[INFO] cloning repository https://github.com/naobservatory/kmer-egd
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/naobservatory/kmer-egd" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 0731f7caf61c3a5f042109627863edf4fb066da6
[INFO] checking naobservatory/kmer-egd against try#b047d5f4496a7526d91d0dddea494c05853f2a7b for pr-122661-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/naobservatory/kmer-egd
[INFO] finished tweaking git repo https://github.com/naobservatory/kmer-egd
[INFO] tweaked toml for git repo https://github.com/naobservatory/kmer-egd written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/naobservatory/kmer-egd on toolchain b047d5f4496a7526d91d0dddea494c05853f2a7b
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b047d5f4496a7526d91d0dddea494c05853f2a7b" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/naobservatory/kmer-egd already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b047d5f4496a7526d91d0dddea494c05853f2a7b" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+b047d5f4496a7526d91d0dddea494c05853f2a7b" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 0862fa24177dd938a1fc13d423ef95c16bc021a4608023d4dde370b02f43f383
[INFO] running `Command { std: "docker" "start" "-a" "0862fa24177dd938a1fc13d423ef95c16bc021a4608023d4dde370b02f43f383", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "0862fa24177dd938a1fc13d423ef95c16bc021a4608023d4dde370b02f43f383", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0862fa24177dd938a1fc13d423ef95c16bc021a4608023d4dde370b02f43f383", kill_on_drop: false }`
[INFO] [stdout] 0862fa24177dd938a1fc13d423ef95c16bc021a4608023d4dde370b02f43f383
[INFO] checking naobservatory/kmer-egd against try#b047d5f4496a7526d91d0dddea494c05853f2a7b for pr-122661-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] [stderr] error: unable to write file rothman.unenriched.counts
[INFO] [stderr] error: unable to write file rothman.unenriched.simple
[INFO] [stderr] error: unable to write file rothman.unenriched_samples
[INFO] [stderr] error: unable to write file run-iterative-assembler.sh
[INFO] [stderr] error: unable to write file run-spike-in.sh
[INFO] [stderr] error: unable to write file sars-cov-2.fasta
[INFO] [stderr] error: unable to write file score-hash-output-parallel.sh
[INFO] [stderr] error: unable to write file score-hash-output-single.sh
[INFO] [stderr] error: unable to write file score-shm-output.sh
[INFO] [stderr] error: unable to write file score-trie-output-parallel.sh
[INFO] [stderr] error: unable to write file score-trie-output-single.sh
[INFO] [stderr] error: unable to write file score-trie-output.sh
[INFO] [stderr] error: unable to write file select-mod-lines.py
[INFO] [stderr] error: unable to write file shm-common.h
[INFO] [stderr] error: unable to write file shm-dump-all.c
[INFO] [stderr] error: unable to write file shm-egd.c
[INFO] [stderr] error: unable to write file shm-examples.c
[INFO] [stderr] error: unable to write file shm-hist.c
[INFO] [stderr] error: unable to write file simple-assemble.py
[INFO] [stderr] error: unable to write file simple-sample.py
[INFO] [stderr] error: unable to write file simplify_metadata.py
[INFO] [stderr] error: unable to write file simulate-HTP.py
[INFO] [stderr] error: unable to write file simulate-one-kmer.py
[INFO] [stderr] error: unable to write file simulate-spikes.sh
[INFO] [stderr] error: unable to write file tsamv.NC_030229.1.fasta
[INFO] [stderr] error: unable to write file util.h
[INFO] [stderr] error: unable to write file virtual-spike-in.py
[INFO] [stderr] error: unable to write file wtps.txt
[INFO] [stderr] fatal: unable to checkout working tree
[INFO] [stderr] warning: Clone succeeded, but checkout failed.
[INFO] [stderr] You can inspect what was checked out with 'git status'
[INFO] [stderr] and retry with 'git restore --source=HEAD :/'
[INFO] [stderr] 
[INFO] checking naobservatory/kmer-egd against try#b047d5f4496a7526d91d0dddea494c05853f2a7b for pr-122661-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] [stderr] error: unable to write file rothman.unenriched.counts
[INFO] [stderr] error: unable to write file rothman.unenriched.simple
[INFO] [stderr] error: unable to write file rothman.unenriched_samples
[INFO] [stderr] error: unable to write file run-iterative-assembler.sh
[INFO] [stderr] error: unable to write file run-spike-in.sh
[INFO] [stderr] error: unable to write file sars-cov-2.fasta
[INFO] [stderr] error: unable to write file score-hash-output-parallel.sh
[INFO] [stderr] error: unable to write file score-hash-output-single.sh
[INFO] [stderr] error: unable to write file score-shm-output.sh
[INFO] [stderr] error: unable to write file score-trie-output-parallel.sh
[INFO] [stderr] error: unable to write file score-trie-output-single.sh
[INFO] [stderr] error: unable to write file score-trie-output.sh
[INFO] [stderr] error: unable to write file select-mod-lines.py
[INFO] [stderr] error: unable to write file shm-common.h
[INFO] [stderr] error: unable to write file shm-dump-all.c
[INFO] [stderr] error: unable to write file shm-egd.c
[INFO] [stderr] error: unable to write file shm-examples.c
[INFO] [stderr] error: unable to write file shm-hist.c
[INFO] [stderr] error: unable to write file simple-assemble.py
[INFO] [stderr] error: unable to write file simple-sample.py
[INFO] [stderr] error: unable to write file simplify_metadata.py
[INFO] [stderr] error: unable to write file simulate-HTP.py
[INFO] [stderr] error: unable to write file simulate-one-kmer.py
[INFO] [stderr] error: unable to write file simulate-spikes.sh
[INFO] [stderr] error: unable to write file ska-hash-count.cpp
[INFO] [stderr] error: unable to write file sort-bucket-evaluations.sh
[INFO] [stderr] error: unable to write file spike-in-growth.py
[INFO] [stderr] error: unable to write file spike-pipeline.sh
[INFO] [stderr] fatal: cannot create directory at 'src': No space left on device
[INFO] [stderr] warning: Clone succeeded, but checkout failed.
[INFO] [stderr] You can inspect what was checked out with 'git status'
[INFO] [stderr] and retry with 'git restore --source=HEAD :/'
[INFO] [stderr] 
[INFO] checking naobservatory/kmer-egd against try#b047d5f4496a7526d91d0dddea494c05853f2a7b for pr-122661-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] [stderr] error: unable to write file find-min-hcu-poisson-p-values.sh
[INFO] [stderr] error: unable to write file find-reads-single.sh
[INFO] [stderr] error: unable to write file find-reads.sh
[INFO] [stderr] error: unable to write file find-spikes.py
[INFO] [stderr] error: unable to write file find-subsetted-kmers.sh
[INFO] [stderr] error: unable to write file flat_hash_map.hpp
[INFO] [stderr] error: unable to write file generate-unenriched-count-cdfs.py
[INFO] [stderr] error: unable to write file group-spikes.py
[INFO] [stderr] error: unable to write file growth-rate-comparison.py
[INFO] [stderr] error: unable to write file hash-count-rothman.cpp
[INFO] [stderr] error: unable to write file hash-count-single.cpp
[INFO] [stderr] error: unable to write file hash-count-union.cpp
[INFO] [stderr] error: unable to write file hash-count-variable.cpp
[INFO] [stderr] error: unable to write file hash-count.cpp
[INFO] [stderr] error: unable to write file hc-HTP-full-summary
[INFO] [stderr] error: unable to write file hiv.fasta
[INFO] [stderr] error: unable to write file iterative-assembler-clean-up.py
[INFO] [stderr] error: unable to write file iterative-assembler.c
[INFO] [stderr] error: unable to write file iterative-assembler.py
[INFO] [stderr] error: unable to write file iterative-assembler.sh
[INFO] [stderr] error: unable to write file kmer-distribution-pipeline.sh
[INFO] [stderr] error: unable to write file log-memory.sh
[INFO] [stderr] error: unable to write file longest-timeseries.tsv
[INFO] [stderr] error: unable to write file ma-biobot-original.tsv
[INFO] [stderr] error: unable to write file ma-biobot-revised.tsv
[INFO] [stderr] error: unable to write file make-cdf.py
[INFO] [stderr] error: unable to write file merge-best-seeds.py
[INFO] [stderr] error: unable to write file merge-counted-kmers-inner.sh
[INFO] [stderr] error: unable to write file merge-counted-kmers.py
[INFO] [stderr] error: unable to write file merge-counted-kmers.sh
[INFO] [stderr] error: unable to write file merge-counts.py
[INFO] [stderr] error: unable to write file merge-counts.sh
[INFO] [stderr] error: unable to write file merge-individual-histograms.py
[INFO] [stderr] error: unable to write file merge-per-prefix-counts.py
[INFO] [stderr] error: unable to write file merge-uniq-to-cdf.py
[INFO] [stderr] error: unable to write file mnsv.AB232926.1.fasta
[INFO] [stderr] error: unable to write file open-shm.c
[INFO] [stderr] error: unable to write file order-by-position.py
[INFO] [stderr] error: unable to write file ov2.OK428619.1.fasta
[INFO] [stderr] error: unable to write file partition-spikes.py
[INFO] [stderr] error: unable to write file partition-spikes.sh
[INFO] [stderr] error: unable to write file pmmov.ON493797.1.fasta
[INFO] [stderr] error: unable to write file print-kmer-simulated-day.py
[INFO] [stderr] error: unable to write file prjna729801.fnames
[INFO] [stderr] error: unable to write file process-diet-single.sh
[INFO] [stderr] error: unable to write file process-diet.sh
[INFO] [stderr] error: unable to write file process-hiv-spikes-single.sh
[INFO] [stderr] error: unable to write file process-socal-hash.sh
[INFO] [stderr] error: unable to write file process-socal-trie.sh
[INFO] [stderr] error: unable to write file process-socal.sh
[INFO] [stderr] error: unable to write file quality-counts.jsons
[INFO] [stderr] error: unable to write file read-shm.c
[INFO] [stderr] error: unable to create file remove-adapter-spikes.py: No space left on device
[INFO] [stderr] error: unable to create file repeatedly-score-trie-output.sh: No space left on device
[INFO] [stderr] error: unable to write file rothman-covid-counts
[INFO] [stderr] error: unable to create file rothman-htp-barcodes: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched.counts: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched.simple: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched_samples: No space left on device
[INFO] [stderr] error: unable to create file run-iterative-assembler.sh: No space left on device
[INFO] [stderr] error: unable to create file run-spike-in.sh: No space left on device
[INFO] [stderr] error: unable to create file sars-cov-2.fasta: No space left on device
[INFO] [stderr] error: unable to create file score-hash-output-parallel.sh: No space left on device
[INFO] [stderr] error: unable to create file score-hash-output-single.sh: No space left on device
[INFO] [stderr] error: unable to create file score-shm-output.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output-parallel.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output-single.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output.sh: No space left on device
[INFO] [stderr] error: unable to create file select-mod-lines.py: No space left on device
[INFO] [stderr] error: unable to create file shm-common.h: No space left on device
[INFO] [stderr] error: unable to create file shm-dump-all.c: No space left on device
[INFO] [stderr] error: unable to create file shm-egd.c: No space left on device
[INFO] [stderr] error: unable to create file shm-examples.c: No space left on device
[INFO] [stderr] error: unable to create file shm-hist.c: No space left on device
[INFO] [stderr] error: unable to create file simple-assemble.py: No space left on device
[INFO] [stderr] error: unable to create file simple-sample.py: No space left on device
[INFO] [stderr] error: unable to create file simplify_metadata.py: No space left on device
[INFO] [stderr] error: unable to create file simulate-HTP.py: No space left on device
[INFO] [stderr] error: unable to create file simulate-one-kmer.py: No space left on device
[INFO] [stderr] error: unable to create file simulate-spikes.sh: No space left on device
[INFO] [stderr] error: unable to create file ska-hash-count.cpp: No space left on device
[INFO] [stderr] error: unable to create file sort-bucket-evaluations.sh: No space left on device
[INFO] [stderr] error: unable to create file spike-in-growth.py: No space left on device
[INFO] [stderr] error: unable to create file spike-pipeline.sh: No space left on device
[INFO] [stderr] fatal: cannot create directory at 'src': No space left on device
[INFO] [stderr] warning: Clone succeeded, but checkout failed.
[INFO] [stderr] You can inspect what was checked out with 'git status'
[INFO] [stderr] and retry with 'git restore --source=HEAD :/'
[INFO] [stderr] 
[INFO] checking naobservatory/kmer-egd against try#b047d5f4496a7526d91d0dddea494c05853f2a7b for pr-122661-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnaobservatory%2Fkmer-egd" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] [stderr] error: unable to write file find-massive-dups.sh
[INFO] [stderr] error: unable to write file find-min-hcu-poisson-p-values.sh
[INFO] [stderr] error: unable to write file find-reads-single.sh
[INFO] [stderr] error: unable to write file find-reads.sh
[INFO] [stderr] error: unable to write file find-spikes.py
[INFO] [stderr] error: unable to write file find-subsetted-kmers.sh
[INFO] [stderr] error: unable to write file flat_hash_map.hpp
[INFO] [stderr] error: unable to write file generate-unenriched-count-cdfs.py
[INFO] [stderr] error: unable to write file group-spikes.py
[INFO] [stderr] error: unable to write file growth-rate-comparison.py
[INFO] [stderr] error: unable to write file hash-count-rothman.cpp
[INFO] [stderr] error: unable to write file hash-count-single.cpp
[INFO] [stderr] error: unable to write file hash-count-union.cpp
[INFO] [stderr] error: unable to write file hash-count-variable.cpp
[INFO] [stderr] error: unable to write file hash-count.cpp
[INFO] [stderr] error: unable to write file hc-HTP-full-summary
[INFO] [stderr] error: unable to write file hiv.fasta
[INFO] [stderr] error: unable to write file iterative-assembler-clean-up.py
[INFO] [stderr] error: unable to write file iterative-assembler.c
[INFO] [stderr] error: unable to write file iterative-assembler.py
[INFO] [stderr] error: unable to write file iterative-assembler.sh
[INFO] [stderr] error: unable to write file kmer-distribution-pipeline.sh
[INFO] [stderr] error: unable to write file log-memory.sh
[INFO] [stderr] error: unable to write file longest-timeseries.tsv
[INFO] [stderr] error: unable to write file ma-biobot-original.tsv
[INFO] [stderr] error: unable to write file ma-biobot-revised.tsv
[INFO] [stderr] error: unable to write file make-cdf.py
[INFO] [stderr] error: unable to write file merge-best-seeds.py
[INFO] [stderr] error: unable to write file merge-counted-kmers-inner.sh
[INFO] [stderr] error: unable to write file merge-counted-kmers.py
[INFO] [stderr] error: unable to write file merge-counted-kmers.sh
[INFO] [stderr] error: unable to write file merge-counts.py
[INFO] [stderr] error: unable to write file merge-counts.sh
[INFO] [stderr] error: unable to write file merge-individual-histograms.py
[INFO] [stderr] error: unable to write file merge-per-prefix-counts.py
[INFO] [stderr] error: unable to write file merge-uniq-to-cdf.py
[INFO] [stderr] error: unable to write file mnsv.AB232926.1.fasta
[INFO] [stderr] error: unable to write file open-shm.c
[INFO] [stderr] error: unable to write file order-by-position.py
[INFO] [stderr] error: unable to write file ov2.OK428619.1.fasta
[INFO] [stderr] error: unable to write file partition-spikes.py
[INFO] [stderr] error: unable to write file partition-spikes.sh
[INFO] [stderr] error: unable to write file pmmov.ON493797.1.fasta
[INFO] [stderr] error: unable to write file print-kmer-simulated-day.py
[INFO] [stderr] error: unable to write file prjna729801.fnames
[INFO] [stderr] error: unable to write file process-diet-single.sh
[INFO] [stderr] error: unable to write file process-diet.sh
[INFO] [stderr] error: unable to write file process-hiv-spikes-single.sh
[INFO] [stderr] error: unable to write file process-socal-hash.sh
[INFO] [stderr] error: unable to write file process-socal-trie.sh
[INFO] [stderr] error: unable to write file process-socal.sh
[INFO] [stderr] error: unable to write file quality-counts.jsons
[INFO] [stderr] error: unable to write file read-shm.c
[INFO] [stderr] error: unable to create file remove-adapter-spikes.py: No space left on device
[INFO] [stderr] error: unable to create file repeatedly-score-trie-output.sh: No space left on device
[INFO] [stderr] error: unable to write file rothman-covid-counts
[INFO] [stderr] error: unable to create file rothman-htp-barcodes: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched.counts: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched.simple: No space left on device
[INFO] [stderr] error: unable to create file rothman.unenriched_samples: No space left on device
[INFO] [stderr] error: unable to create file run-iterative-assembler.sh: No space left on device
[INFO] [stderr] error: unable to create file run-spike-in.sh: No space left on device
[INFO] [stderr] error: unable to create file sars-cov-2.fasta: No space left on device
[INFO] [stderr] error: unable to create file score-hash-output-parallel.sh: No space left on device
[INFO] [stderr] error: unable to create file score-hash-output-single.sh: No space left on device
[INFO] [stderr] error: unable to create file score-shm-output.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output-parallel.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output-single.sh: No space left on device
[INFO] [stderr] error: unable to create file score-trie-output.sh: No space left on device
[INFO] [stderr] fatal: unable to checkout working tree
[INFO] [stderr] warning: Clone succeeded, but checkout failed.
[INFO] [stderr] You can inspect what was checked out with 'git status'
[INFO] [stderr] and retry with 'git restore --source=HEAD :/'
[INFO] [stderr] 


failed to checkout https://github.com/naobservatory/kmer-egd

Caused by:
    command failed: exit status: 128