Missing file at step 10

[mradz19]

[0 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl
  Reading samples from /data/mohammad/full_project/data/00.full_project.samples
  Metagenomes found: 45
  Reading contig length from /data/mohammad/full_project/intermediate/01.full_project.lon
  Reading orf info from /data/mohammad/full_project/results/08.full_project.gff
  Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9)
  Creating reference from contigs
  Working with sample 1: S1
  Getting raw reads
  Aligning to reference with bowtie
  BAM file already found in /data/mohammad/full_project/data/bam/full_project.S1.bam, skipping
  Calculating contig coverage
  Counting with sqm_counter: Opening 12 threads
  11435752 reads counted
  10494702 reads counted
  11437610 reads counted
  9540615 reads counted
  12618761 reads counted
  11406217 reads counted
  10414814 reads counted
  11205437 reads counted
  11629895 reads counted
  9559217 reads counted
  10419199 reads counted
  10957115 reads counted
  Working with sample 2: S2
  Getting raw reads
cp: missing destination file operand after '/data/mohammad/full_project/temp/full_project.S2.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 "/data/mohammad/full_project/temp/full_project.S2.current_1" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
An error occurred during mapping with command       /data/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /data/mohammad/full_project/data/full_project.bowtie  -1 /data/mohammad/full_project/temp/full_project.S2.current_1 -2 /data/mohammad/full_project/temp/full_project.S2.current_2.gz --quiet -p 12 -S /data/mohammad/full_project/data/bam/full_project.S2.sam --very-sensitive-local! at /data/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 267.
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 /data/mradzieta/mohammad/full_project/syslog file (zip it first)
Died at /kusers/ancillary/mradzieta/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941.

Having this issue at step 10, seems like it can't find the relevant file for sample 2?

[jtamames]

syslog and samples file please

[fpusan]

Closing due to lack of activity, feel free to reopen