Error using samtools for downloading bam files
Hi,
I was just trying to run my typical script which downloaded a lot of regions I wanted before, but it stopped all of a sudden presenting the following errors at two different times:
1)
227 Entering Passive Mode (193,62,192,8,185,217).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00119/alignment/HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam".
2)
EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00123/alignment/HG00123.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam"
Does anyone have any idea? The strange thing is that each of the times I ran the code, it presented as errors different bam files which were downloaded before. I looked online but everyone says I should ignore these kind of errors..
Any help would be really appreciated.
Thank you
• 3,048 views
•
link
updated
by
Ram
•
written
by
Maria333 •
•
written
by
Maria333 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
In pysam pileup, discrepancy between stepper all and stepper samtools reads
written by Michael •
-
Mate mismatch errors in 1000genomes CRAM files
written by Mehulsharma.253 •
-
downloading bam files of phase 3 of 1000 genomes project
written by Ana
-
Problem on indexing of sorted BAM file
written by Gaurab2017 •
-
Help with Samtools
written by oma219 •
-
sam to bam conversion
written by sukesh1411 •
-
why I cant have sam, sorted bam or bed by tophat output?
written by zizigolu
-
Filtering nth length from mapped SAM/BAM file.
written by unique379
-
Mapping shorts reads using Bowtie
written by bioinfo
-
Problems Accessing 1000G Data
written by Ahdf-Lell-Kocks •
Can you post your code?
You'll always get the EOF message with FTP, it's hard-coded. I've been meaning to make a pull request to prevent that in fact...
Thank you..So do you suggest that I should continue running the code until it's fixed?
At least for (2) yes. I don't remember (1) also occurring, though I'll check real quick.
I don't get (1). So perhaps you have a networking issue or are using a different version. Make sure you're using the most recent version (1.2 or 1.2.1 I think).
Thank you for that. It seems everything's fine with the code. Don't know what's happening.