popins place-refalign: Location reference not found in contig file

[foggieding]

When running the place-refalign subcommand I get the following error:
ERROR: Location references a contig that was not found in contig file: chr1

However, the contigmap command is finished:
popins contigmap finished in 3421 seconds.

Then I find that the third column of the merged locations.txt file contain some chromosome names, except contig names. Here is an example:
chr8:62201066-62201159 + chr1 - 1 0.333333 Sample_001:1
chr10:9951702-9951767 - chr1 + 1 0.0833333 Sample_002:1

Here are my parameters for contigmap command:
/path/to/popins contigmap
-p ./samples/
-t 5
-r ./ref/genome.fasta
Sample_001

Besides, the supercontig.fa do not contain chr1 while the locations.txt file in the Sample_001 directory contains chr1 :
chr8:62201066-62201159 + chr1 - 1 1

Here is the result for running
samtools view Sample_001/non_ref_new.bam | awk '$3 == "chr8" && $7 == "chr1"' | head -n 1
V300046586L3C002R0640926577 209 chr8 25043222 0 85S54M chr1 145375013 0 AAGGTTTTCTTTTTTTTTTTTTTTTTTATTTTTAAAAGAACTGCTGCCGGGCCCGGGTCCCCCAACCCTTTACCCCCGCCTTTTGGGGAGGCCGAGATGGGCGGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTA 5:*&&8A,+FF<E-E82.315-FDFFFF8@5)E8.36F&,?3;4),):7'B++>)=/(-(4B(+>.0'<?<;B>:&/'-'97&<>.FF<FFF<EF7GFFGFGF:FFFFDFGDGGFFFFCEFFFFEFFFFFGFFFF?F NM:i:0 MD:Z:54 MC:Z:85M4D62M AS:i:54 XS:i:54 SA:Z:chr5,44311905,-,3S30M106S,0,0;

It would be great if you could provide some feedback. Thanks!

[bkehr]

Dear foggieding,

sorry for the late reply and thanks for the detailed info. Looking at the output of the samtools command, my best guess is that some files have been mixed up. In order to help you finding the problem, could you send me the output of the following three commands:

grep "^>" supercontigs.fa | wc -l
samtools view -H Sample_001/non_ref.bam | grep "@SQ" | wc -l
samtools view -H Sample_001/non_ref_new.bam | grep "@SQ" | wc -l

Thanks,
Birte

[bkehr]

Dear foggieding,

could you please check if your error persists with the most recent change 602a504?
You only need to rerun the contigmap command and it should even skip some steps if you have run it before.

Thanks,
Birte

[Krannich479]

Referring to this - I used to have the same error and can confirm that commit 602a504, so far, solved the issue for me in all downstream steps of popins contigmap.