3d-dna error after assemble from juicer
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Jui-Hung
Sep 9, 2022, 9:30:31 AM9/9/22
to 3D Genomics
Hi there,
I am trying on assemble Yeast genome by juicer pipeline.
After I finished running juicer by the command:
juicer.sh -z
MYA3404.genome.fa --assemble
I got the file merged_nodups.txt in the folder ./topDir/aligned/
According to the Genome Assembly Cookbook on page 18, I thought this is the file which should be input in 3d-dna.
Command line is in below:
bash /home/juihung/3d-dna/run-asm-pipeline.sh /home/juihung/juicer/Yeast/genome/MYA3404.genome.fa /home/juihung/juicer/Yeast/topDir/aligned/merged_nodups.txt
3d-dna gave me the messages as below:
/home/juihung/3d-dna/run-asm-pipeline.sh ../genome/MYA3404.genome.fa ../topDir/aligned/merged_nodups.txt
version: 180922
../../../3d-dna/run-asm-pipeline.sh: line 656 ： [: too many arguments
###############
Starting iterating scaffolding with editing:
...starting round 0 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.0.cprops
...Using merged_nodups file: MYA3404.genome.mnd.0.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 0 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.0.asm_mnd.txt does not exist or does not contain any reads.
...detecting misjoins in round 0 assembly:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 25000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 125000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 25000 resolution matrix
Could not read hic file: null
:( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
:) -w flag was triggered, performing cursory search for repeat at 25000 resolution
:) -t flag was triggered, flagging regions with coverage higher than 2
...Dumping 25000 resolution coverage track
Could not read hic file: null
:( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
mv: cannot stat 'depletion_score_wide.wig': No such file or directory
mv: cannot stat 'depletion_score_narrow.wig': No such file or directory
mv: cannot stat 'mismatch_wide.bed': No such file or directory
mv: cannot stat 'mismatch_narrow.bed': No such file or directory
mv: cannot stat 'coverage_wide.wig': No such file or directory
mv: cannot stat 'repeats_wide.bed': No such file or directory
cat: mismatch_narrow.at.step.0.bed: No such file or directory
cat: repeats_wide.at.step.0.bed: No such file or directory
...-p flag was triggered. Running with GNU Parallel support parameter set to true.
...-r flag was triggered, output will be labeled as *.1.*
...applying edits to cprops file
...applying edits to mnd file
...starting round 1 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.1.cprops
...Using merged_nodups file: MYA3404.genome.mnd.1.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 1 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.1.asm_mnd.txt does not exist or does not contain any reads.
...detecting misjoins in round 1 assembly:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 25000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 125000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 25000 resolution matrix
Could not read hic file: null
:( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
:) -w flag was triggered, performing cursory search for repeat at 25000 resolution
:) -t flag was triggered, flagging regions with coverage higher than 2
...Dumping 25000 resolution coverage track
Could not read hic file: null
:( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
mv: cannot stat 'depletion_score_wide.wig': No such file or directory
mv: cannot stat 'depletion_score_narrow.wig': No such file or directory
mv: cannot stat 'mismatch_wide.bed': No such file or directory
mv: cannot stat 'mismatch_narrow.bed': No such file or directory
mv: cannot stat 'coverage_wide.wig': No such file or directory
mv: cannot stat 'repeats_wide.bed': No such file or directory
cat: mismatch_narrow.at.step.1.bed: No such file or directory
cat: repeats_wide.at.step.1.bed: No such file or directory
...-p flag was triggered. Running with GNU Parallel support parameter set to true.
...-r flag was triggered, output will be labeled as *.2.*
...applying edits to cprops file
...applying edits to mnd file
...starting round 2 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.2.cprops
...Using merged_nodups file: MYA3404.genome.mnd.2.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 2 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.2.asm_mnd.txt does not exist or does not contain any reads.
:( No resolved files are found. Please rerun the pipeline to include the scaffold segment. Exiting!
version: 180922
../../../3d-dna/run-asm-pipeline.sh: line 656 ： [: too many arguments
###############
Starting iterating scaffolding with editing:
...starting round 0 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.0.cprops
...Using merged_nodups file: MYA3404.genome.mnd.0.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 0 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.0.asm_mnd.txt does not exist or does not contain any reads.
...detecting misjoins in round 0 assembly:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 25000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 125000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 25000 resolution matrix
Could not read hic file: null
:( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
:) -w flag was triggered, performing cursory search for repeat at 25000 resolution
:) -t flag was triggered, flagging regions with coverage higher than 2
...Dumping 25000 resolution coverage track
Could not read hic file: null
:( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
mv: cannot stat 'depletion_score_wide.wig': No such file or directory
mv: cannot stat 'depletion_score_narrow.wig': No such file or directory
mv: cannot stat 'mismatch_wide.bed': No such file or directory
mv: cannot stat 'mismatch_narrow.bed': No such file or directory
mv: cannot stat 'coverage_wide.wig': No such file or directory
mv: cannot stat 'repeats_wide.bed': No such file or directory
cat: mismatch_narrow.at.step.0.bed: No such file or directory
cat: repeats_wide.at.step.0.bed: No such file or directory
...-p flag was triggered. Running with GNU Parallel support parameter set to true.
...-r flag was triggered, output will be labeled as *.1.*
...applying edits to cprops file
...applying edits to mnd file
...starting round 1 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.1.cprops
...Using merged_nodups file: MYA3404.genome.mnd.1.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 1 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.1.asm_mnd.txt does not exist or does not contain any reads.
...detecting misjoins in round 1 assembly:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 25000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 125000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 25000 resolution matrix
Could not read hic file: null
:( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
:) -w flag was triggered, performing cursory search for repeat at 25000 resolution
:) -t flag was triggered, flagging regions with coverage higher than 2
...Dumping 25000 resolution coverage track
Could not read hic file: null
:( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!
mv: cannot stat 'depletion_score_wide.wig': No such file or directory
mv: cannot stat 'depletion_score_narrow.wig': No such file or directory
mv: cannot stat 'mismatch_wide.bed': No such file or directory
mv: cannot stat 'mismatch_narrow.bed': No such file or directory
mv: cannot stat 'coverage_wide.wig': No such file or directory
mv: cannot stat 'repeats_wide.bed': No such file or directory
cat: mismatch_narrow.at.step.1.bed: No such file or directory
cat: repeats_wide.at.step.1.bed: No such file or directory
...-p flag was triggered. Running with GNU Parallel support parameter set to true.
...-r flag was triggered, output will be labeled as *.2.*
...applying edits to cprops file
...applying edits to mnd file
...starting round 2 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: MYA3404.genome.2.cprops
...Using merged_nodups file: MYA3404.genome.mnd.2.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
:) DONE!
...visualizing round 2 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to true.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.MYA3404.genome.2.asm_mnd.txt does not exist or does not contain any reads.
:( No resolved files are found. Please rerun the pipeline to include the scaffold segment. Exiting!
How do I solve this problem?
Thank you very much.
Best regards,
Jui-Hung Tai
Olga Dudchenko
Sep 22, 2022, 3:06:54 PM9/22/22
to 3D Genomics
this line: [: too many arguments
Best,
Olga
Jui-Hung
Oct 6, 2022, 12:17:15 PM10/6/22
to 3D Genomics
Dear Olga,
I upgraded the bash version to 4.4.20.
That "too many arguments" did not showed again, but the remaining error message still showing.
Is there anything I can do to figure out the problems?
Thank for helping.
Best,
Jui-Hung
Olga Dudchenko 在 2022年9月23日 星期五凌晨3:06:54 [UTC+8] 的信中寫道：
Olga Dudchenko
Oct 6, 2022, 12:23:48 PM10/6/22
to 3D Genomics
Hi Jui-Hung,
What remaining error message? You'll need to be a bit more specific. This one?
temp.MYA3404.genome.0.asm_mnd.txt does not exist or does not contain any reads.
Does your merged_nodups.txt file contain any data? Also check that your fasta does not contain any special characters in the headers.
Best,
Olga
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