unable to find header and no output file generated

[mrinal mishra]

Hello,

I am new to Juicer. I am trying to use Juicer with my Hi-C data and draft assembly. I am using CPU version of Juicer.sh. When I am running it. I am getting error that there is no header file in Output (named as Aligned) folder. There is some problem occurred somewhere in creating sorted align files. I am attaching a snippet of the Error which I am getting. It will be great help if somebody let me know where is the problem and how to resolve it. 

Mrinals-MacBook-Pro:juicer MadMac$ /Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh -g draft -s HindIII -z /Volumes/Storage/sleeper_hi_c/juicer/CPU/references/draft.fasta -y /Volumes/Storage/sleeper_hi_c/juicer/CPU/restriction_sites/draft_HindIII.txt -p assembly -S merge

(-: Looking for fastq files...fastq files exist

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 315: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 321: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 325: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 326: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 327: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 328: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 329: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 330: /Volumes/Storage/sleeper_hi_c/juicer/aligned/header: No such file or directory

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 491: /Volumes/Storage/sleeper_hi_c/juicer/aligned/merged_sort.txt: No such file or directory

***! Some problems occurred somewhere in creating sorted align files.

[Olga Dudchenko]

Hi Mrinal,

It might be of help if you show what your original output looks like: it seems that what you are showing is what happens on your rerun -S merge attempt.

Best,

Olga

[mrinal mishra]

On Saturday, 1 September 2018 14:16:17 UTC-4, Olga Dudchenko wrote:

Hi Mrinal,

It might be of help if you show what your original output looks like: it seems that what you are showing is what happens on your rerun -S merge attempt.

Best,

Olga

On Saturday, September 1, 2018 at 12:56:51 PM UTC-5, mrinal mishra wrote:

Hello Olga,

Thank you for your reply. The original output which I am getting is - 

Mrinals-MacBook-Pro:juicer MadMac$ /Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh -g draft -s HindIII -z /Volumes/Storage/sleeper_hi_c/juicer/CPU/references/draft.fasta -y /Volumes/Storage/sleeper_hi_c/juicer/CPU/restriction_sites/draft_HindIII.txt -p assembly

(-: Looking for fastq files...fastq files exist

(-: Aligning files matching /Volumes/storage/sleeper_hi_c/juicer/fastq/*_R*.fastq*

 to genome draft with site file /Volumes/Storage/sleeper_hi_c/juicer/CPU/restriction_sites/draft_HindIII.txt

---  Using already created files in /Volumes/storage/sleeper_hi_c/juicer/splits

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 365: /opt/juicer/scripts/common/countligations.sh: No such file or directory

Running command bwa mem -t 4 /Volumes/Storage/sleeper_hi_c/juicer/CPU/references/draft.fasta /Volumes/storage/sleeper_hi_c/juicer/splits/RHC00904C_L1_R1.fastq.gz > /Volumes/storage/sleeper_hi_c/juicer/splits/RHC00904C_L1_R1.fastq.gz.sam

/Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 381: bwa: command not found

***! Alignment of /Volumes/storage/sleeper_hi_c/juicer/splits/RHC00904C_L1_R1.fastq.gz failed.

Mrinals-MacBook-Pro:juicer MadMac$ /Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh -g draft -s HindIII -z /Volumes/Storage/sleeper_hi_c/juicer/CPU/references/draft.fasta -y /Volumes/Storage/sleeper_hi_c/juicer/CPU/restriction_sites/draft_HindIII.txt -p assembly

(-: Looking for fastq files...fastq files exist

***! Move or remove directory "/Volumes/storage/sleeper_hi_c/juicer/aligned" before proceeding.

***! Type "juicer.sh -h " for help 

Best, 

Mrinal

[Olga Dudchenko]

Mrinal,

It seems you do not have bwa in your path: /Volumes/Storage/sleeper_hi_c/juicer/CPU/juicer.sh: line 381: bwa: command not found

Also note that there is something of an issue with your installation as the scripts seems to be in /volumes/storage/sleeper_hic_c while core scripts are assumed to be in /opt/juicer

Take a look at https://github.com/theaidenlab/juicer/wiki/Installation

Best,
Olga

[mrinal mishra]

Dear Olga,

Thank you for your reply. I successfully solved the previous problems that was occuring while running Juicer. But I am now stuck at another error. Here is the error which I am getting now. It will be great if you could help. 

Mrinals-MacBook-Pro:juicer MadMac$ /opt/juicer/juicer.sh -D /opt/juicer -g draft -s MboI -z /opt/juicer/references/draft.fasta  -y /opt/juicer/restriction_sites/draft_MboI.txt  -p assembly

(-: Looking for fastq files...fastq files exist

(-: Aligning files matching /opt/juicer/fastq/*_R*.fastq*

 to genome draft with site file /opt/juicer/restriction_sites/draft_MboI.txt

(-: Created /opt/juicer/splits and /opt/juicer/aligned.

Running command bwa mem -t 4 /opt/juicer/references/draft.fasta /opt/juicer/splits/RHC00904-C_L1_R1.fastq.gz > /opt/juicer/splits/RHC00904-C_L1_R1.fastq.gz.sam

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 266668 sequences (40000200 bp)...

[M::process] read 266668 sequences (40000200 bp)...

[M::mem_process_seqs] Processed 266668 reads in 175.991 CPU sec, 65.229 real sec

[M::process] read 266668 sequences (40000200 bp)...

[M::mem_process_seqs] Processed 266668 reads in 172.875 CPU sec, 57.883 real sec

[M::process] read 266668 sequences (40000200 bp)...

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -t 4 /opt/juicer/references/draft.fasta /opt/juicer/splits/RHC00904-C_L1_R1.fastq.gz

[main] Real time: 1171.519 sec; CPU: 3049.921 sec

(-:  Align of /opt/juicer/splits/RHC00904-C_L1_R1.fastq.gz.sam done successfully

Running command bwa mem -t 4 /opt/juicer/references/draft.fasta /opt/juicer/splits/RHC00904-C_L1_R2.fastq.gz > /opt/juicer/splits/RHC00904-C_L1_R2.fastq.gz.sam

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 266668 sequences (40000200 bp)...

[M::process] read 266668 sequences (40000200 bp)...

[M::mem_process_seqs] Processed 266668 reads in 192.200 CPU sec, 77.310 real sec

[M::process] read 266668 sequences (40000200 bp)...

[M::mem_process_seqs] Processed 266668 reads in 193.446 CPU sec, 73.930 real sec

[M::process] read 266668 sequences (40000200 bp)...

[M::mem_process_seqs] Processed 266668 reads in 196.267 CPU sec, 71.152 real sec

[M::process] read 266668 sequences (40000200 bp)...

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -t 4 /opt/juicer/references/draft.fasta /opt/juicer/splits/RHC00904-C_L1_R2.fastq.gz

[main] Real time: 1360.634 sec; CPU: 3431.047 sec

(-: Mem align of /opt/juicer/splits/RHC00904-C_L1_R2.fastq.gz.sam done successfully

(-: Sort read 1 aligned file by readname completed.

(-: Sort read 2 aligned file by readname completed.

(-: /opt/juicer/splits/RHC00904-C_L1.fastq.gz.sam created successfully.

awk: calling undefined function and

 input record number 4, file /opt/juicer/splits/RHC00904-C_L1.fastq.gz.sam

 source line number 98

***! Failure during chimera handling of /opt/juicer/splits/RHC00904-C_L1.fastq.gz

Best,

Mrinal

[Olga Dudchenko]

Hi Mrina,

Not sure. Can you send an ls -lht on your splits folder to see what you've got there?

Olga