marbl
Generating .hic file with convert.sh
I have loaded juicer_tools_1.22.01.jar to the JUICER_JAR variable like as following: JUICER_JAR=/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/SALSA-master/juicer_tools_1.22.01.jar and i run the program like
convert.sh scaffolds #here, scaffolds is the directory where the final fasta, agp file and other file are located what had been generated in default by the program
The error is like as following:
scaffolds//alignments_sorted.txt does not exist or does not contain any reads.
I have checked the alignments_sorted.txt file and nothing was inside of it. Can i get some help information to solve this issue? Thanks in advance.
It sounds like the scaffolds folder is missing some expected files required for conversion. What is the full contents of the scaffolds folder you're running on? There should be a alignment_iteration_1.bed as well as an alignments.txt file.
Hi,
I experienced the same issue. After I ran ./convert.sh scaffolding I got the error
./convert.sh: line 14: python: command not found
WARN [2021-10-05T20:08:39,686] [Globals.java:138] [main] Development mode is enabled
Using 1 CPU thread(s)
scaffolding/alignments_sorted.txt does not exist or does not contain any reads.
Therefore, the problem was that the command python in line 14 of the convert.sh-script was not found.
For me, modifying line 14 of convert.sh from
python ${SCRIPT_PATH}/alignments2txt.py -b ${SALSA_OUT_DIR}/alignment_iteration_1.bed -a ${SALSA_OUT_DIR}/scaffolds_FINAL.agp -l ${SALSA_OUT_DIR}/scaffold_length_iteration_1 > ${SALSA_OUT_DIR}/alignments.txt
to
python2 ${SCRIPT_PATH}/alignments2txt.py -b ${SALSA_OUT_DIR}/alignment_iteration_1.bed -a ${SALSA_OUT_DIR}/scaffolds_FINAL.agp -l ${SALSA_OUT_DIR}/scaffold_length_iteration_1 > ${SALSA_OUT_DIR}/alignments.txt
did the trick.
Best wishes, Isabel
@kishor2019 You're using the wrong PYTHON version (v 3.x), you have to use PYTHON 2 (e.g. 2.6), or fix the script like @CIWa has suggested.
