Jake VanCampen

If you want to extract all interactions over a range of coordinates, try omitting r2: ``` cooler dump $cool -t pixels --join -r "$chr1:$start1-$end2" --balanced ```

Interesting, yeah appears to be the same error with just one ``` $ ./TRUST4/run-trust4 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcodeRange 0 15 +...

Yup that works ``` $ trust4-clean/run-trust4 -t 8 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --repseq [Thu Nov 18 18:18:42 2021] TRUST4 begins. [Thu Nov 18 18:18:42...

same same ``` $ trust4-clean/run-trust4 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcodeRange 0 15 + --UMI data/B-A1_S6_L001_R1_001.fastq.gz --umiRange 16 25 + --repseq --barcodeWhitelist refs/737K-august-2016.txt...

It's also worth noting that I got a segfault with the conda install, but I can file that as a separate issue

``` $ cat /etc/os-release NAME="Ubuntu" VERSION="21.04 (Hirsute Hippo)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 21.04" VERSION_ID="21.04" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=hirsute UBUNTU_CODENAME=hirsute ``` ``` $ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa...

Ahh there we are, okay so without --barcodeWhiteList we are cookin with heat. ``` trust4-clean/run-trust4 -t 8 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/*_R2_*.fastq.gz --barcode data/*_R1_*.fastq.gz --barcodeRange...

Just kidding that eventually failed also with: ``` system /trust4-clean/trust4 -f refs/hg38_bcrtcr.fa --trimLevel 2 --skipMateExtension -t 16 -o ./foxlab-trust4/run1 -u ./foxlab-trust4/run1_toassemble.fq --barcode ./foxlab-trust4/run1_toassemble_bc.fa --UMI ./foxlab-trust4/run1_toassemble_umi.fa failed: 9 at trust4-clean/run-trust4 line...

I did recompile with -O, then switched to a machine with more memory and the run finished. After observing the memory usage during runtime, it appears the machine didn't have...

I have experienced the same `OSError: [Errno 18] Invalid cross-device link:` error when hg-tmp is on a different filesystem, and the commit referenced above is how I fixed it (works...