Hi lauren I will continue this problem
First I use kneaddata 0.7.2 it give me unpaired reads
singularity --debug exec
/software/kneaddata_0.7.2.sif kneaddata \
--remove-intermediate-output --threads 4 --bypass-trim \
--input ../raw_data/SRR527911_1.fastq.gz --input ../raw_data/SRR527911_2.fastq.gz \
--output ../temp/01_kneaddata --reference-db ../databases/kneaddata/human_genome \
--bowtie2-options "--very-sensitive --dovetail"
paired 1 737M and paired 2 82M are not same
-rw-r--r-- 1 ckzhu sample_lib 0 Jul 17 09:07 SRR527911_1_kneaddata_unmatched_2.fastq
-rw-r--r-- 1 ckzhu sample_lib 0 Jul 17 09:07 SRR527911_1_kneaddata_Homo_sapiens_bowtie2_unmatched_1_contam.fastq
-rw-r--r-- 1 ckzhu sample_lib 13K Jul 17 09:07 SRR527911_1_kneaddata_unmatched_1.fastq
-rw-r--r-- 1 ckzhu sample_lib 82M Jul 17 09:07 SRR527911_1_kneaddata_paired_2.fastq
-rw-r--r-- 1 ckzhu sample_lib 737M Jul 17 09:07 SRR527911_1_kneaddata_paired_1.fastq
-rw-r--r-- 1 ckzhu sample_lib 1.4K Jul 17 09:07 SRR527911_1_kneaddata_Homo_sapiens_bowtie2_unmatched_2_contam.fastq
-rw-r--r-- 1 ckzhu sample_lib 448 Jul 17 09:07 SRR527911_1_kneaddata_Homo_sapiens_bowtie2_paired_contam_2.fastq
-rw-r--r-- 1 ckzhu sample_lib 4.0K Jul 17 09:07 SRR527911_1_kneaddata_Homo_sapiens_bowtie2_paired_contam_1.fastq
-rw-r--r-- 1 ckzhu sample_lib 11K Jul 17 09:07 SRR527911_1_kneaddata.log
Then I use kneaddata 0.10.0 from docker images
I get new error
singularity --debug exec
/software/kneaddata_0.10.0.sif kneaddata \
--remove-intermediate-output --threads 4 --bypass-trim \
--input ../raw_data/SRR527911_1.fastq.gz --input ../raw_data/SRR527911_2.fastq.gz \
--output ../temp/01_kneaddata --reference-db ../databases/kneaddata/human_genome \
--bowtie2-options "--very-sensitive --dovetail"
Decompressing gzipped file ...
Decompressing gzipped file ...
Reformatting file sequence identifiers ...
Reformatting file sequence identifiers ...
Initial number of reads ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiers8t6864hl_decompressed_zex5i232_SRR527911_1 ): 1921490.0
Initial number of reads ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersrphkmryn_decompressed_gf1ann04_SRR527911_2 ): 1921490.0
Bypass trimming
Total reads after trimming ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiers8t6864hl_decompressed_zex5i232_SRR527911_1 ): 1921490.0
Total reads after trimming ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersrphkmryn_decompressed_gf1ann04_SRR527911_2 ): 1921490.0
ERROR: Unable to write file: /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiers8t6864hl_decompressed_zex5i232_SRR527911_1
DEBUG [U=5169,P=28402] Master() Child exited with exit status 1
why I can’t write tmp file in that dir? should root to run singularity?
If I use conda ,I also can’t write
conda create -n kneaddata kneaddata=0.10.0
source activate kneaddata
kneaddata \
--remove-intermediate-output --threads 4 --bypass-trim \
--input ../raw_data/SRR527911_1.fastq.gz --input ../raw_data/SRR527911_2.fastq.gz \
--output ../temp/01_kneaddata --reference-db ../databases/kneaddata/human_genome \
--bowtie2-options "--very-sensitive --dovetail"
Decompressing gzipped file ...
Decompressing gzipped file ...
Reformatting file sequence identifiers ...
Reformatting file sequence identifiers ...
Initial number of reads ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersjsysc7lb_decompressed_sff5u2hr_SRR527911_1 ): 1921490.0
Initial number of reads ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersf3j5gvzj_decompressed_hab_axlq_SRR527911_2 ): 1921490.0
Bypass trimming
Total reads after trimming ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersjsysc7lb_decompressed_sff5u2hr_SRR527911_1 ): 1921490.0
Total reads after trimming ( /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersf3j5gvzj_decompressed_hab_axlq_SRR527911_2 ): 1921490.0
ERROR: Unable to write file: /public/home/sample_lib/ckzhu/software/Snakemake_singularity/test/pipeline/temp/01_kneaddata/reformatted_identifiersjsysc7lb_decompressed_sff5u2hr_SRR527911_1