I am running REAPR version 1.0.18 (and also the older 1.0.17) to check for correctness of my genome assemblies.

However, I am getting a run error with the "smaltmap" step, and this error suggests that the input files are not in the correct format. Syntax used was:

reapr smaltmap a5miseq_EthFoc11_LOCAL.fsa EthFoc-11_S285_L007_R1_001.fastq.gz EthFoc-11_S285_L007_R2_001.fastq.gz a5miseq_EthFoc11_RawReads_mapped.bam

The complete STDOUT/STDERR is at this page - http://textuploader.com/djam1. Towards the end of the message, it reads (with BOTH versions)

# =-=-= End of Hash Index Stats =-=-=
# Sampling insert size distribution ...
[0] smalt.c:750 ERROR: wrong FASTQ/FASTA format 
[REAPR smaltmap] Error in system call:
/share/apps/reapr-1.0.17/src/smalt sample -u 1000 -o a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9652.smaltmap.smalt_sample a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9652.smaltmap.smalt_index EthFoc-11_S285_L007_R1_001.fastq.gz EthFoc-11_S285_L007_R2_001.fastq.gz
srun: error: c9-72: task 0: Exited with exit code 1

Despite the error message, outputs are generated, as shown below:

-rw-rw-r-- 1 aksrao aksrao    0 Sep 11 01:44 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9777.smaltmap.smalt_sample
-rw-rw-r-- 1 aksrao aksrao 318M Sep 11 01:44 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9777.smaltmap.smalt_index.smi
-rw-rw-r-- 1 aksrao aksrao  21M Sep 11 01:44 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9777.smaltmap.smalt_index.sma
-rw-rw-r-- 1 aksrao aksrao    0 Sep 11 01:31 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9652.smaltmap.smalt_sample
-rw-rw-r-- 1 aksrao aksrao 318M Sep 11 01:31 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9652.smaltmap.smalt_index.smi
-rw-rw-r-- 1 aksrao aksrao  21M Sep 11 01:30 a5miseq_EthFoc11_RawReads_mapped.bam.tmp.9652.smaltmap.smalt_index.sm

Interestingly, I've used these same input files successfully (PE 2*150 HiSeq4K R1, R2 files) with other software / tools including Trimmomatic, ALLPATHS-LG, bbduk.sh / tadpole.sh.

Importantly, I've used these same input files for the "perfectmap" step of reapr analyses, without any run errors! The syntax was:

reapr perfectmap a5miseq_EthFoc11_LOCAL.fsa EthFoc-11_S285_L007_R1_001.fastq.gz EthFoc-11_S285_L007_R2_001.fastq.gz 150 perfect

and generated the following outputs:

-rw-rw-r-- 1 aksrao aksrao  51K Sep 11 01:08 perfect.perfect_cov.gz.tbi
-rw-rw-r-- 1 aksrao aksrao  946 Sep 11 01:08 perfect.hist
-rw-rw-r-- 1 aksrao aksrao 153M Sep 11 01:08 perfect.perfect_cov.gz

So I am not sure what this "wrong FASTQ/FASTA format" error message means, and why it even appears. Could someone help me debug this please? Thank you!