Bowtie2-build critical error when using --taxonomic-profile


I am using this command below:

humann --input-format fastq.gz --input /scratch/RNAseq/processed_seqs/711-508.fastq.gz
–output /scratch/RNAseq/test/711-508
–taxonomic-profile /scratch/MPA-MAX.txt
–memory-use maximum

And I get this error:

CRITICAL ERROR: Error executing: /home/bin/miniconda3/envs/biobakery/bin/bowtie2-build -f /scratch/RNAseq/test/711-508/711-508_humann_temp/711-508_custom_chocophlan_database.ffn /scratch/RNAseq/test/711-508/711-508_humann_temp/711-508_bowtie2_index

I am not sure what I am doing wrong. So any tips or tricks would help!


Hello, Thanks for posting the command and the detailed error message. Can you try running the sub-command that failed (the command after “Error executing:” ) and see what error message it returns? Also you could check out the log file to see if it has more information about the error.


Hi Lauren,

Here is the output when I run the sub-command that failed:

(biobakery) bash-4.2$ /home/GRAuser/bin/miniconda3/envs/biobakery/bin/bowtie2-build -f /scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_custom_chocophlan_database.ffn /scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_bowtie2_index
  Output files: "/scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_bowtie2_index.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
Building a SMALL index
Reading reference sizes
  Time reading reference sizes: 00:00:18
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:16
bmax according to bmaxDivN setting: 505265048
Using parameters --bmax 378948786 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 378948786 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:54
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:16
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:31
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.02106e+09 (target: 378948785)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
  No samples; assembling all-inclusive block

Here is what the log file says:

03/01/2022 10:41:39 AM - humann.utilities - CRITICAL: TRACEBACK: 
Traceback (most recent call last):
  File "/home/GRAuser/.local/lib/python3.7/site-packages/humann/", line 754, in execute_command
    p = subprocess.check_call(cmd, stdin=stdin, stdout=stdout, stderr=stderr)
  File "/home/GRAuser/bin/miniconda3/envs/biobakery/lib/python3.7/", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/GRAuser/bin/miniconda3/envs/biobakery/bin/bowtie2-build', '-f', '/scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_custom_chocophlan_database.ffn', '/scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_bowtie2_index']' returned non-zero exit status 247.