Missing columns in *.transposon.sorted.unique.bigWig.summary

[blaiseli]

Dear Bo Han,

In one of my analyses, the *.transposon.unique.pdf file is never generated by piPipes chip

I could trace the problem in the error log:

no data in region FBgn0046701_Penelope:0-804 in /home/severine.chambeyron/projet_Abdou/ChIP-Seq/piPipes_chip/shpiwi_rep1/direct_mapping/Chambeyron_8_4_IP_H3K9me3_shpiwi_rep1_S28_L006_R1_001.input.transposon.sorted.unique.bigWig

no data in region FBgn0067418_Helitron:0-564 in /home/severine.chambeyron/projet_Abdou/ChIP-Seq/piPipes_chip/shpiwi_rep1/direct_mapping/Chambeyron_8_4_IP_H3K9me3_shpiwi_rep1_S28_L006_R1_001.input.transposon.sorted.unique.bigWig

Loading required package: parallel
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 580255 did not have 4 elements
Calls: read.table -> scan
Execution halted
2016-May-04 17:47:17 - Attempting to read '/home/severine.chambeyron/projet_Abdou/ChIP-Seq/piPipes_chip/shpiwi_rep1/direct_mapping/Chambeyron_8_4_IP_H3K9me3_shpiwi_rep1_S28_L006_R1_001.IP.transposon.bam' in BAM format...

The problematic zone in the *.transposon.sorted.unique.bigWig file is the following:

FBgn0067418_Helitron    551 0.0000000   0.0000000
FBgn0067418_Helitron    552 0.0000000   0.0000000
FBgn0067418_Helitron    553 0.0000000   0.0000000
FBgn0067418_Helitron    554 0.0000000   0.0000000
FBgn0067418_Helitron    555 0.0000000   0.0000000
FBgn0067418_Helitron    556 0.0000000   0.0000000
FBgn0067418_Helitron    557 0.0000000   0.0000000
FBgn0067418_Helitron    558 0.0000000   0.0000000
FBgn0067418_Helitron    559 0.0000000   0.0000000
FBgn0067418_Helitron    560 0.0000000   0.0000000
FBgn0067418_Helitron    561 0.0000000   0.0000000
FBgn0067418_Helitron    562 0.0000000   0.0000000
FBgn0067418_Helitron    563 0.0000000   0.0000000
FBgn0067418_Helitron    564 0.0000000   0.0000000
    FBgn0067418_Helitron    565
    FBgn0067418_Helitron    566
    FBgn0067418_Helitron    567
    FBgn0067418_Helitron    568
    FBgn0067418_Helitron    569
    FBgn0067418_Helitron    570
    FBgn0067418_Helitron    571
    FBgn0067418_Helitron    572
    FBgn0067418_Helitron    573
    FBgn0067418_Helitron    574
    FBgn0067418_Helitron    575

The problem does not happen with data from another replicate of the same experiment.
Here is the corresponding error log portion:

Number of  Commands: 252
no data in region FBgn0046701_Penelope:0-804 in /home/severine.chambeyron/projet_Abdou/ChIP-Seq/piPipes_chip/shpiwi_rep2/direct_mapping/Chambeyron_12_8_IP_H3K9me3_shpiwi_rep2_S32_L006_R1_001.IP.transposon.sorted.unique.bigWig

no data in region FBgn0046701_Penelope:0-804 in /home/severine.chambeyron/projet_Abdou/ChIP-Seq/piPipes_chip/shpiwi_rep2/direct_mapping/Chambeyron_12_8_IP_H3K9me3_shpiwi_rep2_S32_L006_R1_001.input.transposon.sorted.unique.bigWig

Loading required package: parallel
$FBgn0000004_17.6
null device 
          1 

$FBgn0000005_297

In the corresponding *.transposon.sorted.unique.bigWig file, the "Helitron" zone stops at position 564 instead of continuing with missing data in the problematic replicate:

FBgn0067418_Helitron    551 0.1344920   0.0000000
FBgn0067418_Helitron    552 0.1344920   0.0000000
FBgn0067418_Helitron    553 0.1344920   0.0000000
FBgn0067418_Helitron    554 0.1008690   0.0000000
FBgn0067418_Helitron    555 0.1008690   0.0000000
FBgn0067418_Helitron    556 0.1008690   0.0000000
FBgn0067418_Helitron    557 0.1008690   0.0000000
FBgn0067418_Helitron    558 0.1008690   0.0000000
FBgn0067418_Helitron    559 0.1008690   0.0000000
FBgn0067418_Helitron    560 0.1008690   0.0000000
FBgn0067418_Helitron    561 0.0672460   0.0000000
FBgn0067418_Helitron    562 0.0672460   0.0000000
FBgn0067418_Helitron    563 0.0672460   0.0000000
FBgn0067418_Helitron    564 0.0336230   0.0000000
FBgn0067419_G7  1   0.4370990   0.0000000
FBgn0067419_G7  2   0.5043450   0.0000000
FBgn0067419_G7  3   0.5043450   0.0000000
FBgn0067419_G7  4   0.5379680   0.0000000
FBgn0067419_G7  5   0.6388370   0.0000000
FBgn0067419_G7  6   0.7060830   0.0000000
FBgn0067419_G7  7   0.7733290   0.0000000
FBgn0067419_G7  8   0.7733290   0.0000000
FBgn0067419_G7  9   0.8069520   0.0000000
FBgn0067419_G7  10  0.9078210   0.0000000
FBgn0067419_G7  11  1.0086900   0.0000000

Could the problem be related to the "no data in region" warnings ?

There were no mention of missing data for Helitron in the error log for the well-behaving replicate.
For the problematic replicate, there was a mention of missing data in the Helitron zone preceding the wrong lines., but only in the input, not in the IP.

[bowhan]

Can you please run git log -1 and let me know the version of piPipes you have?

[blaiseli]

Hi,

Here is the output of git log -1:

commit cd5f1cfb33e67ddf2926cea7ad57212b17695e27
Author: bowhan <[email protected]>
Date:   Wed Oct 14 20:06:11 2015 -0400

    improve miRNA unique-/multi-mapper determination