Generating .hic file with convert.sh

[kishor2019]

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.

[carolhsb]

Hi,

I'm having the same issue.

[skoren]

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.

[CIWa]

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

[cement-head]

@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.