No output given by FastANI

[neelam19051]

fastANI --threads 2 -q /home/neel@m95/Desktop/AMR/annotated/fna1/fna -r /home/neel@m95/Desktop/AMR/annotated/fna1/fna --fragLen 50 --matrix -o outdir/all_out

Reference = [/home/neel@m95/Desktop/AMR/annotated/fna1/fna] Query = [/home/neel@m95/Desktop/AMR/annotated/fna1/fna] Kmer size = 16 Fragment length = 50 Threads = 2 ANI output file = outdir/all_out

INFO [thread 0], skch::main, Count of threads executing parallel_for : 2 INFO [thread 0], skch::Sketch::build, window size for minimizer sampling = 1 INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 0 INFO [thread 0], skch::Sketch::index, unique minimizers = 0 INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (0, 0) ... Segmentation fault (core dumped)

[cjain7]

You may want to double-check the input genome file paths provided using -q and -r option

[neelam19051]

fastANI --threads 8 --ql /home/neel@m95/Desktop/AMR/ref/query_list --rl /home/neel@m95/Desktop/AMR/ref/ref_list --fragLen 50 --matrix -o /home/neel@m95/Desktop/AMR/annotated/faa/all_out If i did this above command it shows error like- ERROR, skch::validateInputFiles, Could not open 1_

please help me i am stuck in this command from past 2 weeks.

[cjain7]

This normally happens when the file path is not accessible by the file parser. My guess is that the absolute file paths which you are providing has some issue.

[Yang-Wang-2020]

same issue. the output file is empty with no error message.

[cjain7]

@Yang-Wang-2020 Please see https://github.com/ParBLiSS/FastANI/issues/19