Hi there, wondering if any ideas on the following.
I'm running calib installed with conda on a Linux server. I've successfully run the calib command and generated a cluster file. The problem occurs when I try to run calib_cons. The following is the full command and output:
calib_cons -c B5-testgz.cluster -q B5_3_1_S5_L001_R1_UMI_full.fastq B5_3_1_S5_L001_R2_UMI_full.fastq -t 4 -o B5gz-R1 B5gz-R2
Reading cluster file: B5-testgz.cluster
Reading fastq file: B5_3_1_S5_L001_R1_UMI_full.fastq
Writing output files: B5gz-R1
Illegal instruction (core dumped)
I end up with 6 empty files in my directory (.msa, .msa1, .fastq and .fast0/1/2).
A factor here is that some preprocessing occurred before the data was passed to me and the UMIs had been removed from the front of the read sequences - I have had to copy them back to the sequence start from the read header and put dummy characters (!!!!!!!!!!!) in the quality scores line so that the lengths match the sequences. Not sure if something here could be problematic. An example read:
@A01439:100:HC3VHDRX2:1:2101:2808:1000:CTTGCATCTTA 1:N:0:CGGCATTA+TGACTGAC CTTGCATCTTACTTAAAAACCTACAAATGAAACCCAGCATGCATACACACACCCCTCCATACCCTCACATAAATTATATATACCCTTATCTATACTAACTATAAAATGTAT + !!!!!!!!!!!F:F:FFF,:F,:F::FFFF::FF:F,,FFFFF:FFF,F:FF,:FFFFF,FFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFF
results of head B5-testgz.cluster if it helps:
26551449 34947546 10 @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTAGTCAGTTTTCTAAATCTATAATGGAAAAGAAAATCGAATCTCGTCTTTATTTTTAAAAAGGGAAGGATGTTCAAGATCGGAAGAGCACACGTCTGAA !!!!!!!!!!!FF::FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTTGAACATCCTTCCCTTTTTAAAAATAAAGACGAGATTCGATTTTCTTTTCCATTATAGATTTAGAAAACTGACTTAGATCGGAAGAGCGTCGTGTAGGGAA !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 11104884 14491263 46 @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAGTACTGGAAAGTCCCATTTTTCTCTGCACTGAACAGCCAGAAAAAGAAACAACGTTTCTAACTTAATTGGCTAGATCGGAAGAGCACACGTCTGAACTC !!!!!!!!!!!,,FF:FFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAAGCCAATTAAGTTAGAAACGTTGTTTCTTTTTCTGGCTGTTCAGTGCAGAGAAAAATGGGACTTTCCAGTACAAGATCGGAAGAGCGTCGTGTTGGGAAAG !!!!!!!!!!!FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF,FF,,FF,,:F 15253236 19933987 47 @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTGCATAACACAGCAGAGCCACTATGAAATTCAGCTCTTATAGCAAACATTTAAATGATTTTTGTTGGATATTTTCTCTCAGTTGGCATGTGAACAAATGTG !!!!!!!!!!!F,,,FFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTCACATTTGTTCACATGCCAACTGAGAGAAAATATCCAACAAAAATCATTTAAATGTTTGCTATAAGAGCTGAATTTCATAGTGGCTCTGCTGTGTTATG !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
any thoughts on what may be leading to this error?
Hi there, wondering if any ideas on the following.
I'm running calib installed with conda on a Linux server. I've successfully run the calib command and generated a cluster file. The problem occurs when I try to run calib_cons. The following is the full command and output:
calib_cons -c B5-testgz.cluster -q B5_3_1_S5_L001_R1_UMI_full.fastq B5_3_1_S5_L001_R2_UMI_full.fastq -t 4 -o B5gz-R1 B5gz-R2Reading cluster file: B5-testgz.cluster
Reading fastq file: B5_3_1_S5_L001_R1_UMI_full.fastq
Writing output files: B5gz-R1
Illegal instruction (core dumped)
I end up with 6 empty files in my directory (.msa, .msa1, .fastq and .fast0/1/2).
A factor here is that some preprocessing occurred before the data was passed to me and the UMIs had been removed from the front of the read sequences - I have had to copy them back to the sequence start from the read header and put dummy characters (!!!!!!!!!!!) in the quality scores line so that the lengths match the sequences. Not sure if something here could be problematic. An example read:
@A01439:100:HC3VHDRX2:1:2101:2808:1000:CTTGCATCTTA 1:N:0:CGGCATTA+TGACTGAC CTTGCATCTTACTTAAAAACCTACAAATGAAACCCAGCATGCATACACACACCCCTCCATACCCTCACATAAATTATATATACCCTTATCTATACTAACTATAAAATGTAT + !!!!!!!!!!!F:F:FFF,:F,:F::FFFF::FF:F,,FFFFF:FFF,F:FF,:FFFFF,FFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFresults of head B5-testgz.cluster if it helps:
26551449 34947546 10 @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTAGTCAGTTTTCTAAATCTATAATGGAAAAGAAAATCGAATCTCGTCTTTATTTTTAAAAAGGGAAGGATGTTCAAGATCGGAAGAGCACACGTCTGAA !!!!!!!!!!!FF::FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTTGAACATCCTTCCCTTTTTAAAAATAAAGACGAGATTCGATTTTCTTTTCCATTATAGATTTAGAAAACTGACTTAGATCGGAAGAGCGTCGTGTAGGGAA !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 11104884 14491263 46 @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAGTACTGGAAAGTCCCATTTTTCTCTGCACTGAACAGCCAGAAAAAGAAACAACGTTTCTAACTTAATTGGCTAGATCGGAAGAGCACACGTCTGAACTC !!!!!!!!!!!,,FF:FFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAAGCCAATTAAGTTAGAAACGTTGTTTCTTTTTCTGGCTGTTCAGTGCAGAGAAAAATGGGACTTTCCAGTACAAGATCGGAAGAGCGTCGTGTTGGGAAAG !!!!!!!!!!!FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF,FF,,FF,,:F 15253236 19933987 47 @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTGCATAACACAGCAGAGCCACTATGAAATTCAGCTCTTATAGCAAACATTTAAATGATTTTTGTTGGATATTTTCTCTCAGTTGGCATGTGAACAAATGTG !!!!!!!!!!!F,,,FFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTCACATTTGTTCACATGCCAACTGAGAGAAAATATCCAACAAAAATCATTTAAATGTTTGCTATAAGAGCTGAATTTCATAGTGGCTCTGCTGTGTTATG !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFany thoughts on what may be leading to this error?