I am trying to use SRA toolkit on Kubuntu local terminal to run an accession for Illumina. Every time I get a new error, and so far, I have figured it out, but this time it is saying there is no disk space. I tried rm and rmdir to clear up space. I've used df -h as suggested, but I am not sure what the output means or where to go from here.
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-ubuntu64.tar.gz
--2022-12-08 21:09:05-- https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-ubuntu64.tar.gz
Resolving ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)... 2607:f220:41e:250::7, 2607:f220:41e:250::13, 165.112.9.230, ...
Connecting to ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)|2607:f220:41e:250::7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 85777118 (82M) [application/x-gzip]
Saving to: ‘sratoolkit.3.0.0-ubuntu64.tar.gz’
sratoolkit.3.0.0-ubuntu64.tar.gz 100%[==========================================================>] 81.80M 8.97MB/s in 10s
2022-12-08 21:09:18 (7.93 MB/s) - ‘sratoolkit.3.0.0-ubuntu64.tar.gz’ saved [85777118/85777118]
kbailey48@penguin:~$ SRR
-bash: SRR: command not found
kbailey48@penguin:~$ tar -zxvf sratoolkit.3.0.0-ubuntu64.tar.gz
sratoolkit.3.0.0-ubuntu64/
sratoolkit.3.0.0-ubuntu64/bin/
sratoolkit.3.0.0-ubuntu64/bin/abi-dump
sratoolkit.3.0.0-ubuntu64/bin/abi-dump.3
sratoolkit.3.0.0-ubuntu64/bin/abi-load
sratoolkit.3.0.0-ubuntu64/bin/abi-load.3
sratoolkit.3.0.0-ubuntu64/bin/align-info
sratoolkit.3.0.0-ubuntu64/bin/align-info.3
sratoolkit.3.0.0-ubuntu64/bin/bam-load
sratoolkit.3.0.0-ubuntu64/bin/bam-load.3
sratoolkit.3.0.0-ubuntu64/bin/cache-mgr
sratoolkit.3.0.0-ubuntu64/bin/cache-mgr.3
sratoolkit.3.0.0-ubuntu64/bin/cg-load
sratoolkit.3.0.0-ubuntu64/bin/cg-load.3
sratoolkit.3.0.0-ubuntu64/bin/dump-ref-fasta
sratoolkit.3.0.0-ubuntu64/bin/dump-ref-fasta.3
sratoolkit.3.0.0-ubuntu64/bin/fasterq-dump
sratoolkit.3.0.0-ubuntu64/bin/fasterq-dump.3
sratoolkit.3.0.0-ubuntu64/bin/fasterq-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/fastq-dump
sratoolkit.3.0.0-ubuntu64/bin/fastq-dump.3
sratoolkit.3.0.0-ubuntu64/bin/fastq-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/fastq-load
sratoolkit.3.0.0-ubuntu64/bin/fastq-load.3
sratoolkit.3.0.0-ubuntu64/bin/helicos-load
sratoolkit.3.0.0-ubuntu64/bin/helicos-load.3
sratoolkit.3.0.0-ubuntu64/bin/illumina-dump
sratoolkit.3.0.0-ubuntu64/bin/illumina-dump.3
sratoolkit.3.0.0-ubuntu64/bin/illumina-load
sratoolkit.3.0.0-ubuntu64/bin/illumina-load.3
sratoolkit.3.0.0-ubuntu64/bin/kar
sratoolkit.3.0.0-ubuntu64/bin/kar.3
sratoolkit.3.0.0-ubuntu64/bin/kdbmeta
sratoolkit.3.0.0-ubuntu64/bin/kdbmeta.3
sratoolkit.3.0.0-ubuntu64/bin/latf-load
sratoolkit.3.0.0-ubuntu64/bin/latf-load.3
sratoolkit.3.0.0-ubuntu64/bin/pacbio-load
sratoolkit.3.0.0-ubuntu64/bin/pacbio-load.3
sratoolkit.3.0.0-ubuntu64/bin/prefetch
sratoolkit.3.0.0-ubuntu64/bin/prefetch.3
sratoolkit.3.0.0-ubuntu64/bin/prefetch.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/rcexplain
sratoolkit.3.0.0-ubuntu64/bin/rcexplain.3
sratoolkit.3.0.0-ubuntu64/bin/sam-dump
sratoolkit.3.0.0-ubuntu64/bin/sam-dump.3
sratoolkit.3.0.0-ubuntu64/bin/sam-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sff-dump
sratoolkit.3.0.0-ubuntu64/bin/sff-dump.3
sratoolkit.3.0.0-ubuntu64/bin/sff-load
sratoolkit.3.0.0-ubuntu64/bin/sff-load.3
sratoolkit.3.0.0-ubuntu64/bin/sra-pileup
sratoolkit.3.0.0-ubuntu64/bin/sra-pileup.3
sratoolkit.3.0.0-ubuntu64/bin/sra-pileup.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-search
sratoolkit.3.0.0-ubuntu64/bin/sra-search.3
sratoolkit.3.0.0-ubuntu64/bin/sra-sort
sratoolkit.3.0.0-ubuntu64/bin/sra-sort-cg
sratoolkit.3.0.0-ubuntu64/bin/sra-sort-cg.3
sratoolkit.3.0.0-ubuntu64/bin/sra-sort.3
sratoolkit.3.0.0-ubuntu64/bin/sra-stat
sratoolkit.3.0.0-ubuntu64/bin/sra-stat.3
sratoolkit.3.0.0-ubuntu64/bin/srapath
sratoolkit.3.0.0-ubuntu64/bin/srapath.3
sratoolkit.3.0.0-ubuntu64/bin/srapath.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/srf-load
sratoolkit.3.0.0-ubuntu64/bin/srf-load.3
sratoolkit.3.0.0-ubuntu64/bin/test-sra
sratoolkit.3.0.0-ubuntu64/bin/test-sra.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-config
sratoolkit.3.0.0-ubuntu64/bin/vdb-config.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-copy
sratoolkit.3.0.0-ubuntu64/bin/vdb-copy.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-decrypt
sratoolkit.3.0.0-ubuntu64/bin/vdb-decrypt.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-dump
sratoolkit.3.0.0-ubuntu64/bin/vdb-dump.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-encrypt
sratoolkit.3.0.0-ubuntu64/bin/vdb-encrypt.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-lock
sratoolkit.3.0.0-ubuntu64/bin/vdb-lock.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-unlock
sratoolkit.3.0.0-ubuntu64/bin/vdb-unlock.3
sratoolkit.3.0.0-ubuntu64/bin/vdb-validate
sratoolkit.3.0.0-ubuntu64/bin/vdb-validate.3
sratoolkit.3.0.0-ubuntu64/bin/ncbi/
sratoolkit.3.0.0-ubuntu64/bin/ncbi/certs.kfg
sratoolkit.3.0.0-ubuntu64/bin/ncbi/default.kfg
sratoolkit.3.0.0-ubuntu64/bin/ncbi/vdb-copy.kfg
sratoolkit.3.0.0-ubuntu64/bin/srapath-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sratools.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/srf-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/test-sra.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-config.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-copy.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-decrypt.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-dump-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-encrypt.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-lock.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-unlock.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/vdb-validate.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/abi-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/abi-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/align-info.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/bam-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/cache-mgr.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/cg-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/dump-ref-fasta.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/fasterq-dump-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/fastq-dump-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/fastq-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/helicos-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/illumina-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/illumina-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/kar.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/kdbmeta.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/latf-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/pacbio-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/prefetch-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/rcexplain.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sam-dump-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sff-dump.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sff-load.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-pileup-orig.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-search.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-sort-cg.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-sort.3.0.0
sratoolkit.3.0.0-ubuntu64/bin/sra-stat.3.0.0
sratoolkit.3.0.0-ubuntu64/example/
sratoolkit.3.0.0-ubuntu64/example/perl/
sratoolkit.3.0.0-ubuntu64/example/perl/base-stats.pl
sratoolkit.3.0.0-ubuntu64/example/perl/dump-reference.pl
sratoolkit.3.0.0-ubuntu64/example/perl/gene-lookup.pl
sratoolkit.3.0.0-ubuntu64/example/perl/mismatch-stats.pl
sratoolkit.3.0.0-ubuntu64/example/perl/quality-stats.pl
sratoolkit.3.0.0-ubuntu64/example/perl/simplefastq.pl
sratoolkit.3.0.0-ubuntu64/example/perl/splitfastq.pl
sratoolkit.3.0.0-ubuntu64/README-blastn
sratoolkit.3.0.0-ubuntu64/README-vdb-config
sratoolkit.3.0.0-ubuntu64/schema/
sratoolkit.3.0.0-ubuntu64/schema/align/
sratoolkit.3.0.0-ubuntu64/schema/align/align.vschema
sratoolkit.3.0.0-ubuntu64/schema/align/mate-cache.vschema
sratoolkit.3.0.0-ubuntu64/schema/align/pileup-stats.vschema
sratoolkit.3.0.0-ubuntu64/schema/align/qstat.vschema
sratoolkit.3.0.0-ubuntu64/schema/align/refseq.vschema
sratoolkit.3.0.0-ubuntu64/schema/align/seq.vschema
sratoolkit.3.0.0-ubuntu64/schema/csra2/
sratoolkit.3.0.0-ubuntu64/schema/csra2/csra2.vschema
sratoolkit.3.0.0-ubuntu64/schema/csra2/read.vschema
sratoolkit.3.0.0-ubuntu64/schema/csra2/reference.vschema
sratoolkit.3.0.0-ubuntu64/schema/csra2/stats.vschema
sratoolkit.3.0.0-ubuntu64/schema/insdc/
sratoolkit.3.0.0-ubuntu64/schema/insdc/insdc.vschema
sratoolkit.3.0.0-ubuntu64/schema/insdc/seq.vschema
sratoolkit.3.0.0-ubuntu64/schema/insdc/sra.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/
sratoolkit.3.0.0-ubuntu64/schema/ncbi/clip.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/ncbi.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/pnbrdb.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/seq-graph.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/seq.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/spotname.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/sra.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/stats.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/trace.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/varloc.vschema
sratoolkit.3.0.0-ubuntu64/schema/ncbi/wgs-contig.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/
sratoolkit.3.0.0-ubuntu64/schema/sra/454.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/abi.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/generic-fastq.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/helicos.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/illumina.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/ion-torrent.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/nanopore.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/pacbio.vschema
sratoolkit.3.0.0-ubuntu64/schema/sra/pevents.vschema
sratoolkit.3.0.0-ubuntu64/schema/vdb/
sratoolkit.3.0.0-ubuntu64/schema/vdb/built-in.vschema
sratoolkit.3.0.0-ubuntu64/schema/vdb/vdb.vschema
sratoolkit.3.0.0-ubuntu64/CHANGES
sratoolkit.3.0.0-ubuntu64/README.md
kbailey48@penguin:~$ export PATH=$PATH:~/bin/sratoollkit.3.0.0-ubuntu64/bin
kbailey48@penguin:~$ SRR=SRR21726463
kbailey48@penguin:~$ prefetch $SRR
-bash: prefetch: command not found
kbailey48@penguin:~$ export PATH=$PATH:$PWD/sratoolkit.3.0.0-ubuntu64/bin
kbailey48@penguin:~$ which fastq-dump
/home/kbailey48/sratoolkit.3.0.0-ubuntu64/bin/fastq-dump
kbailey48@penguin:~$ SRR=SRR21726463
kbailey48@penguin:~$ prefetch $SRR
2022-12-09T02:12:26 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-12-09T02:12:28 prefetch.3.0.0: 1) Downloading 'SRR21726463'...
2022-12-09T02:12:28 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-12-09T02:12:28 prefetch.3.0.0: Downloading via HTTPS...
2022-12-09T02:13:30 prefetch.3.0.0: HTTPS download succeed
2022-12-09T02:13:30 prefetch.3.0.0: 'SRR21726463' is valid
2022-12-09T02:13:30 prefetch.3.0.0: 1) 'SRR21726463' was downloaded successfully
2022-12-09T02:13:30 prefetch.3.0.0: 'SRR21726463' has 0 unresolved dependencies
kbailey48@penguin:~$ fasterq-dump $SRR --threads 1 --outdir reads/$SRR --split-files --skip-technical
disk-limit exeeded!
to see limits: re-run with '-x' option.
fasterq-dump quit with error code 3
kbailey48@penguin:~$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/vdb 10G 8.5G 1.4G 87% /
none 492K 4.0K 488K 1% /dev
/dev/vdb 10G 8.5G 1.4G 87% /dev/kvm
tmpfs 100K 0 100K 0% /dev/lxd
run 1.4G 32K 1.4G 1% /dev/.host_ip
/dev/root 421M 288M 124M 70% /dev/.ssh/sshd_config
9p 1.9G 1.0M 1.9G 1% /mnt/chromeos
tmpfs 1.4G 0 1.4G 0% /mnt/external
/dev/vda 57M 57M 0 100% /opt/google/cros-containers
fonts 3.1G 2.8G 307M 91% /usr/share/fonts/chromeos
tmpfs 100K 0 100K 0% /dev/.lxd-mounts
devtmpfs 1.4G 0 1.4G 0% /dev/tty
tmpfs 1.4G 0 1.4G 0% /dev/shm
tmpfs 557M 112K 557M 1% /run
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 4.0M 0 4.0M 0% /sys/fs/cgroup
tmpfs 279M 16K 279M 1% /run/user/1000
