelCount.txt
-rw-r--r-- 1 enrique enrique 40519788 Jul 9 05:16 fungal _T9_kmer.softmasked.fasta
-rw-r--r-- 1 enrique enrique 7203 Jul 9 05:13 fungal _T9_kmer.summaryPie.pdf
-rw-r--r-- 1 enrique enrique 112749 Jul 9 05:16 fungal _T9_kmer_combined_library.fasta

My log file:

<<< Generating Summary Plots >>>
 [1] "/home/enrique/miniconda3/envs/earlgrey/lib/R/bin/exec/R"                                                                                                 
 [2] "--no-echo"                                                                                                                                                   
 [3] "--no-restore"                                                                                                                                                
 [4] "--file=/home/enrique/miniconda3/envs/earlgrey/share/earlgrey-4.2.4-1/scripts//autoPie.R"                                                                 
 [5] "--args"                                                                                                                                                      
 [6] "/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_mergedRepeats/looseMerge/fungal _T9_kmer.filteredRepeats.bed"
 [7] "/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_mergedRepeats/looseMerge/fungal _T9_kmer.filteredRepeats.gff"
 [8] "39853892"                                                                                                                                                    
 [9] "/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_summaryFiles/fungal _T9_kmer.summaryPie.pdf"                 
[10] "/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_summaryFiles/fungal _T9_kmer.highLevelCount.txt"             
Splitting repeat library
Reading in gff
Starting calculations
WARNING. chromosome (contig_8) was not found in the FASTA file. Skipping.
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/home/enrique/miniconda3/envs/earlgrey/share/earlgrey-4.2.4-1/scripts//divergenceCalc/divergence_calc.py", line 116, in outer_func
    a = a.sequence(fi=genome_path, fo=query_path, s=True)
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/site-packages/pybedtools/bedtool.py", line 907, in decorated
    result = method(self, *args, **kwargs)
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/site-packages/pybedtools/bedtool.py", line 388, in wrapped
    stream = call_bedtools(
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/site-packages/pybedtools/helpers.py", line 456, in call_bedtools
    raise BEDToolsError(subprocess.list2cmdline(cmds), stderr)
pybedtools.helpers.BEDToolsError: 
Command was:

	bedtools getfasta -s -fo tmp//qseqs/808 -fi /home/enrique/earlgrey/fungal _T9_kmer.fasta -bed /tmp/pybedtools.vjri15g4.tmp

Error message was:
[E::fai_read] Could not understand FASTA index /home/enrique/earlgrey/fungal _T9_kmer.fasta.fai line 131
[E::fai_load3_core] Failed to read FASTA index /home/enrique/earlgrey/fungal _T9_kmer.fasta.fai
Warning: malformed fasta index file /home/enrique/earlgrey/fungal _T9_kmer.fasta

"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/enrique/miniconda3/envs/earlgrey/share/earlgrey-4.2.4-1/scripts//divergenceCalc/divergence_calc.py", line 203, in <module>
    results = pool.map(func, chunks)
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/home/enrique/miniconda3/envs/earlgrey/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
pybedtools.helpers.BEDToolsError: 
Command was:

	bedtools getfasta -s -fo tmp//qseqs/808 -fi /home/enrique/earlgrey/fungal _T9_kmer.fasta -bed /tmp/pybedtools.vjri15g4.tmp

Error message was:
[E::fai_read] Could not understand FASTA index /home/enrique/earlgrey/fungal _T9_kmer.fasta.fai line 131
[E::fai_load3_core] Failed to read FASTA index /home/enrique/earlgrey/fungal _T9_kmer.fasta.fai
Warning: malformed fasta index file /home/enrique/earlgrey/fungal _T9_kmer.fasta

Error in open.connection(con, open) : cannot open the connection
Calls: %>% ... connection -> connectionForResource -> open -> open.connection
In addition: Warning message:
In open.connection(con, open) :
  cannot open file '/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_RepeatLandscape/fungal _T9_kmer.filteredRepeats.withDivergence.gff': No such file or directory
Execution halted
cp: cannot stat '/home/enrique/earlgrey/earlGreyOutputs/fungal _T9_kmer_EarlGrey/fungal _T9_kmer_RepeatLandscape/*.pdf': No such file or directory