When I attempt to open a remote file for viewing from the thousand genomes project ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/dat a/HG00149/alignment/HG00149.mapped.ILLUMINA.bwa.GBR.low_coverage.201011 23.bam I recieve the following error and am unable to view the file:
samtools view ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/data /HG00149/alignment/HG00149.mapped.ILLUMINA.bwa.GBR.low_coverage.2010112 3.bam [kftp_connect_file] 213 9133937880 [W::bam_hdr_read] bgzf_check_EOF: Success [E::bam_hdr_read] invalid BAM binary header [main_samview] fail to read the header from "ftp://ftp-trace.ncbi.nih.g ov/1000genomes/ftp/phase1/data/HG00149/alignment/HG00149.mapped.ILLUMIN A.bwa.GBR.low_coverage.20101123.bam". This only happens with files larger than round 5 Gb. For anything smaller the command runs successfully I have tried on multiple machines with multiple operating systems from multiple different networks. (Centos6.4, Ubuntu 16.04, Centos 7). I have tried on a server with 120 Gb of RAM which makes me suspect that this is not an insufficient memory issue. If I ftp copy the file to my server and try the samtools view command locally it works as expected. Thinking that this could have been an issue with the 1000genomes ftp server I tried several other ftp servers hosting bam files and encountered the same problem. (Large files fail when I try to samtools view ftp://..... ) (Small files work). Again, if I copy the large files and samtools view them locally it works. I am wondering if anyone has any suggestions as to what could be causing this issue. Thank you ! ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
