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

Microbial community profiling HUMAnN
1

Hello.

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!

Thanks.

2

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.

Thanks!
Lauren

3

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
Settings:
  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:
  /scratch/GRAuser/RNAseq/test/711-508/711-508_humann_temp/711-508_custom_chocophlan_database.ffn
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/utilities.py", 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/subprocess.py", 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.

Thanks!