/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.1.0/bin/bundle clean ==> Testing brewsci/bio/trinity ==> /usr/local/Cellar/trinity/2.11.0/bin/Trinity --no_distributed_trinity_exec --bypass_java_version_check --seqType fq --max_memory 1G --SS_lib_type RF --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.11.0 Left read files: $VAR1 = [ 'reads.left.fq.gz', 'reads2.left.fq.gz' ]; Right read files: $VAR1 = [ 'reads.right.fq.gz', 'reads2.right.fq.gz' ]; Trinity version: Trinity-v2.11.0 -ERROR: couldn't parse latest version tag info from github: {"message":"API rate limit exceeded for 13.105.117.53. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)","documentation_url":"https://docs.github.com/rest/overview/resources-in-the-rest-api#rate-limiting"} Thursday, February 29, 2024: 09:49:26 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/Cellar/trinity/2.11.0/libexec/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Duser.home=/Users/runner/Library/Caches/Homebrew/java_cache -Djava.io.tmpdir=/private/tmp Thursday, February 29, 2024: 09:49:27 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/Cellar/trinity/2.11.0/libexec/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Duser.home=/Users/runner/Library/Caches/Homebrew/java_cache -Djava.io.tmpdir=/private/tmp Thursday, February 29, 2024: 09:49:27 CMD: mkdir -p /private/tmp/trinity-test-20240229-37816-j239uq/trinity_out_dir Thursday, February 29, 2024: 09:49:27 CMD: mkdir -p /private/tmp/trinity-test-20240229-37816-j239uq/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 200 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/private/tmp/trinity-test-20240229-37816-j239uq/reads.left.fq.gz', '/private/tmp/trinity-test-20240229-37816-j239uq/reads2.left.fq.gz' ], [ '/private/tmp/trinity-test-20240229-37816-j239uq/reads.right.fq.gz', '/private/tmp/trinity-test-20240229-37816-j239uq/reads2.right.fq.gz' ] ]; Thursday, February 29, 2024: 09:49:27 CMD: /usr/local/Cellar/trinity/2.11.0/libexec/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 2 --output /private/tmp/trinity-test-20240229-37816-j239uq/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /private/tmp/trinity-test-20240229-37816-j239uq/reads.left.fq.gz,/private/tmp/trinity-test-20240229-37816-j239uq/reads2.left.fq.gz --right /private/tmp/trinity-test-20240229-37816-j239uq/reads.right.fq.gz,/private/tmp/trinity-test-20240229-37816-j239uq/reads2.right.fq.gz --pairs_together --PARALLEL_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /private/tmp/trinity-test-20240229-37816-j239uq/reads.left.fq.gz) >> left.fa CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /private/tmp/trinity-test-20240229-37816-j239uq/reads.right.fq.gz) >> right.fa CMD finished (0 seconds) CMD: seqtk-trinit