How change the path of tmp files

[microbial-cookie]

Hi developers,

I would like to know how to change the path where intermediate files are stored during the execution of CoverM. Due to limited personal tmp storage space on the server, when I run CoverM to calculate the abundance of MAGs, it exceeds the maximum value for cache files. How can I change it to another path? Alternatively, do you have any suggestions to reduce the storage space occupied by intermediate files? This issue has caused frequent errors and no results when running the analysis on a sample with a single-sequence file of 11GB. Thank you very much!!!

[2023-12-12T04:47:12Z ERROR coverm::bam_generator] Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.Xjny75gjMWOC/foo.pipe": unable to open SAM/BAM/CRAM file at /tmp/coverm_fifo.Xjny75gjMWOC/foo.pipe
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] Error when running mapping process. Exitstatus was ExitStatus(unix_wait_status(256)). Command run was: ["bash -c "set -e -o pipefail; minimap2 --split-prefix /tmp/.tmp6CfAL7 -a -x sr -t 64 '/tmp/.tmplxyL0M' 'S10-sample_rmRNA_1.fastq' 'S10-sample_rmRNA_2.fastq' 2>/tmp/.tmpJ09Vw7 | remove_minimap2_duplicated_headers 2>/tmp/.tmpURlAiq| samtools sort -T '/tmp/coverm_fifo.Xjny75gjMWOC/coverm-make-samtools-sortYGl602' -l0 -@ 63 2>/tmp/.tmpwMMs8N |tee "/tmp/coverm_fifo.Xjny75gjMWOC/foo.pipe" |samtools view -@ 63 -b -o '/opt/shared/ruiwenhu/coverm-genome.S10-sample_rmRNA_1.fastq.bam' 2>/tmp/.tmpH4qSWY""]
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] The STDERR for the MINIMAP2_SR part was: [M::mm_idx_gen::3.5091.52] collected minimizers
[M::mm_idx_gen::5.1111.78] sorted minimizers
[M::main::5.1111.78] loaded/built the index for 21048 target sequence(s)
[M::mm_mapopt_update::5.1111.78] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 21048
[M::mm_idx_stat::5.3291.75] distinct minimizers: 24420302 (88.16% are singletons); average occurrences: 1.149; average spacing: 6.019; total length: 168891417
[M::worker_pipeline::7.4953.34] mapped 342626 sequences
[M::worker_pipeline::8.9684.43] mapped 341828 sequences
[M::worker_pipeline::9.6865.57] mapped 341156 sequences
[M::worker_pipeline::10.4876.54] mapped 340744 sequences
[M::worker_pipeline::11.1147.47] mapped 340464 sequences
[M::worker_pipeline::11.7288.27] mapped 340206 sequences
[M::worker_pipeline::12.2989.01] mapped 339824 sequences
[M::worker_pipeline::12.9139.67] mapped 339402 sequences
[M::worker_pipeline::13.51410.25] mapped 338982 sequences
[M::worker_pipeline::14.06710.82] mapped 338738 sequences
[M::worker_pipeline::14.67511.35] mapped 338430 sequences
[M::worker_pipeline::15.19711.86] mapped 338332 sequences
[M::worker_pipeline::15.75612.31] mapped 338218 sequences
[M::worker_pipeline::16.49012.60] mapped 338236 sequences
[M::worker_pipeline::17.15812.91] mapped 338272 sequences
[M::worker_pipeline::17.95113.10] mapped 338472 sequences
[M::worker_pipeline::18.56913.41] mapped 341754 sequences
[M::worker_pipeline::19.25213.67] mapped 341312 sequences
[M::worker_pipeline::19.93013.91] mapped 340408 sequences
[M::worker_pipeline::20.73014.04] mapped 340362 sequences
[M::worker_pipeline::21.50814.17] mapped 340046 sequences
[M::worker_pipeline::22.44814.19] mapped 339830 sequences
[M::worker_pipeline::23.34914.25] mapped 339434 sequences
[M::worker_pipeline::24.18514.34] mapped 339004 sequences
[M::worker_pipeline::25.08114.39] mapped 338990 sequences
[M::worker_pipeline::26.04914.40] mapped 338752 sequences
[M::worker_pipeline::26.97514.41] mapped 338594 sequences
[M::worker_pipeline::27.98814.39] mapped 338236 sequences
[M::worker_pipeline::28.87514.42] mapped 338236 sequences
[M::worker_pipeline::29.98814.35] mapped 338092 sequences
[M::worker_pipeline::30.99614.33] mapped 338098 sequences
[M::worker_pipeline::32.00214.30] mapped 338300 sequences
[M::worker_pipeline::32.93914.30] mapped 340692 sequences
[M::worker_pipeline::33.81014.35] mapped 341556 sequences
[M::worker_pipeline::34.76714.37] mapped 340876 sequences
[M::worker_pipeline::35.37714.51] mapped 340374 sequences
[M::worker_pipeline::35.91314.67] mapped 340082 sequences
[M::worker_pipeline::36.47814.83] mapped 339728 sequences
[M::worker_pipeline::37.05814.99] mapped 339548 sequences
[M::worker_pipeline::37.57915.16] mapped 339240 sequences
[M::worker_pipeline::38.09115.32] mapped 338994 sequences
[M::worker_pipeline::38.67215.46] mapped 338754 sequences
[M::worker_pipeline::39.21915.60] mapped 338620 sequences
[M::worker_pipeline::39.76115.76] mapped 338288 sequences
[M::worker_pipeline::40.30715.88] mapped 338206 sequences
[M::worker_pipeline::40.83616.01] mapped 338068 sequences
[M::worker_pipeline::41.46916.10] mapped 338182 sequences
[M::worker_pipeline::41.97016.23] mapped 338124 sequences
[M::worker_pipeline::42.58416.33] mapped 338552 sequences
[M::worker_pipeline::43.06916.44] mapped 342064 sequences
[M::worker_pipeline::43.73016.49] mapped 341278 sequences
[M::worker_pipeline::44.45916.52] mapped 340544 sequences
[M::worker_pipeline::45.07316.59] mapped 340150 sequences
[M::worker_pipeline::45.55916.70] mapped 339764 sequences
[M::worker_pipeline::46.14316.78] mapped 339450 sequences
[M::worker_pipeline::46.64816.87] mapped 339320 sequences
[M::worker_pipeline::47.14616.96] mapped 338960 sequences
[M::worker_pipeline::47.72217.03] mapped 338894 sequences
[M::worker_pipeline::48.23117.12] mapped 338570 sequences
[M::worker_pipeline::48.82217.18] mapped 338446 sequences
[M::worker_pipeline::49.38317.27] mapped 338342 sequences
[M::worker_pipeline::49.82717.35] mapped 338028 sequences
[M::worker_pipeline::50.35917.43] mapped 337910 sequences
[M::worker_pipeline::50.83617.52] mapped 338018 sequences
[M::worker_pipeline::51.34617.59] mapped 338202 sequences
[M::worker_pipeline::52.08317.60] mapped 340286 sequences
[M::worker_pipeline::52.76117.62] mapped 341198 sequences
[M::worker_pipeline::53.34917.73] mapped 340566 sequences
[M::worker_pipeline::53.88517.82] mapped 339890 sequences
[M::worker_pipeline::54.55117.87] mapped 339592 sequences
[M::worker_pipeline::55.08317.96] mapped 339260 sequences
[M::worker_pipeline::55.69418.01] mapped 339072 sequences
[M::worker_pipeline::56.20518.10] mapped 338850 sequences
[M::worker_pipeline::56.73518.17] mapped 338818 sequences
[M::worker_pipeline::57.42318.19] mapped 338532 sequences
[M::worker_pipeline::57.99618.25] mapped 338414 sequences
[M::worker_pipeline::60.15518.24] mapped 338180 sequences
[M::worker_pipeline::60.51618.21] mapped 338040 sequences
[M::worker_pipeline::60.95618.31] mapped 337880 sequences
[M::worker_pipeline::61.21518.24] mapped 337916 sequences
[M::worker_pipeline::61.69718.31] mapped 337882 sequences
[M::worker_pipeline::62.32518.36] mapped 338078 sequences
[M::worker_pipeline::62.84318.42] mapped 341242 sequences
[M::worker_pipeline::63.36518.47] mapped 340896 sequences
[M::worker_pipeline::63.92718.52] mapped 340238 sequences
[M::worker_pipeline::64.45418.57] mapped 339592 sequences
[M::worker_pipeline::65.21218.57] mapped 339332 sequences
[M::worker_pipeline::65.70818.62] mapped 339172 sequences
[M::worker_pipeline::66.25818.67] mapped 339112 sequences
[M::worker_pipeline::66.75218.73] mapped 338898 sequences
[M::worker_pipeline::69.75218.50] mapped 338526 sequences
[M::worker_pipeline::70.07018.42] mapped 338542 sequences
[M::worker_pipeline::70.84818.53] mapped 338370 sequences
[M::worker_pipeline::71.58318.59] mapped 338160 sequences
[M::worker_pipeline::71.90318.52] mapped 338066 sequences
[M::worker_pipeline::72.50118.56] mapped 337782 sequences
[M::worker_pipeline::73.06618.60] mapped 337854 sequences
[M::worker_pipeline::73.64018.63] mapped 338148 sequences
[M::worker_pipeline::74.46518.74] mapped 342336 sequences
[M::worker_pipeline::75.22918.76] mapped 356008 sequences
[M::worker_pipeline::75.57118.68] mapped 350428 sequences
[M::worker_pipeline::76.05618.74] mapped 345122 sequences
[M::worker_pipeline::76.67918.76] mapped 347050 sequences
[M::worker_pipeline::77.48418.89] mapped 344848 sequences
[M::worker_pipeline::77.86418.81] mapped 340590 sequences
[M::worker_pipeline::78.43118.84] mapped 339656 sequences
[M::worker_pipeline::78.96518.87] mapped 339166 sequences
[M::worker_pipeline::79.95518.95] mapped 339024 sequences
[M::worker_pipeline::80.65118.93] mapped 339032 sequences
[M::worker_pipeline::81.01618.89] mapped 338522 sequences
[M::worker_pipeline::81.83819.01] mapped 338630 sequences
[M::worker_pipeline::82.15618.95] mapped 338634 sequences
[M::worker_pipeline::82.59618.97] mapped 338556 sequences
[M::worker_pipeline::83.13618.90] mapped 340048 sequences
[M::worker_pipeline::84.37618.78] mapped 342256 sequences
[M::worker_pipeline::85.60118.68] mapped 341792 sequences
[M::worker_pipeline::86.55218.63] mapped 341048 sequences
[M::worker_pipeline::87.77918.53] mapped 340760 sequences
[M::worker_pipeline::88.94018.44] mapped 340990 sequences
[M::worker_pipeline::89.86618.40] mapped 340950 sequences
[M::worker_pipeline::90.87018.35] mapped 339320 sequences
[M::worker_pipeline::92.04018.26] mapped 339362 sequences
[M::worker_pipeline::92.74618.26] mapped 339154 sequences
[M::worker_pipeline::94.01818.16] mapped 339156 sequences
[M::worker_pipeline::95.38718.04] mapped 338984 sequences
[M::worker_pipeline::96.44817.99] mapped 338734 sequences
[M::worker_pipeline::97.70817.90] mapped 338584 sequences
[M::worker_pipeline::98.81717.83] mapped 338690 sequences
[M::worker_pipeline::99.86217.78] mapped 338612 sequences
[M::worker_pipeline::101.05917.71] mapped 338944 sequences
[M::worker_pipeline::101.98317.68] mapped 341308 sequences
[M::worker_pipeline::103.319*
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] The STDERR for the samtools sort part was:
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] The STDERR for the samtools view for cache part was:
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] The STDERR for the remove_minimap2_duplicated_headers part was:
[2023-12-12T04:47:12Z ERROR coverm::bam_generator] Cannot continue since mapping failed.

[rhysnewell]

You can set the TMPDIR environment variable. Either by setting it prior to your coverm command i.e.

TMPDIR=/path/to/bigger/disk/ coverm genome ...

Or by changing it for your entire login session

export TMPDIR=/path/to/bigger/disk

Then you can run coverm as usual:

coverm genome ...