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ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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grid single example test errors: sed: 1: "22p": invalid command code ~ #31

Closed giannamars closed 1 year ago

giannamars commented 1 year ago

Hi,

I am getting an error when running the grid single example test. I've installed bc and ed via brew install on macOS. Thanks for your help, Gianna

(GRiD) user:test user$ grid single -r . -g S_epidermidis.LRKNS118.fna -o output_single single option activated /Users/user/Code/GRiD-1.3/test is present directory /Users/userCode/GRiD-1.3/test is the reads directory /Users/user/Code/GRiD-1.3/test/output_single is the output directory /Users/user/Code/GRiD-1.3/test/S_epidermidis.LRKNS118.fna is the path to reference genome ################ Checking for dependencies ######## parallel found R found bowtie2 found seqtk found samtools found bedtools found bamtools found blastn found pathoscope found mosdepth found All required packages found ################ Checking for required R libraries ######## R libraries ok Output directory ok Creating bowtie index done Running BLAST to dnaA and dif databases Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs done mock_reads Running bowtie 24000 reads; of these: 24000 (100.00%) were unpaired; of these: 13998 (58.33%) aligned 0 times 9899 (41.25%) aligned exactly 1 time 103 (0.43%) aligned >1 times 41.67% overall alignment rate done 8425 reads; of these: 8425 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 8340 (98.99%) aligned exactly 1 time 85 (1.01%) aligned >1 times 100.00% overall alignment rate 8534 reads; of these: 8534 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 8451 (99.03%) aligned exactly 1 time 83 (0.97%) aligned >1 times 100.00% overall alignment rate [samopen] SAM header is present: 84 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated. Running genomeCoverageBed done sed: 1: "2~2p": invalid command code ~ sed: 1: "1~2p": invalid command code ~ [samopen] SAM header is present: 84 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated. Running genomeCoverageBed done sed: 1: "2~2p": invalid command code ~ sed: 1: "1~2p": invalid command code ~ [samopen] SAM header is present: 84 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated. Running genomeCoverageBed done sed: 1: "2~2p": invalid command code ~ sed: 1: "1~2p": invalid command code ~ awk: can't open file mock_reads.main.sam.reorganized.txt source line number 1 grep: mock_reads.main.sam.reorganized.txt: No such file or directory

Parse error: bad token

:1 grep: mock_reads.main.sam.reorganized.txt: No such file or directory grep: mock_reads.main.sam.reorganized.txt: No such file or directory Parse error: bad token :1 Parse error: bad token :1 Parse error: bad token :1 Running GRiD Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: proto Error in getopt(spec) : flag "c" requires an argument Execution halted done rm: mock_reads.sub*.sam.reorganized.txt: No such file or directory rm: mock_reads.main.sam.reorganized.txt: No such file or directory run complete
giannamars commented 1 year ago

This was an error with sed on macOS versus GNU sed: https://stackoverflow.com/questions/22330462/why-does-sed-report-invalid-command-code-for-tilde