search

ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
31 stars 6 forks source link

Error: [bam_header_read] EOF marker is absent. #25

Open SooChing opened 3 years ago

SooChing commented 3 years ago

Dear GRiD Developers,

I'm getting the following error when I am running Grid Multiplex on the mice metagenomic data (from stool) using comprehensive GRiD database. However, I able to receive the output (a heat map in pdf and two tables of results in txt) with the word "run complete".

Error: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_sort_core] merging from 12 files... /usr/bin/bash: -c: line 0: syntax error near unexpected token (' /usr/bin/bash: -c: line 0:bash Anaerotruncus_sp._G3(2012).parallel.sh' [samopen] SAM header is present: 1 sequences.

Example of Warning message: Loading required package: proto Warning message: no DISPLAY variable so Tk is not available geom_smooth() using formula 'y ~ x' Warning messages: 1: Ignoring unknown aesthetics: outfit 2: Removed 62 rows containing non-finite values (stat_smooth). [samopen] SAM header is present: 1 sequences.

Previously, I did not receive this error when I was running the human data on specific environment database (stool_microbes database).

My questions are:

  1. Can I ignore the error since I've successfully received the output?
  2. Can I use the specific environment stool database for mice metagenomic data (from stool)? Or the stool database is only for human stool samples?

Thanks in advance.

Regards, Soo Ching

aemiol commented 3 years ago

Hi Soo Ching,

The warnings are normal but the error is unusual.

I don't see why you can't use the stool database for mice since most of the non-stool microbes in the comprehensive database are environmental microbes.

Thanks, Tunde

SooChing commented 3 years ago

Hi Tunde,

Thanks for your reply.

Unfortunately, the same error is still occurred when I tried the following:

  1. Map the mice stool metagenomics data to stool database.
  2. Map the previous human stool metagenomics data to stool database.

For no.2, it worked without error previously but not now. However, it still generate the similar output as before. I am still figuring out how to solve this.

Thanks.

Soo Ching