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Zac Forsman
Jun 16, 2014, 4:17:13 AM6/16/14
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I've installed dDocent in /usr/local/bin and I ran the install script...but it still doesn't seem to run. The program was looking for aa few scripts in /usr/bin so I copied a few files to that directory as well. Not sure what the problem is.
Here is the program output. -Zac
z@ToBoFox:~/Documents/Plocoraw$ dDocent.FB
dDocent 1.0
Contact jpu...@gmail.com with any problems
2 individuals are detected is this correct? Enter yes or no and press [ENTER]
yes
Proceeding with 2 individuals
Do you want to quality trim your reads?
Type yes or no and press [ENTER]?
yes
Do you want to perform an assembly?
Type yes or no and press [ENTER]?
yes
Reads will be assembled with Rainbow
CD-HIT will cluster reference sequences by similarity. The -c parameter (% similarity to cluster) may need to be changed for your taxa.
Would you like to enter a new c parameter now? Type yes or no and press [ENTER]
no
no
Proceeding with default 0.9 value.
Do you want to map reads? Type yes or no and press [ENTER]
yes
BWA will be used to map reads. You may need to adjust -A -B and -O parameters for your taxa.
Would you like to enter a new parameters now? Type yes or no and press [ENTER]
no
Proceeding with default values for BWA read mapping.
Please enter your email address. dDocent will email you when it is finished running.
Don't worry; dDocent has no financial need to sell your email address to spammers.
dDocent will require input during the assembly stage. Please wait until prompt says it is safe to move program to the background.
Removing the _1 character and replacing with /1 in the name of every sequence
Trimming reads and simultaneously assemblying reference sequences
Trimming Sample PCom1
/usr/local/bin/mergefq.pl: line 1: syntax error near unexpected token `<'
/usr/local/bin/mergefq.pl: line 1: `<html><body>You are being <a href="https://raw.githubusercontent.com/jpuritz/dDocent/master/mergefq.pl">redirected</a>.</body></html>'
mawk: cannot open concat.fasta (No such file or directory)
Warning: empty y range [0:0], adjusting to [-1:1]
Number of Unique Sequences with More than X Occurrences
1 ++---------+----------+----------+----------+----------+----------+----------+----------+----------+---------++
+ + + + + + + + + + +
| |
| |
| |
| |
0.5 ++ ++
| |
| |
| |
| |
| |
0 ++. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .+.
| |
| |
| |
| |
| |
-0.5 ++ ++
| |
| |
| |
| |
+ + + + + + + + + + +
-1 ++---------+----------+----------+----------+----------+----------+----------+----------+----------+---------++
0 5 10 15 20 25 30 35 40 45 50
Please choose data cutoff. Pick point right before assymptote, probably between 10 and 30.
It approximates the expected coverage per RAD fragment.
20
At this point, all configuration information has been enter and dDocent may take several hours to run.
It is recommended that you move this script to a background operation and disable terminal input and output.
All data and logfiles will still be recorded.
To do this:
Press control and Z simultaneously
Type 'bg' without the quotes and press enter
Type 'disown -h' again without the quotes and press enter
Now sit back, relax, and wait for your analysis to finish.
unknown file type
/usr/local/bin/dDocent.FB: line 372: 16023 Aborted (core dumped) rainbow cluster -m 6 -1 uniq.F.fasta -2 uniq.RC.fasta > rcluster
Use of uninitialized value $dseq in split at /usr/bin/select_best_rbcontig_plus_read1.pl line 20.
Use of uninitialized value in transliteration (tr///) at /usr/bin/select_best_rbcontig_plus_read1.pl line 85.
Use of uninitialized value $seqs[1] in reverse at /usr/bin/select_best_rbcontig_plus_read1.pl line 86.
/usr/local/bin/dDocent.FB: line 372: 16031 Segmentation fault (core dumped) samtools faidx reference.fasta
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.5a-r405
[main] CMD: bwa index reference.fasta
[main] Real time: 0.339 sec; CPU: 0.003 sec
Trimming Sample PLob1
Using BWA to map reads.
/usr/local/bin/dDocent.FB: line 181: 16083 Segmentation fault (core dumped) samtools faidx reference.fasta
/usr/local/bin/dDocent.FB: line 235: 16088 Segmentation fault (core dumped) bwa mem reference.fasta $i.R1.fq $i.R2.fq -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" 2> bwa.$i.log
16089 (core dumped) | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2> $i.bam.log
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
/usr/local/bin/dDocent.FB: line 235: 16099 Segmentation fault (core dumped) samtools sort -@$NUMProc $i.bam $i
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
/usr/local/bin/dDocent.FB: line 235: 16105 Segmentation fault (core dumped) bwa mem reference.fasta $i.R1.fq $i.R2.fq -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" 2> bwa.$i.log
16106 (core dumped) | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2> $i.bam.log
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
/usr/local/bin/dDocent.FB: line 235: 16120 Segmentation fault (core dumped) samtools sort -@$NUMProc $i.bam $i
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
Creating alignment intervals
Reading data from:
fwaa and
rwaa
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
/usr/local/bin/dDocent.FB: line 529: 16148 Aborted (core dumped) clone_filter -1 fwaa -2 rwaa
Reading data from:
fwab and
rwab
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
/usr/local/bin/dDocent.FB: line 529: 16151 Aborted (core dumped) clone_filter -1 fwab -2 rwab
Reading data from:
fwac and
rwac
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
/usr/local/bin/dDocent.FB: line 529: 16153 Aborted (core dumped) clone_filter -1 fwac -2 rwac
Reading data from:
fwad and
rwad
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
/usr/local/bin/dDocent.FB: line 529: 16155 Aborted (core dumped) clone_filter -1 fwad -2 rwad
cat: *.fq_1: No such file or directory
cat: *.fq_2: No such file or directory
rm: cannot remove ‘*.fq_1’: No such file or directory
rm: cannot remove ‘*.fq_2’: No such file or directory
Reading data from:
fw and
rw
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
/usr/local/bin/dDocent.FB: line 529: 16160 Aborted (core dumped) clone_filter -1 fw -2 rw
mv: cannot stat ‘fw.fil.fq_1’: No such file or directory
mv: cannot stat ‘rw.fil.fq_2’: No such file or directory
[M::main_mem] read 833994 sequences (80000055 bp)...
/usr/local/bin/dDocent.FB: line 529: 16164 Segmentation fault (core dumped) bwa mem reference.fasta forward1 reverse1 -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:cat\tSM:cat\tPL:Illumina"
16165 (core dumped) | samtools view -q1 -@ $NUMProc -SbT reference.fasta - > cat.bam 2> cat.bam.log
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
/usr/local/bin/dDocent.FB: line 529: 16180 Segmentation fault (core dumped) samtools sort -@$NUMProc cat.bam cat
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
Failed to open BAM file cat-RRG.bam
Error: The requested bed file (map.bed) could not be opened. Exiting!
split: 0: invalid number of lines
Try 'split --help' for more information.
ls: cannot access splitmap*: No such file or directory
mv: cannot stat ‘raw.1.vcf’: No such file or directory
mv: cannot stat ‘raw.2.vcf’: No such file or directory
mv: cannot stat ‘raw.3.vcf’: No such file or directory
mv: cannot stat ‘raw.4.vcf’: No such file or directory
mv: cannot stat ‘raw.5.vcf’: No such file or directory
mv: cannot stat ‘raw.6.vcf’: No such file or directory
mv: cannot stat ‘raw.7.vcf’: No such file or directory
mv: cannot stat ‘raw.8.vcf’: No such file or directory
mv: cannot stat ‘raw.9.vcf’: No such file or directory
/usr/local/bin/dDocent.FB: line 313: vcfcombine: command not found
/usr/local/bin/dDocent.FB: line 314: vcfglxgt: command not found
/usr/local/bin/dDocent.FB: line 314: vcffixup: command not found
Using VCFtools to parse SNPS.vcf for SNPS that are called in at least 90% of individuals
Please install an MTA on this system if you want to use sendmail!
adrienne...@eagles.usm.edu
Jun 25, 2014, 11:49:25 AM6/25/14
to ddo...@googlegroups.com
Hi Zac,
Are you still having this problem? I have been working through the installation process and I ran into the same issue. If you look at the mergefq.pl file, does it say something like "<html><body>You are being <a href="https://raw.githubusercontent.com/jpuritz/dDocent/master/mergefq.pl">redirected</a>.</body></html>" (same thing as your error after "Trimming Sample PCom1")?
For some reason, curl didn't grab mergefq.pl correctly (though the usage in the installation script looks fine to me) and it threw everything else off. That's my best guess, at least. To fix it, I removed the existing text in the mergefq.pl file, copied the script from https://raw.githubusercontent.com/jpuritz/dDocent/master/mergefq.pl, and pasted it into the empty file. There's probably a better way to do it, but it seems to have worked okay.
Hopefully that helps a bit! I had some other problems down the line, but it could have just been my setup.
Cheers,
Adrienne Norrell
Are you still having this problem? I have been working through the installation process and I ran into the same issue. If you look at the mergefq.pl file, does it say something like "<html><body>You are being <a href="https://raw.githubusercontent.com/jpuritz/dDocent/master/mergefq.pl">redirected</a>.</body></html>" (same thing as your error after "Trimming Sample PCom1")?
For some reason, curl didn't grab mergefq.pl correctly (though the usage in the installation script looks fine to me) and it threw everything else off. That's my best guess, at least. To fix it, I removed the existing text in the mergefq.pl file, copied the script from https://raw.githubusercontent.com/jpuritz/dDocent/master/mergefq.pl, and pasted it into the empty file. There's probably a better way to do it, but it seems to have worked okay.
Hopefully that helps a bit! I had some other problems down the line, but it could have just been my setup.
Cheers,
Adrienne Norrell
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