My apologies for the delay, and hopefully you have figured out your
problem. If not, a similar topic has been discussed previously on this
list. A quick google search found this:
https://sourceforge.net/p/samtools/mailman/message/31305332/
While the BAM file is not corrupt, many command line tools in Picard will
want read group identifiers for records, and so there is a warning. More
concerning are the errors about the strand flags not being set correctly
across ends in a pair. I would ask the upstream authors or tool about
these types of issues. I would further suggest using
MergeBamAlignments.jar to clean up any such issues, which are frequently
caused by even the most popular aligners.
Nils
On Fri, Sep 5, 2014 at 2:51 PM, María Teresa Chávez <matere...@gmail.com>
wrote:
> I ran the following command in terminal:
>
> $java -Xmx8g -jar ValidateSamFile.jar I=NIST7086_CGTACTAG_L001.sorted.bam
>
>
>
> It gave the following error:
>
> ERROR: Read groups is empty
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1465:2067, A record is
> missing a read group
>
> ERROR: Record 1, Read name HWI-D00119:50:H7AP8ADXX:1:1101:1465:2067, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1465:2067, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1471:2105, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1471:2105, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1313:2126, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1313:2126, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1323:2185, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1323:2185, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1610:2026, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1610:2026, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1743:2071, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1743:2071, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1522:2074, A record is
> missing a read group
>
> ERROR: Record 13, Read name HWI-D00119:50:H7AP8ADXX:1:1101:1522:2074, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1522:2074, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1592:2093, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1592:2093, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1693:2111, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1693:2111, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1578:2148, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1578:2148, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1549:2148, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1549:2148, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1983:2046, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1983:2046, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1837:2054, A record is
> missing a read group
>
> ERROR: Record 25, Read name HWI-D00119:50:H7AP8ADXX:1:1101:1837:2054, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1837:2054, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1917:2098, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1917:2098, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1907:2147, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1907:2147, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1981:2174, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1981:2174, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1792:2208, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1792:2208, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1776:2218, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1776:2218, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1921:2235, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1921:2235, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1974:2236, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:1974:2236, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2207:2023, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2207:2023, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2235:2047, A record is
> missing a read group
>
> ERROR: Record 43, Read name HWI-D00119:50:H7AP8ADXX:1:1101:2235:2047, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2235:2047, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2154:2083, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2154:2083, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2179:2146, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2179:2146, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2146:2190, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2146:2190, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2448:2024, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2448:2024, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2355:2053, A record is
> missing a read group
>
> ERROR: Record 53, Read name HWI-D00119:50:H7AP8ADXX:1:1101:2355:2053, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2355:2053, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2292:2094, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2292:2094, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2339:2138, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2339:2138, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2497:2150, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2497:2150, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2458:2205, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2458:2205, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2690:2039, A record is
> missing a read group
>
> ERROR: Record 63, Read name HWI-D00119:50:H7AP8ADXX:1:1101:2690:2039, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2690:2039, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2586:2050, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2586:2050, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2535:2057, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2535:2057, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2728:2059, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2728:2059, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2579:2067, A record is
> missing a read group
>
> ERROR: Record 71, Read name HWI-D00119:50:H7AP8ADXX:1:1101:2579:2067, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2579:2067, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2683:2105, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2683:2105, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2713:2134, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2713:2134, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2505:2135, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2505:2135, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2749:2185, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2749:2185, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2702:2213, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2702:2213, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2871:2052, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2871:2052, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2760:2052, A record is
> missing a read group
>
> ERROR: Record 85, Read name HWI-D00119:50:H7AP8ADXX:1:1101:2760:2052, Mate
> negative strand flag does not match read negative strand flag of mate
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2760:2052, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2972:2062, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2972:2062, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2911:2087, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2911:2087, A record is
> missing a read group
>
> WARNING: Read name HWI-D00119:50:H7AP8ADXX:1:1101:2954:2103, A record is
> missing a read group
>
> Maximum output of [100] errors reached.
>
>
> I thought maybe the file was corrupt so I tried
>
>
> $samtools index NIST7086_CGTACTAG_L001.sorted.bam
>
> but that completed without errors.
>
>
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
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>
>
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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