Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally Line no 18

[vmevada102]

I am receiving following error

--- SAMPLE AJTDEW -------- Contig tax file /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/intermediate/09.AJTDEW.contiglog already found, skipping step 9 [0 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl Can't find SqueezeMeta_conf.pl in /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW. Is the project path ok? at /home/vishal/miniconda3/envs/squeezemeta/SqueezeMeta/scripts/10.mapsamples.pl line 18. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally sh: /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/syslog: No such file or directory sh: /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/syslog: No such file or directory

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/syslog file (zip it first)

As the original Path for the analysis is /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/

Why this tool is asking for /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJDEW

Kindly help to resolve this issue.

[vmevada102]

I have copied all files to /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJDEW for testing purpose. However, following error received.

[0 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl Reading samples from /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/data/00.AJTDEW.samples Metagenomes found: 1 Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9) Found reference in /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/data/AJTDEW.bowtie.1.bt2, skipping Working with sample 1: AJTDEW Getting raw reads cp: missing destination file operand after ‘/home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/temp/AJTDEW.AJTDEW.current_1’ Try 'cp --help' for more information. Aligning to reference with bowtie stat: No such file or directory Warning: Could not open read file "/home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/temp/AJTDEW.AJTDEW.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 stat: No such file or directory Warning: Could not open read file "/home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/temp/AJTDEW.AJTDEW.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 An error occurred during mapping! at /home/vishal/miniconda3/envs/squeezemeta/SqueezeMeta/scripts/10.mapsamples.pl line 179. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW/AJTDEW/syslog file (zip it first) Died at /home/vishal/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl line 921.

[jtamames]

I guess you tried to restart the process from the project directory /home/vishal/Desktop/squeezemetarun/anjana/anjana_td/AJTDEW, instead of the upper directory /home/vishal/Desktop/squeezemetarun/anjana/anjana_td. Otherwise it is not possible that the pipeline crashes in 10 complaining of a missing conf file while having run correctly the previous steps

[vmevada102]

I have already tried from the upper directory /home/vishal/Desktop/squeezemetarun/anjana/anjana_td as mentioned in the first comment

[jtamames]

Please remember to share the syslog file with us. Sorry to ask, but are you sure you did nothing else to the project, like moving the files and restarting in a different computer? As I said, it is not possible that the process misses the SqueezeMeta_conf.pl file in step 10, and not in previous ones, since that file is checked in every step