kallisto 0.46.1

Usage: kallisto <CMD> [arguments] ..

Where <CMD> can be one of:

    index         Builds a kallisto index 
    quant         Runs the quantification algorithm 
    bus           Generate BUS files for single-cell data 
    pseudo        Runs the pseudoalignment step 
    merge         Merges several batch runs 
    h5dump        Converts HDF5-formatted results to plaintext
    inspect       Inspects and gives information about an index
    version       Prints version information
    cite          Prints citation information

Running kallisto <CMD> without arguments prints usage information for <CMD>

/Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks

cbai_transcriptome_31          kallisto-4libraries.ipynb
cbai_transcriptome_v3.1.fasta  readme.md
kallisto/

--2020-08-12 11:58:06--  https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v3.1.fasta
Resolving owl.fish.washington.edu (owl.fish.washington.edu)... 128.95.149.83
Connecting to owl.fish.washington.edu (owl.fish.washington.edu)|128.95.149.83|:443... connected.
WARNING: cannot verify owl.fish.washington.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
  Unable to locally verify the issuer's authority.
HTTP request sent, awaiting response... 200 OK
Length: 145648199 (139M)
Saving to: ‘cbai_transcriptome_v3.1.fasta’

cbai_transcriptome_ 100%[===================>] 138.90M  10.4MB/s    in 13s     

2020-08-12 11:58:21 (10.5 MB/s) - ‘cbai_transcriptome_v3.1.fasta’ saved [145648199/145648199]

[build] loading fasta file cbai_transcriptome_v3.1.fasta
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 12560 target sequences
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 303833 contigs and contains 43881871 k-mers 

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 78,649
[index] number of k-mers: 43,881,871
[index] number of equivalence classes: 213,585
[quant] running in paired-end mode
[quant] will process pair 1: /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380822_S3_L001_R1_001.fastp-trim.202004144409.fq.gz
                             /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380822_S3_L001_R2_001.fastp-trim.202004144409.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 9,369,940 reads, 6,141,882 reads pseudoaligned
[quant] estimated average fragment length: 160.365
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,119 rounds

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 78,649
[index] number of k-mers: 43,881,871
[index] number of equivalence classes: 213,585
[quant] running in paired-end mode
[quant] will process pair 1: /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380823_S4_L001_R1_001.fastp-trim.202004144852.fq.gz
                             /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380823_S4_L001_R2_001.fastp-trim.202004144852.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 8,760,917 reads, 5,426,016 reads pseudoaligned
[quant] estimated average fragment length: 164.564
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,249 rounds

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 78,649
[index] number of k-mers: 43,881,871
[index] number of equivalence classes: 213,585
[quant] running in paired-end mode
[quant] will process pair 1: /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380824_S5_L001_R2_001.fastp-trim.202004145320.fq.gz
                             /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380824_S5_L001_R1_001.fastp-trim.202004145320.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 9,861,054 reads, 6,460,364 reads pseudoaligned
[quant] estimated average fragment length: 173.524
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,206 rounds

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 78,649
[index] number of k-mers: 43,881,871
[index] number of equivalence classes: 213,585
[quant] running in paired-end mode
[quant] will process pair 1: /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380825_S6_L001_R1_001.fastp-trim.202004145835.fq.gz
                             /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380825_S6_L001_R2_001.fastp-trim.202004145835.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 10,184,344 reads, 6,441,322 reads pseudoaligned
[quant] estimated average fragment length: 160.804
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,259 rounds

####################################################################################
#
# Usage:  /Applications/bioinfo/trinityrnaseq-v2.8.6/util/abundance_estimates_to_matrix.pl --est_method <method>  sample1.results sample2.results ...
#
#      or  /Applications/bioinfo/trinityrnaseq-v2.8.6/util/abundance_estimates_to_matrix.pl --est_method <method> --quant_files file.listing_target_files.txt
#
#      Note, if only a single input file is given, it's expected to contain the paths to all the target abundance estimation files.
#
# Required:
#            
#  --est_method <string>           RSEM|eXpress|kallisto|salmon  (needs to know what format to expect)
#
#  --gene_trans_map <string>           the gene-to-transcript mapping file. (if you don't want gene estimates, indicate 'none'.
#
#
# Options:
#
#  --cross_sample_norm <string>         TMM|UpperQuartile|none   (default: TMM)
#
#  --name_sample_by_basedir             name sample column by dirname instead of filename
#      --basedir_index <int>            default(-2)
#
#  --out_prefix <string>                default: value for --est_method
#
#  --quant_files <string>              file containing a list of all the target files.
#
######################################################################################

-reading file: /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380822_cold_uninfected/abundance.tsv
-reading file: /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380823_cold_infected/abundance.tsv
-reading file: /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380824_warm_uninfected/abundance.tsv
-reading file: /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380825_warm_infected/abundance.tsv


* Outputting combined matrix.

/Applications/bioinfo/trinityrnaseq-v2.8.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TPM.not_cross_norm > /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q < /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TPM.not_cross_norm.runTMM.R 1>&2 
dyld: Library not loaded: @rpath/libreadline.6.2.dylib
  Referenced from: /Users/graciecrandall/anaconda/lib/R/lib/libR.dylib
  Reason: image not found
sh: line 1:  5170 Abort trap: 6           R --no-save --no-restore --no-site-file --no-init-file -q < /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TPM.not_cross_norm.runTMM.R 1>&2
Error, cmd: R --no-save --no-restore --no-site-file --no-init-file -q < /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TPM.not_cross_norm.runTMM.R 1>&2  died with ret (34304)  at /Applications/bioinfo/trinityrnaseq-v2.8.6/util/support_scripts/run_TMM_scale_matrix.pl line 105.
Error, CMD: /Applications/bioinfo/trinityrnaseq-v2.8.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TPM.not_cross_norm > /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.TMM.EXPR.matrix died with ret 6400 at /Applications/bioinfo/trinityrnaseq-v2.8.6/util/abundance_estimates_to_matrix.pl line 385.

	380822_cold_uninfected	380823_cold_infected	380824_warm_uninfected	380825_warm_infected
TRINITY_DN9654_c0_g1_i1	269	195	271	245
TRINITY_DN2423_c0_g1_i5	70.0962	54.7109	113.331	102.982
TRINITY_DN35884_c0_g1_i1	17	11	12	9
TRINITY_DN51908_c0_g1_i1	3	4	7	4
TRINITY_DN10230_c0_g1_i5	0	0	0	0
TRINITY_DN556_c1_g1_i4	0	23.6851	29.7852	9.53139
TRINITY_DN6709_c0_g1_i8	0	0	0	0
TRINITY_DN25396_c0_g1_i5	0	0	0	1.00319
TRINITY_DN881_c3_g1_i1	806	864	1449	1267