create_consensus.sh error

[AlejandroMS17]

Hello Adam,

I am trying to use the new version of create_consensus.sh and I am getting this error:

`amorales@dacelo:/disks/dacelo/data/analyses/RB7_data_analysis/merged_bams_alignment_3$ bash create_consensus_20_04_2017.sh -t 30 -o RB7_3.fa -r /disks/dacelo/data/analyses/RB7_data_analysis/merged_bams_alignment_2/RB7_2.fa -i /disks/dacelo/data/analyses/RB7_data_analysis/merged_bams_alignment_3/RB7_3_alignment_marked_duplicates.bam Academic tradition requires you to cite works you base your article on. When using programs that use GNU Parallel to process data for publication please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid mpileup: option requires an argument -- 'f'

Usage: samtools mpileup [options] in1.bam [in2.bam [...]]

Input options: -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding -A, --count-orphans do not discard anomalous read pairs -b, --bam-list FILE list of input BAM filenames, one per line -B, --no-BAQ disable BAQ (per-Base Alignment Quality) -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0] -d, --max-depth INT max per-file depth; avoids excessive memory usage [250] -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs -f, --fasta-ref FILE faidx indexed reference sequence file -G, --exclude-RG FILE exclude read groups listed in FILE -l, --positions FILE skip unlisted positions (chr pos) or regions (BED) -q, --min-MQ INT skip alignments with mapQ smaller than INT [0] -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13] -r, --region REG region in which pileup is generated -R, --ignore-RG ignore RG tags (one BAM = one sample) --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [] --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP] -x, --ignore-overlaps disable read-pair overlap detection

Output options: -o, --output FILE write output to FILE [standard output] -g, --BCF generate genotype likelihoods in BCF format -v, --VCF generate genotype likelihoods in VCF format

Output options for mpileup format (without -g/-v): -O, --output-BP output base positions on reads -s, --output-MQ output mapping quality

Output options for genotype likelihoods (when -g/-v is used): -t, --output-tags LIST optional tags to output: DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR [] -u, --uncompressed generate uncompressed VCF/BCF output

SNP/INDEL genotype likelihoods options (effective with -g/-v): -e, --ext-prob INT Phred-scaled gap extension seq error probability [20] -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002] -h, --tandem-qual INT coefficient for homopolymer errors [100] -I, --skip-indels do not perform indel calling -L, --max-idepth INT maximum per-file depth for INDEL calling [250] -m, --min-ireads INT minimum number gapped reads for indel candidates [1] -o, --open-prob INT Phred-scaled gap open seq error probability [40] -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity -P, --platforms STR comma separated list of platforms for indels [all] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null]

Notes: Assuming diploid individuals. filter: option requires an argument -- 'e'

About: Apply fixed-threshold filters. Usage: bcftools filter [options]

Options: -e, --exclude exclude sites for which the expression is true (see man page for details) -g, --SnpGap filter SNPs within base pairs of an indel -G, --IndelGap filter clusters of indels separated by or fewer base pairs allowing only one to pass -i, --include include only sites for which the expression is true (see man page for details -m, --mode [+x] "+": do not replace but add to existing FILTER; "x": reset filters at sites which pass --no-version do not append version and command line to the header -o, --output write output to a file [standard output] -O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v] -r, --regions restrict to comma-separated list of regions -R, --regions-file restrict to regions listed in a file -s, --soft-filter annotate FILTER column with or unique filter name ("Filter%d") made up by the program ("+") -S, --set-GTs <.|0> set genotypes of failed samples to missing (.) or ref (0) -t, --targets similar to -r but streams rather than index-jumps -T, --targets-file similar to -R but streams rather than index-jumps --threads number of extra output compression threads [0]

Failed to open -: unknown file type Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid mpileup: option requires an argument -- 'f'`

[adamjorr]

this looks like it works now, try it out when you get the chance and let me know

[AlejandroMS17]

It was running the first part, but I got another error. Please see the attached file, thanks!. create_consensus_error_21_04_2017.txt

[adamjorr]

You ran out of space writing the bam with marked duplicates. You can try changing your temporary directory to somewhere else, but make sure you have enough storage space for your results.

[AlejandroMS17]

Hey Adam, I made some space and I got the same problem. How much space would I need?, how can I change the temporary directory?.

[AlejandroMS17]

https://www.biostars.org/p/42613/

https://gatkforums.broadinstitute.org/gatk/discussion/6083/picard-tools-markduplicates-spilling-to-disk

[adamjorr]

good catch, try now and see what happens