I got some errors from irap.

[joshuakwon]

I'm trying to analyse my rna-seq data with irap.
However, I got some errors during the analysis.
Please, give me some solutions and help me.
Very many thanks.


----------------------------
[irap@localhost ~]$ irap conf=human_ex.conf de_method=deseq
*****************************************************
* IRAP 0.4.0
* Developed by Nuno Fonseca (authorname (at) acm.org)
* This pipeline is distributed under the terms of the GNU General Public License 3
*
* Initializing...
* Trying to load configuration file human_ex.conf...
* Configuration loaded.
*
* Required Parameters:
* name=human_ex
* data_dir=/run/media/irap/KSH/Human
* species=homo_sapiens
* reference=Homo_sapiens.GRCh37.74.dna.toplevel.fa.gz
* gtf_file = Homo_sapiens.GRCh37.74.gtf.gz
* gff3_file = Homo_sapiens.GRCh37.74.gff3
* Transcripts = /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.cdna.all.fa
* pe=myLib1 myLib2 myLib3 myLib4 myLib5
* debug * fastq_files=/home/irap/730-mono-TSP1_1.fastq /home/irap/730-mono-TSP1_2.fastq /home/irap/730-M1-TSP1_1.fastq /home/irap/730-M1-TSP1_2.fastq /home/irap/730-M2a-TSP1_1.fastq /home/irap/730-M2a-TSP1_2.fastq /home/irap/730-M2b-TSP1_1.fastq /home/irap/730-M2b-TSP1_2.fastq /home/irap/730-M2c-TSP1_1.fastq /home/irap/730-M2c-TSP1_2.fastq
* myLib1_sd=60
* myLib2_sd=60
* myLib3_sd=60
* myLib4_sd=60
* myLib5_sd=60
* myLib1_ins=350
* myLib2_ins=350
* myLib3_ins=350
* myLib4_ins=350
* myLib5_ins=350
* myLib1_rs=101
* myLib2_rs=101
* myLib3_rs=101
* myLib4_rs=101
* myLib5_rs=101
* myLib1_qual=33
* myLib2_qual=33
* myLib3_qual=33
* myLib4_qual=33
* myLib5_qual=33
* contrasts=GAvsGB GBvsGA
* GAvsGB=GA GB
* GA=myLib1
* GB=myLib2 myLib3 myLib4 myLib5
* GBvsGA=GB GA
* GB=myLib2 myLib3 myLib4 myLib5
* GA=myLib1
* groups= parameter not defined, using the groups in the contrasts (if defined).
* technical.replicates=NONE
*
* Optional Parameters:
* max_threads=16
* tmp_dir=/run/media/irap/KSH/Human/tmp (temporary directory)
* mapper=tophat1
* quant_method=htseq2
* exon_quant=n
* transcript_quant=y
* quant_norm_method=deseq
* mapper_splicing=yes
* de_method=deseq
* gse_tool=piano
* gse_method=fisher
* gse_pvalue=0.05
* gse_minsize=3 (minimum number of genes)
* gse_minedge=3 (used in the GSE related plots)
* gse_top=Inf (used in the GSE related plots)
*========================================================
DEBUG
reference_prefix=/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
gtf_file_abspath=/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf
index_files= /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.1.ebwt
file_indexed=/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
17:14:02 14/01/2015 * [DONE] Initialization
17:14:02 14/01/2015 * [DONE] Directory structure created
gunzip -c /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz > /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.tmp && mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.tmp /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf
gtf2geneclass.sh /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf > /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gene_class.txt.tmp && mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gene_class.txt.tmp /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gene_class.txt
cp /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gene_class.txt human_ex/data/gene_class.txt.tmp && mv human_ex/data/gene_class.txt.tmp human_ex/data/gene_class.txt
gunzip -c /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.gz > /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.tmp && mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.tmp /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
19:41:31 14/01/2015 * INDEXING

irap_map.sh bowtie1 bowtie-build --offrate 3 /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
Wrapper: bowtie-build --offrate 3 /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
Settings:
Output files: "/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.*.ebwt"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 3 (one in 8)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa
Reading reference sizes
Time reading reference sizes: 02:57:34
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 02:25:43
bmax according to bmaxDivN setting: 747254778
Using parameters --bmax 560441084 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 560441084 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:03:21
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:39
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:01:34
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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Binary sorting into buckets time: 00:02:20
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:01:59
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 3.73627e+08 (target: 560441083)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:39
Sorting block of length 532692084
(Using difference cover)
Sorting block time: 00:13:20
Returning block of 532692085
Getting block 2 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:45
Sorting block of length 305168893
(Using difference cover)
Sorting block time: 00:07:44
Returning block of 305168894
Getting block 3 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:52
Sorting block of length 497342339
(Using difference cover)
Sorting block time: 00:13:34
Returning block of 497342340
Getting block 4 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:54
Sorting block of length 326395284
(Using difference cover)
Sorting block time: 00:08:55
Returning block of 326395285
Getting block 5 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:55
Sorting block of length 336824268
(Using difference cover)
Sorting block time: 00:09:55
Returning block of 336824269
Getting block 6 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:55
Sorting block of length 382684617
(Using difference cover)
Sorting block time: 00:09:40
Returning block of 382684618
Getting block 7 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:54
Sorting block of length 496777301
(Using difference cover)
Sorting block time: 00:12:57
Returning block of 496777302
Getting block 8 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:32
Sorting block of length 111134319
(Using difference cover)
Sorting block time: 00:02:57
Returning block of 111134320
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 881098029
fchr[G]: 1493792045
fchr[T]: 2106926216
fchr[$]: 2989019112
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 858235346 bytes to primary EBWT file: /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.1.ebwt
Wrote 1494509564 bytes to secondary EBWT file: /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2989019112
bwtLen: 2989019113
sz: 747254778
bwtSz: 747254779
lineRate: 6
linesPerSide: 1
offRate: 3
offMask: 0xfffffff8
isaRate: -1
isaMask: 0xffffffff
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 373627390
offsSz: 1494509560
isaLen: 0
isaSz: 0
lineSz: 64
sideSz: 64
sideBwtSz: 56
sideBwtLen: 224
numSidePairs: 6671918
numSides: 13343836
numLines: 13343836
ebwtTotLen: 854005504
ebwtTotSz: 854005504
reverse: 0
Total time for call to driver() for forward index: 07:16:50
Reading reference sizes
Time reading reference sizes: 02:03:56
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 02:02:31
bmax according to bmaxDivN setting: 747254778
Using parameters --bmax 560441084 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 560441084 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:03:17
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:39
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:01:38
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:02:21
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 3.73627e+08 (target: 560441083)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:32
Sorting block of length 269521119
(Using difference cover)
Sorting block time: 00:06:28
Returning block of 269521120
Getting block 2 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:43
Sorting block of length 539929538
(Using difference cover)
Sorting block time: 00:13:42
Returning block of 539929539
Getting block 3 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:51
Sorting block of length 470436118
(Using difference cover)
Sorting block time: 00:12:15
Returning block of 470436119
Getting block 4 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:53
Sorting block of length 344556343
(Using difference cover)
Sorting block time: 00:08:54
Returning block of 344556344
Getting block 5 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:49
Sorting block of length 287564152
(Using difference cover)
Sorting block time: 00:07:58
Returning block of 287564153
Getting block 6 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:54
Sorting block of length 317250824
(Using difference cover)
Sorting block time: 00:07:52
Returning block of 317250825
Getting block 7 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:53
Sorting block of length 457404276
(Using difference cover)
Sorting block time: 00:11:34
Returning block of 457404277
Getting block 8 of 8
Reserving size (560441084) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:36
Sorting block of length 302356735
(Using difference cover)
Sorting block time: 00:07:35
Returning block of 302356736
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 881098029
fchr[G]: 1493792045
fchr[T]: 2106926216
fchr[$]: 2989019112
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 858235346 bytes to primary EBWT file: /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.rev.1.ebwt
Wrote 1494509564 bytes to secondary EBWT file: /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.dna.toplevel.fa.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2989019112
bwtLen: 2989019113
sz: 747254778
bwtSz: 747254779
lineRate: 6
linesPerSide: 1
offRate: 3
offMask: 0xfffffff8
isaRate: -1
isaMask: 0xffffffff
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 373627390
offsSz: 1494509560
isaLen: 0
isaSz: 0
lineSz: 64
sideSz: 64
sideBwtSz: 56
sideBwtLen: 224
numSidePairs: 6671918
numSides: 13343836
numLines: 13343836
ebwtTotLen: 854005504
ebwtTotSz: 854005504
reverse: 0
Total time for backward call to driver() for mirror index: 05:54:11
irap_check_gtf /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf && touch /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.checked
Features found: CDS exon start_codon stop_codon
File '/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf' looks ok.
gtf_add_exon_id.pl /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf > /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.exon_id.gtf.tmp && mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.exon_id.gtf.tmp /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.exon_id.gtf
Loading /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf
tophat2_gtf_juncs /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf > human_ex/data/Homo_sapiens.GRCh37.74.gtf.juncs.tmp
mv human_ex/data/Homo_sapiens.GRCh37.74.gtf.juncs.tmp human_ex/data/Homo_sapiens.GRCh37.74.gtf.juncs
gtf_juncs v2.0.9 (3067M)
---------------------------
Extracted 375869 junctions from /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf
irap_gtf2mapping --gtf /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.gtf --out /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.tmp --cores 16 && \
mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.tmp.Rdata /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.Rdata && \
mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.tmp_exons.tsv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping_exons.tsv && \
mv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.tmp_trans.tsv /run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping_trans.tsv
Error in `$<-.data.frame`(`*tmp*`, "source", value = c("processed_transcript;transcribed_unprocessed_pseudogene", :
replacement has 234790 rows, data has 1306656
Calls: $<- -> $<-.data.frame
Execution halted
make: *** [/run/media/irap/KSH/Human/reference/homo_sapiens/Homo_sapiens.GRCh37.74.mapping.Rdata] Error 1

[nfonseca]

Hi,
I noticed that you are using version 0.4. Did you get the same problem in the latest version?
Regards,
Nuno

[joshuakwon]

I've never succeed to run iRAP.

Hi,
I noticed that you are using version 0.4. Did you get the same problem in the latest version?
Regards,
Nuno

Hi Nuno,

I got the error from version 0.4.
Unfortunately, I've never succeed to setup and run the latest version of iRAP.
As you mentioned on google code, I ran irap_install.sh but it made many of errors.
So, I'm running irap 0.4 using virtualbox.
It runs well, however it stopped in the table reading process.
Do you have any clue? or suggestion?

[nfonseca]

Hi Joshua,

I released a new version of iRAP which should have the installation issues from version 0.4 solved. The virtualbox image now contains the latest version installed and, alternatively, you may run iRAP on a docker container. I do not recommend using the virtualbox image to run intensive computational analysis since it will be considerably slow.

Thanks,

Nuno

Hi Nuno,

I got the error from version 0.4.
Unfortunately, I've never succeed to setup and run the latest version of iRAP.
As you mentioned on google code, I ran irap_install.sh but it made many of errors.
So, I'm running irap 0.4 using virtualbox.
It runs well, however it stopped in the table reading process.
Do you have any clue? or suggestion?