Kneaddata upaires reads

Infrastructure and utilities KneadData
1

I use kneaddata v.0.12 installed from bioconda.

It unpairs my paire-en reads durin the bowtie run. Before most reads waire paired end after all were single end.

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3

kneaddate explicitly runs a unpair option!

INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 bowtie2 --threads 8 -x kneaddata-0.7.6/database/cat/cat --mode strict --bowtie2-op
tions “–very-sensitive-local --phred33” -1 /tmp/sample1.trimmed.1.fastq -2 /tmp/sample1.trimmed.2.fastq --un-pair /tmp/sample1_cat_bowtie2_paired_clean_%.fa
stq --al-pair /tmp/sample1_cat_bowtie2_paired_contam_%.fastq -U /tmp/sample1.trimmed.single.1.fastq,/tmp/sample1.trimmed.single.2.fastq --un-single /tmp/samp
le1_cat_bowtie2_unmatched_%clean.fastq --al-single /tmp/sample1_cat_bowtie2_unmatched%_contam.fastq -S /dev/null

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4

My reads have the folowing heders

@VH00415:2:AAAKHCJHV:1:1101:30994:1000 1:N:0:AACCATAGAA+CCATCTCGCC
CTCCGGCAGGGTTCCGCAGTCAGCGATGTGATTCCAAAATAAAGCGCCTTCGATCTTGCAATGATATAAAAGGGAATCTCTTCTTTTCGCAGACAGGTATCTGCCCCCGGTTTTCTGGCAAAAGAAAATTTCCTGTCCCCATTTTTATCCA
+
-C;;C;;;CC;-CCCCCCCCCCC;C-CCC-CCCC-C;C-CCC-C;C;;CCCCCCC-CCCCCCCCCCCCCCC-CCCC;CCCCCCCCC;;C;;C-C-CCCCCCCC;;-C;;CC-CC-C-C-CC;CC-C-;CC-CCC;CCC-CCC;CC-CCCC-
@VH00415:2:AAAKHCJHV:1:1101:34592:1000 1:N:0:AACCATAGAA+CCATCTCGCC
CTGCTATGACCGCAGATAATGGTACCATCCTCCAACTCAATGGCAGAAGAGGTATGACCCGTCTCCTTCTTATGATTCTTGGCAGCTACCGTCACCTTGCGGTAATCAGTAGTAATCTTAGCCTGATTGAAGAGCATCTGAATCTTATTGA
+
CCCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-;CCCC;CCCCCCCCCC-CCCCC-CCCCCCCCCCCCCCCCCCCCC-CC-CCCCC-C-CC-CCC;
@VH00415:2:AAAKHCJHV:1:1101:35614:1000 1:N:0:AACCATAGAA+CCATCTCGCC
CCAGCAGCACCACCGCCAACAACAATAACTTTACGCATTATTTATCTCCTATTTTTTTACGCAAACGCAATAATTCAGTTTCAGTTAATTTTCTATATTCTCCACGTTTTAATTTACTCAAAGTAAGACCTGCAAAAGCTATGGGTTTTAA
(base) [rdkiesersi1@gate Debug_biobackery]$ zcat test_reads/sample1_R2.fastq.gz | head 
@VH00415:2:AAAKHCJHV:1:1101:30994:1000 2:N:0:AACCATAGAA+CCATCTCGCC
GTCCCTGATAGATTTTACATATCAGGGAAAGGATACGCAGGGATTTCCGCTTTTACTGGGTCATCCGGGAGGAGCACCGGCAAATTTTCTTGGGGCGATGGCGGTTTTTGGAGCGGCCGGCGCATTGATCACAAAACTAGGAGAAGATATG
+
C-C;C-C-;-CC--CC;-CC-CCC-;C;CCCC-;;;-----CC-CC---C;;C-C---;-C;-C;-CCC-C--;-;C;C-CC-CCCC-CCC--CCCC--CC--C;;--;C-C;--C;CCC;-CCCC;CCC;-C-C--CCC-C;-CC;;;CC
@VH00415:2:AAAKHCJHV:1:1101:34592:1000 2:N:0:AACCATAGAA+CCATCTCGCC
GTTCGAGGGTATCTATGGTAGCAATCCATACAAGTCGCCTACAGATATGGGGGTGAACATGGTAGGTTTCTGTATCTCTGATGATGAGGCTTGCTGCGAGGCATCCAAGAATGAGATTGTCCGCCGTTACTATGCGGCTACCACCAAGATG
+
CC-;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-C;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC;CCCCCCCCCCCCCC;;-CCCCCCC-CC-CC-;C;CCCC
@VH00415:2:AAAKHCJHV:1:1101:35614:1000 2:N:0:AACCATAGAA+CCATCTCGCC
GCTTTAGGATATGAAGTTAAAGCTTTAAAACGCATAGCTTTTGCAGGTCTTACTTTGAGTAAATTAAAACGTGGAGAATATAGAAAATTAACTGAAACTGAATTATTGCGTTTGCGTAAAAAAATTGGAGATAAATAATGCGTAACGTTAT
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5

I think I might be running into an issue cause by this - I updated from v0.10 to v0.12 recently, and now I end up with nothing in my _paired_ files, everything is dumped into _unmatched_…

As an example

v0.10

$ ls -lLh
-rw-rw-r-- 1 vanja1 vanja1 230K Jul  5 18:35 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 237K Jul  5 18:35 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  26K Jul  5 18:35 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  25K Jul  5 18:35 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  17K Jul  5 18:35 FG02839_S64_kneaddata.log
-rw-rw-r-- 1 vanja1 vanja1 269M Jul  5 18:35 FG02839_S64_kneaddata_paired_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 279M Jul  5 18:35 FG02839_S64_kneaddata_paired_2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 274M Jul  5 18:35 FG02839_S64_kneaddata.repeats.removed.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 292M Jul  5 18:35 FG02839_S64_kneaddata.repeats.removed.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  16M Jul  5 18:35 FG02839_S64_kneaddata.repeats.removed.unmatched.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 7.3M Jul  5 18:35 FG02839_S64_kneaddata.repeats.removed.unmatched.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 287M Jul  5 18:35 FG02839_S64_kneaddata.trimmed.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 298M Jul  5 18:35 FG02839_S64_kneaddata.trimmed.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  16M Jul  5 18:35 FG02839_S64_kneaddata.trimmed.single.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 7.4M Jul  5 18:35 FG02839_S64_kneaddata.trimmed.single.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  21M Jul  5 18:35 FG02839_S64_kneaddata_unmatched_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  21M Jul  5 18:35 FG02839_S64_kneaddata_unmatched_2.fastq.gz

v0.12

$ ls -lLh
-rw-rw-r-- 1 vanja1 vanja1   85 Jul  5 10:39 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1   85 Jul  5 10:39 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 281K Jul  5 10:39 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 289K Jul  5 10:39 FG02839_S64_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  17K Jul  5 10:39 FG02839_S64_kneaddata.log
-rw-rw-r-- 1 vanja1 vanja1   57 Jul  5 10:39 FG02839_S64_kneaddata_paired_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1   57 Jul  5 10:39 FG02839_S64_kneaddata_paired_2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 295M Jul  5 10:39 FG02839_S64_kneaddata.repeats.removed.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 313M Jul  5 10:39 FG02839_S64_kneaddata.repeats.removed.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  12M Jul  5 10:39 FG02839_S64_kneaddata.repeats.removed.unmatched.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 4.7M Jul  5 10:39 FG02839_S64_kneaddata.repeats.removed.unmatched.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 311M Jul  5 10:39 FG02839_S64_kneaddata.trimmed.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 321M Jul  5 10:39 FG02839_S64_kneaddata.trimmed.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1  12M Jul  5 10:39 FG02839_S64_kneaddata.trimmed.single.1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 4.8M Jul  5 10:39 FG02839_S64_kneaddata.trimmed.single.2.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 306M Jul  5 10:39 FG02839_S64_kneaddata_unmatched_1.fastq.gz
-rw-rw-r-- 1 vanja1 vanja1 317M Jul  5 10:39 FG02839_S64_kneaddata_unmatched_2.fastq.gz
6

Hi @kescobo and @SilasK ,
I am looking into this issue. Thanks for posting.

Regards,
Sagun

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7

Replying to follow the post as I have the same issue as @kescobo with kneaddata v.0.12.0.

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