command failed with exit status = 127

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Alberto L'Abbate

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Oct 18, 2017, 9:49:42 AM10/18/17

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Hi,

is there anyone that has faced the same error?

I'm running JAFFA with the test dataset as follows:

/lustrehome/alabbate/JAFFA-version-1.09/tools/bin/bpipe run /lustrehome/alabbate/JAFFA-version-1.09/JAFFA_assembly.groovy /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/BT474-demo_*.fastq.gz /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/MCF7-demo_*.fastq.gz

====================================================================================================

| Starting Pipeline at 2017-10-18 15:18 |

====================================================================================================

========================================= Stage run_check ==========================================

Running JAFFA version 1.09

Checking for required data files...

/lustrehome/alabbate/JAFFA-version-1.09/hg38_genCode22.fa

/lustrehome/alabbate/JAFFA-version-1.09/hg38_genCode22.tab

/lustrehome/alabbate/JAFFA-version-1.09/known_fusions.txt

/lustrehome/alabbate/JAFFA-version-1.09/hg38.fa

/lustrehome/alabbate/JAFFA-version-1.09/Masked_hg38.1.bt2

/lustrehome/alabbate/JAFFA-version-1.09/hg38_genCode22.1.bt2

All looking good

================================= Stage prepare_reads (MCF7-demo) ==================================

================================= Stage prepare_reads (BT474-demo) =================================

TrimmomaticPE: Started with arguments: -threads 16 -phred33 /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/BT474-demo_1.fastq.gz /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/BT474-demo_2.fastq.gz /lustrehome/alabbate/JAFFA-version-1.09/prova/BT474-demo/tempp1.fq /dev/null /lustrehome/alabbate/JAFFA-version-1.09/prova/BT474-demo/tempp2.fq /dev/null LEADING:0 TRAILING:0 MINLEN:35

TrimmomaticPE: Started with arguments: -threads 16 -phred33 /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/MCF7-demo_1.fastq.gz /opt/exp_soft/bio/storlazzi/JAFFA-version-1.09/data/MCF7-demo_2.fastq.gz /lustrehome/alabbate/JAFFA-version-1.09/prova/MCF7-demo/tempp1.fq /dev/null /lustrehome/alabbate/JAFFA-version-1.09/prova/MCF7-demo/tempp2.fq /dev/null LEADING:0 TRAILING:0 MINLEN:35

Input Read Pairs: 83014 Both Surviving: 83014 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)

TrimmomaticPE: Completed successfully

Input Read Pairs: 85723 Both Surviving: 85723 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)

TrimmomaticPE: Completed successfully

83014 reads; of these:

83014 (100.00%) were paired; of these:

1136 (1.37%) aligned concordantly 0 times

81878 (98.63%) aligned concordantly exactly 1 time

0 (0.00%) aligned concordantly >1 times

98.63% overall alignment rate

85723 reads; of these:

85723 (100.00%) were paired; of these:

2104 (2.45%) aligned concordantly 0 times

83619 (97.55%) aligned concordantly exactly 1 time

0 (0.00%) aligned concordantly >1 times

97.55% overall alignment rate

2104 reads; of these:

2104 (100.00%) were paired; of these:

1650 (78.42%) aligned concordantly 0 times

454 (21.58%) aligned concordantly exactly 1 time

0 (0.00%) aligned concordantly >1 times

21.58% overall alignment rate

================================== Stage run_assembly (MCF7-demo) ==================================

/lustrehome/alabbate/JAFFA-version-1.09/tools/bin/velveth directory 19,36,4 -fastq -separate ../../MCF7-demo/MCF7-demo_filtered_reads.fastq.1.gz ../../MCF7-demo/MCF7-demo_filtered_reads.fastq.2.gz >> log_velveth

Running Assembly for k=19

Running Assembly for k=23

Running Assembly for k=27

Running Assembly for k=31

Running Assembly for k=35

Oases K-mer=19 assembly succeeded

Oases K-mer=23 assembly succeeded

Oases K-mer=27 assembly succeeded

Oases K-mer=31 assembly succeeded

Oases K-mer=35 assembly succeeded

Oases mergeAssembly succeeded

real 1m30.563s

user 0m40.298s

sys 0m1.188s

======================== Stage align_transcripts_to_annotation (MCF7-demo) =========================

1136 reads; of these:

1136 (100.00%) were paired; of these:

1109 (97.62%) aligned concordantly 0 times

27 (2.38%) aligned concordantly exactly 1 time

0 (0.00%) aligned concordantly >1 times

2.38% overall alignment rate

================================= Stage run_assembly (BT474-demo) ==================================

/lustrehome/alabbate/JAFFA-version-1.09/tools/bin/velveth directory 19,36,4 -fastq -separate ../../BT474-demo/BT474-demo_filtered_reads.fastq.1.gz ../../BT474-demo/BT474-demo_filtered_reads.fastq.2.gz >> log_velveth

Running Assembly for k=19

Running Assembly for k=23

Running Assembly for k=27

Loaded 297165649 letters in 195175 sequences

Searched 314792 bases in 255 sequences

real 1m15.656s

user 0m14.434s

sys 0m0.402s

=============================== Stage filter_transcripts (MCF7-demo) ===============================

ERROR: Command failed with exit status = 127 :

time --vanilla --args MCF7-demo/MCF7-demo.psl MCF7-demo/MCF7-demo.txt 1000 /lustrehome/alabbate/JAFFA-version-1.09/hg38_genCode22.tab < /lustrehome/alabbate/JAFFA-version-1.09/process_transcriptome_blat_table.R &> /lustrehome/alabbate/JAFFA-version-1.09/prova/MCF7-demo/log_filter

Running Assembly for k=31

Running Assembly for k=35

Oases K-mer=19 assembly succeeded

Oases K-mer=23 assembly succeeded

Oases K-mer=27 assembly succeeded

Oases K-mer=31 assembly succeeded

Oases K-mer=35 assembly succeeded

Oases mergeAssembly succeeded

real 1m42.137s

user 0m32.114s

sys 0m0.991s

======================== Stage align_transcripts_to_annotation (BT474-demo) ========================

Loaded 297165649 letters in 195175 sequences

Searched 374043 bases in 238 sequences

real 0m13.234s

user 0m12.890s

sys 0m0.326s

============================== Stage filter_transcripts (BT474-demo) ===============================

ERROR: Command failed with exit status = 127 :

time --vanilla --args BT474-demo/BT474-demo.psl BT474-demo/BT474-demo.txt 1000 /lustrehome/alabbate/JAFFA-version-1.09/hg38_genCode22.tab < /lustrehome/alabbate/JAFFA-version-1.09/process_transcriptome_blat_table.R &> /lustrehome/alabbate/JAFFA-version-1.09/prova/BT474-demo/log_filter

========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

Branch BT474-demo in stage Unknown reported message:

Command failed with exit status = 127 :

Branch MCF7-demo in stage Unknown reported message:

Command failed with exit status = 127 :

Use 'bpipe errors' to see output from failed commands.

Do you have any suggestion to fix the issue?

Thank you in advance.

ALberto

Nadia Davidson

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Oct 20, 2017, 2:40:17 AM10/20/17

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Hi Alberto,

It looks to me like the path to R has not been set in your tools.groovy file in the directory where JAFFA was installed. You will need to install R if you don't already have it on your system and then edit the file tools.groovy with the path to R. If it's installed globally (or with modules), you can just add:

R="R"

Cheers,

Nadia.

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