run-asm-pipeline.sh with awk error

[shimiao12345]

Hi , I ran 3d-dna for a plant genome with the command: sh 3d-dna/run-asm-pipeline.sh 9201_Genome_Scaffold.fasta merged_nodups.txt

I got error infomation as follows:

awk: 3d-dna-master/utils/generate-sorted-cprops-file.awk:15: fatal: 3 is invalid as number of arguments for asorti 3d-dna-master/run-asm-pipeline.sh: line 634: 1 + / 2100000000 : syntax error: operand expected (error token is "/ 2100000000 ")

Do you know what cause this problem? Thank you very much!

[dudcha]

Please check your ask version. It should be at least 4.0.2.

Best, Olga

On Feb 12, 2019, at 3:17 AM, shimiao12345 notifications@github.com wrote:

Hi , I ran 3d-dna for a plant genome with the command: sh 3d-dna/run-asm-pipeline.sh 9201_Genome_Scaffold.fasta merged_nodups.txt

I got error infomation as follows:

awk: 3d-dna-master/utils/generate-sorted-cprops-file.awk:15: fatal: 3 is invalid as number of arguments for asorti 3d-dna-master/run-asm-pipeline.sh: line 634: 1 + / 2100000000 : syntax error: operand expected (error token is "/ 2100000000 ")

Do you know what cause this problem? Thank you very much!

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[shimiao12345]

Thanks for your reply. When I ran the older version,there is no this problem. But it takes an extremely long time when generating the 9201_Genome_HERA_Scaffold.rawchrom.fasta file.Then I see that the merged_nodups.txt which was generated by juicer is 155GB. So big is the file! Is that the reason why 9201_Genome_HERA_Scaffold.rawchrom.fasta file was slowly generated?The genome size is 1Gb and the HIC data is 100Gb. Why it happened? I was confused.

3ddna cmd: sh run-pipeline.sh -c 20 9201_Genome_HERA_Scaffold.fasta merged_nodups.txt

juicer cmd: sh juicer.sh \ -g IGT-9201 \ -z 9201_Genome_HERA_Scaffold.fasta \ -d analysis \ -s "MboI" \ -p 9201_Genome_HERA_Scaffold.fasta.size \ -y IGT-9201_MboI.txt \ -t 50

[dudcha]

Most likely your original fasta is not wrapped, i.e. all sequences are listed in a single line. Use 3d-dna/utils/wrap-fasta.awk to wrap you draft and pass that as input into appropriate stage.

Best, Olga

On Feb 15, 2019, at 1:55 AM, shimiao12345 notifications@github.com wrote:

Thanks for your reply. When I ran the older version,there is no this problem. But it takes an extremely long time when generating the 9201_Genome_HERA_Scaffold.rawchrom.fasta file.Then I see that the merged_nodups.txt which was generated by juicer is 155GB. So big is the file! Is that the reason why 9201_Genome_HERA_Scaffold.rawchrom.fasta file was slowly generated?The genome size is 1Gb and the HIC data is 100Gb. Why it happened? I was confused.

3ddna cmd: sh run-pipeline.sh -c 20 9201_Genome_HERA_Scaffold.fasta merged_nodups.txt

juicer cmd: sh juicer.sh -g IGT-9201 -z 9201_Genome_HERA_Scaffold.fasta -d analysis -s "MboI" -p 9201_Genome_HERA_Scaffold.fasta.size -y IGT-9201_MboI.txt -t 50

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[wuxiaopei0509]

I have the same problem "awk: 3d-dna-master/utils/generate-sorted-cprops-file.awk:15: fatal: 3 is invalid as number of arguments for asorti 3d-dna-master/run-asm-pipeline.sh: line 634: 1 + / 2100000000 : syntax error: operand expected (error token is "/ 2100000000 ") How could you change the awk version ？ I have no root permission. Thank you!

[woshi0655]

Hi, I also got the same error, and my awk version is >=4.0.2, but still can not work. What can I do?