05. Output

Output Directories

pipesnake generates a lot of outputs, so let's unpack them.

Depending on the specifications of your config file (e.g. see lines 197-226 here), you may have all or none of the directories below in your --outdir. The config file makes it easy to change which files to keep from which processes. For example, changing iqtree_keep_output = true to iqtree_keep_output = false will mean no iqtree/ or files will be displayed in your output directory.

Note: process names (e.g. ASTER) refer to steps in the pipesnake.nf workflow file.

Directory	Description	Output Directory/Files	Explanation
aster/	output of ASTER process	aster_tree_final	hybrid-ASTRAL species tree
bbmap/	output of BBMAP_DEDUPE and BBMAP_REFORMAT processes	(6 per sample) sample_id_deduped.fastq.gz sample_id_duplicates.fastq.gz sample_id_R1_bbmap.fastq.gz sample_id_R1_reformated.fastq.gz sample_id_R2_bbmap.fastq.gz sample_id_R2_reformated.fastq.gz	deduplicated and reformatted read files
blat/	output of BLAT process contigs-to-targets	(1 per sample) sample_id_to_probes	results of forward BLAT search
blat2/	output of BLAT process targets-to-probes	(1 per sample) sample_id_from_probes	results of reverse BLAT search
concatenate/	output of CONCATENATE and TRIMMOMATIC processes	(3 per sample) sample_id_concatenated_R1.fastq.gz sample_id_concatenated_R2.fastq.gz sample_id_trimmed_unpaired_concatenated.fastq.gz
concatenate2/	output of CONCATENATE2 and TRIMMOMATIC_CLEAN_PE processes	(1 per sample) sample_id_trimmed_unpaired_pe_seconcatenated.fastq.gz
concatenate3/	output of CONCATENATE2 and BBMAP_FILTER processes	(1 per sample) sample_id_trinity_r1_unpaired_concatenated.fastq.gz
gblocks/	output of GBLOCKS process	(1 per locus) [locus_name].fasta.aln-gb	GBLOCKS trimmed alignments
iqtree/	output of IQTREE process (if used)	(9 per locus) locus_id...fasta.bionj locus_id...fasta.ckp.gz locus_id...fasta.contree locus_id...fasta.iqtree locus_id...fasta.log locus_id...fasta.mldist locus_id...fasta.model.gz locus_id...fasta.splits.nex locus_id...fasta.treefile	IQTREE locus trees and associated files
make/	output of MAKE_PRG process	(1 per sample) [lineage].fasta	results in a pseudo-reference genome file of final matched sequences
merge/	output of MERGE_TREES process	AllLoci.trees	concatenated locus trees into a single file
parse/	output of PARSE_BLAT_RESULTS process	(1 per sample) sample_id_matches.csv
pear/	output of PEAR process	(4 per sample) sample_id.assembled.fastq.gz sample_id.discarded.fastq.gz sample_id.unassembled.forward.fastq.gz sample_id.unassembled.reverse.fastq.gz	paired, unpaired, and discarded read files
phylogeny/	output of PHYLOGENY_MAKE_ALIGNMENTS process	(1 per locus) locus_id.fasta	'raw' alignments (unaligned)
prepare/	output of PREPARE_ADAPTOR process	(1 per sample) sample_id.fa	makes adapter file for trimming (input for trimmomatic)
quality/	output of QUALITY_2_ASSEMBLY process	(1 per sample) sample_id_assemblyquality.csv	basic statistics on sample quality from contig and assembled loci
raxml/	output of RAXML process (if used)	(5 per locus) RAxML_bestTree.locus_id...fasta RAxML_bipartitions.locus_id...fasta RAxML_bipartitionsBranchLabels.locus_id...fasta RAxML_bootstrap.locus_id...fasta RAxML_info.locus_id...fasta	RAxML locus trees and associated files
trimmomatic/	output of TRIMMOMATIC or TRIMMOMATIC_CLEAN_PE processes?	(9 per sample) sample_id_R1_paired_trimmed_cleaned.fastq.gz sample_id_R1_paired.trimmed.fastq.gz sample_id_R1_unpaired_trimmed_cleaned.fastq.gz sample_id_R1_unpaired_trimmed.fastq.gz sample_id_R2_paired_trimmed_cleaned.fastq.gz sample_id_R2_paired.trimmed.fastq.gz sample_id_R2_unpaired_trimmed_cleaned.fastq.gz sample_id_R2_unpaired_trimmed.fastq.gz sample_id_unpaired_trimmed_cleaned_se.fastq.gz
trinity/	output of TRINITY and TRINITY_POSTPROCESSING processes	(2 per sample) sample_id_trinity/ sample_id_trinity_processed.fasta

Chronology

We can follow the creation of output directories chronologically. This might be useful for troubleshooting purposes.

• BBMAP_DEDUPE
• PREPARE_ADAPTOR
• INPUT_CHECK
• PREPARE_SAMPLESHEET
• BBMAP_REFORMAT
• TRIMMOMATIC
• PEAR
• CONCATENATE
• CONCATENATE2
• CONCATENATE3
• TRIMMOMATIC_CLEAN_PE
• TRIMMOMATIC_CLEAN_SE
• BBMAP_FILTER
• TRINITY
• TRINITY_POSTPROCESSING
• BLAT
• BLAT2
• PARSE_BLAT_RESULTS
• MAFFT
• MACSE
• PERL_CLEANUP
• MAKE_PRG
• QUALITY_2_ASSEMBLY
• PHYLOGENY_MAKE_ALIGNMENTS
• GBLOCKS
• RAXML / IQTREE
• SED
• BBMAP_REFORMAT
• MERGE_TREES
• ASTER