I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to index my .BAM file it gives me this error:

[E::hts_idx_push] NO_COOR reads not in a single block at the end 1652 -1.

Here is my code:

source /opt/asn/etc/asn-bash-profiles-special/modules.sh
module load samtools/1.3.1

cd ~/gz_files/soapdenovo
###SAM to BAM and sort 

samtools faidx soapdenovo.fa 
samtools view -b -T soapdenovo.fa -o sample${r}bowtiemapping.bam sample${r}bowtiemapping.sam
samtools sort -n -T ~/gz_files/soapdenovo/temp -o sample${r}bowtiemapping_sorte$
samtools index sample${r}bowtiemapping_sorted.bam

################LETS MAKE THE ABUNDANCE TABLES###########################$
samtools view -c -f 4  sample${r}bowtiemapping_sorted.bam > sample${r}alignment$

samtools idxstats sample${r}bowtiemapping_sorted.bam >  sample${r}idxstats.txt

#git clone https://github.com/metajinomics/mapping_tools.git
#python mapping_tools/get_count_table.py *.idxstats.txt > contig_counts.tsv
##less contig_counts.tsv

Any help would be appreciated!

Notes on pipeline

  • samtools import was replaced with samtools view
  • faidxcorrected
  • Instructions used are here on github
  • Suggestion for future trouble shooting is given here by @winni2k
  • $\begingroup$ In you code, which is the line that is causing trouble? I cannot see any samtools index for indexing the bam, as you say. $\endgroup$
    – Poshi
    Sep 21, 2018 at 7:25
  • 1
    $\begingroup$ More comments... samtools import has been deprecated for 8 years. Use samtools view instead. $\endgroup$
    – Poshi
    Sep 21, 2018 at 7:30
  • 1
    $\begingroup$ Finally, the second samtools faidx makes no sense: there are no fasta files to index! $\endgroup$
    – Poshi
    Sep 21, 2018 at 7:31
  • 1
    $\begingroup$ Which is the command that fails? Which one is giving that message? Again, I'm seeing several errors. faidx have too many parameters (what are you trying to achieve?), view will complain about not having a bam input, and sort have no input file given and the shell will complain about an orphan dollar sign. Four errors in for different lines. Better go step by step and check that one step works before going to the next. $\endgroup$
    – Poshi
    Sep 24, 2018 at 17:47
  • 1
    $\begingroup$ Try upgrading to the most recent version of samtools, this bug may have been squashed already. $\endgroup$
    – Devon Ryan
    Nov 2, 2018 at 8:05

1 Answer 1


By now this will be of little interest to the original poster, but for future reference:

$ samtools sort -n -T ~/[etc] -o sample${r}bowtiemapping_sorted.bam [etc]
$ samtools index sample${r}bowtiemapping_sorted.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 1652 -1.

This error message indicates (admittedly somewhat obscurely) that the reads are not sorted by coordinate — in particular, there are mapped reads appearing after the unplaced unmapped reads (those with RNAME *) that should be at the very end of the file.

This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.

  • $\begingroup$ Hi @JohnMarshall agreed but it certainly of interest to many of us. $\endgroup$
    – M__
    Jul 14, 2020 at 12:40

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