Could not find output of previous scripts. Please rerun full pipeline.

[vunguyen1907]

Hi.

I follow instructions to install AFLAP on my computer and try to run fastq data with approximately 560 genotyped animals belonging to 40 families. I used below code to run

t_n044@lsp-bioinfo01:~/AFLAP$ ./AFLAP.sh -P stripedcatfish_fastq/pedigree.txt -m 31 -t 4 -d 50 -D 100 -k -x -U

There an error as " Could not find output of previous scripts. Please rerun full pipeline."

How can I fix it to make it run?

Thanks heap,

Vu

And the running outcomes as below:

Beginning Step 1/6 jellyfish 2.3.0 detected 47 parents detected. Not so simple! Determining crosses 40 crosses identified: 100 100 100 2246910 100 2246917 2246940 2246927 2246941 2246912 2246942 2246935 2246943 2246933 2246944 2246939 2246945 2246911 2246946 2246920 2246947 2246910 2246948 2246921 2246949 2246929 2246950 2246918 2246951 2246938 2246953 2246930 2246954 2246937 2246955 2246922 2246956 2246919 2246957 2246930 2246959 2246923 2246960 2246917 2246961 2246921 2246962 2246932 2246963 2246936 2246964 2246918 2246965 100 2246966 2246924 2246967 2246916 2246968 2246927 2246969 2246926 2246970 2246914 2246971 2246913 2246972 2246909 2246973 2246931 2246974 2246925 2246975 2246928 2246976 2246922 2246977 2246926 2246978 2246916 40 F1 cross(es) identified. 100x100 100x2246910 100x2246917 2246940x2246927 2246941x2246912 2246942x2246935 2246943x2246933 2246944x2246939 2246945x2246911 2246946x2246920

We are in buisness! Linkage analysis will be performed on markers derived from 47 F0: 2246909 2246910 2246911 2246912 2246913 2246914 2246915 2246916 2246917 2246918 2246919 2246920 2246921 2246922 2246923 2246924 2246925 2246926 2246927 2246928 2246929 2246930 2246931 2246932 2246933 2246934 2246935 2246936 2246937 2246938 2246939 2246976 2247099 2247100 2247102 2247103 2247104 2247105 2247106 2247107 2247108 2247109 2247110 2247111 2247112 2247113 2247114 Moving onto k-mer counting

Begining k-mer counting for 47 parents Begining k-mer counting for 2246909 file stripedcatfish_fastq/high-density/2246909.fastq.gz not found, terminating

Running Kmer kinship

Could not find output of previous scripts. Please rerun full pipeline.

[kfletcher88]

Hi, My interpretation of the above is that AFLAP failed to locate the file stripedcatfish_fastq/high-density/2246909.fastq.gz detailed in the pedigree file. Would you mind showing me that line of the pedigree file? A quick fix may be to put absolute paths to the files.

The print of Running Kmer kinship looks like a bug as AFLAP did not get that far into the pipeline, I will look into that.

[vunguyen1907]

Thanks.

I have corrected the path in the pedigree file and it read every fastq file, but there is still an issue. I copied some last lines for the run as below.

In the AFLAP_tmp folder with 01, 02, 03 and KmerKin subfolder. NO folder names as 04, 05......

I run Ubuntu in window 10. I think it maybe due to missing some package of

Thanks for your help.

Vu

---

Libraries gplots and proxy loaded successfully

Beginning data import, this may take a few minutes Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'AFLAP_tmp/05/2247111_m31_L15U30.Filtered.Genotypes.MarkerID.tsv': No such file or directory Execution halted cat: AFLAP_tmp/03/2247112_CrossedTo.txt: No such file or directory

Libraries gplots and proxy loaded successfully

Beginning data import, this may take a few minutes Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'AFLAP_tmp/05/2247112_m31_L15U30.Filtered.Genotypes.MarkerID.tsv': No such file or directory Execution halted cat: AFLAP_tmp/03/2247113_CrossedTo.txt: No such file or directory

Libraries gplots and proxy loaded successfully

Beginning data import, this may take a few minutes Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'AFLAP_tmp/05/2247113_m31_L15U30.Filtered.Genotypes.MarkerID.tsv': No such file or directory Execution halted cat: AFLAP_tmp/03/2247114_CrossedTo.txt: No such file or directory

Libraries gplots and proxy loaded successfully

Beginning data import, this may take a few minutes Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'AFLAP_tmp/05/2247114_m31_L15U30.Filtered.Genotypes.MarkerID.tsv': No such file or directory Execution halted

[vunguyen1907]

Dear Fletcher,

I sent my log file when running my data of the recent run, including my pedigree file for you to check if there is anything wrong with it.

It seemed that it lacks dependence packages of ABYSS? I have downloaded ABYSS and jellyfish into the AFLAP folder and also install them using instructions from GitHub https://github.com/bcgsc/abyss

log.txt pedigree.txt

Thanks and regards,

Vu