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Hi. I'm having a problem of not getting out.circ_report.
My commands and results are as follows:
$circminer -r ./references/Human/GRCh38.104/Homo_sapiens.GRCh38.dna.primary_assembly.fa -g /./references/Human/GRCh38.104/Homo_sapiens.GRCh38.104.gtf -1 ../fastq_files/C1_1.trimmed.fq -2 ../fastq_files/C1_2.trimmed.fq Wed Dec 22 11:17:01 2021 [INFO] Number of threads: 1 Wed Dec 22 11:17:01 2021 [INFO] Input file type: Paired-end Wed Dec 22 11:17:02 2021 [INFO] Kmer size obtained from index: 20 Wed Dec 22 11:17:02 2021 [INFO] Loading GTF file... Wed Dec 22 11:17:24 2021 [INFO] Completed! (CPU time: 21.86s; Real time: 22.44s) Wed Dec 22 11:17:24 2021 [INFO] Genome index type: Full Wed Dec 22 11:17:24 2021 [INFO] Starting read extraction Wed Dec 22 11:17:24 2021 [INFO] + Loading genome index... Wed Dec 22 11:18:12 2021 [INFO] + Completed! (CPU time: 8.19s; Real time: 48.30s) Wed Dec 22 11:18:12 2021 [INFO] + Loading genome sequence... Wed Dec 22 11:18:13 2021 [INFO] + Completed! (CPU time: 1.10s; Real time: 1.10s) Wed Dec 22 11:18:13 2021 [INFO] + Starting pseudo-alignment (Round 1) Wed Dec 22 11:58:13 2021 [INFO] + Completed round 1! (CPU time: 2198.78s; Real time: 2399.62s) Wed Dec 22 11:58:13 2021 [INFO] + Loading genome index... Wed Dec 22 11:59:12 2021 [INFO] + Completed! (CPU time: 7.41s; Real time: 59.11s) Wed Dec 22 11:59:12 2021 [INFO] + Loading genome sequence... Wed Dec 22 11:59:12 2021 [INFO] + Completed! (CPU time: 0.73s; Real time: 0.74s) Wed Dec 22 11:59:12 2021 [INFO] + Starting pseudo-alignment (Round 2) Wed Dec 22 12:36:37 2021 [INFO] + Completed round 2! (CPU time: 2024.90s; Real time: 2244.38s) Wed Dec 22 12:36:37 2021 [INFO] + Loading genome index... Wed Dec 22 12:37:35 2021 [INFO] + Completed! (CPU time: 7.11s; Real time: 58.29s) Wed Dec 22 12:37:35 2021 [INFO] + Loading genome sequence... Wed Dec 22 12:37:36 2021 [INFO] + Completed! (CPU time: 0.74s; Real time: 0.74s) Wed Dec 22 12:37:36 2021 [INFO] + Starting pseudo-alignment (Round 3) Wed Dec 22 13:07:08 2021 [INFO] + Completed round 3! (CPU time: 1620.36s; Real time: 1771.96s) Wed Dec 22 13:07:08 2021 [INFO] Starting circRNA detection Wed Dec 22 13:07:08 2021 [INFO] + Sorting remaining read mappings using GNU sort... Wed Dec 22 13:07:23 2021 [INFO] + Completed! (CPU time: 0.00s; Real time: 14.45s) Wed Dec 22 13:07:23 2021 [INFO] + Loading genome sequence... Wed Dec 22 13:07:29 2021 [INFO] + Completed! (CPU time: 1.96s; Real time: 6.04s) Wed Dec 22 13:08:14 2021 [INFO] + Loading genome sequence... Wed Dec 22 13:08:19 2021 [INFO] + Completed! (CPU time: 1.40s; Real time: 5.51s) Segmentation fault (core dumped)
The following files were generated but NOT out.circ_report:
output_1_remain_R1.fastq output_1_remain_R2.fastq output_2_remain_R1.fastq output_2_remain_R2.fastq output_3_remain_R1.fastq output_3_remain_R1.fastq.srt output_3_remain_R2.fastq output_3_remain_R2.fastq.srt output.candidates.pam
What am I doing wrong here?
The text was updated successfully, but these errors were encountered:
No branches or pull requests
Hi. I'm having a problem of not getting out.circ_report.
My commands and results are as follows:
$circminer -r ./references/Human/GRCh38.104/Homo_sapiens.GRCh38.dna.primary_assembly.fa -g /./references/Human/GRCh38.104/Homo_sapiens.GRCh38.104.gtf -1 ../fastq_files/C1_1.trimmed.fq -2 ../fastq_files/C1_2.trimmed.fq
Wed Dec 22 11:17:01 2021 [INFO] Number of threads: 1
Wed Dec 22 11:17:01 2021 [INFO] Input file type: Paired-end
Wed Dec 22 11:17:02 2021 [INFO] Kmer size obtained from index: 20
Wed Dec 22 11:17:02 2021 [INFO] Loading GTF file...
Wed Dec 22 11:17:24 2021 [INFO] Completed! (CPU time: 21.86s; Real time: 22.44s)
Wed Dec 22 11:17:24 2021 [INFO] Genome index type: Full
Wed Dec 22 11:17:24 2021 [INFO] Starting read extraction
Wed Dec 22 11:17:24 2021 [INFO] + Loading genome index...
Wed Dec 22 11:18:12 2021 [INFO] + Completed! (CPU time: 8.19s; Real time: 48.30s)
Wed Dec 22 11:18:12 2021 [INFO] + Loading genome sequence...
Wed Dec 22 11:18:13 2021 [INFO] + Completed! (CPU time: 1.10s; Real time: 1.10s)
Wed Dec 22 11:18:13 2021 [INFO] + Starting pseudo-alignment (Round 1)
Wed Dec 22 11:58:13 2021 [INFO] + Completed round 1! (CPU time: 2198.78s; Real time: 2399.62s)
Wed Dec 22 11:58:13 2021 [INFO] + Loading genome index...
Wed Dec 22 11:59:12 2021 [INFO] + Completed! (CPU time: 7.41s; Real time: 59.11s)
Wed Dec 22 11:59:12 2021 [INFO] + Loading genome sequence...
Wed Dec 22 11:59:12 2021 [INFO] + Completed! (CPU time: 0.73s; Real time: 0.74s)
Wed Dec 22 11:59:12 2021 [INFO] + Starting pseudo-alignment (Round 2)
Wed Dec 22 12:36:37 2021 [INFO] + Completed round 2! (CPU time: 2024.90s; Real time: 2244.38s)
Wed Dec 22 12:36:37 2021 [INFO] + Loading genome index...
Wed Dec 22 12:37:35 2021 [INFO] + Completed! (CPU time: 7.11s; Real time: 58.29s)
Wed Dec 22 12:37:35 2021 [INFO] + Loading genome sequence...
Wed Dec 22 12:37:36 2021 [INFO] + Completed! (CPU time: 0.74s; Real time: 0.74s)
Wed Dec 22 12:37:36 2021 [INFO] + Starting pseudo-alignment (Round 3)
Wed Dec 22 13:07:08 2021 [INFO] + Completed round 3! (CPU time: 1620.36s; Real time: 1771.96s)
Wed Dec 22 13:07:08 2021 [INFO] Starting circRNA detection
Wed Dec 22 13:07:08 2021 [INFO] + Sorting remaining read mappings using GNU sort...
Wed Dec 22 13:07:23 2021 [INFO] + Completed! (CPU time: 0.00s; Real time: 14.45s)
Wed Dec 22 13:07:23 2021 [INFO] + Loading genome sequence...
Wed Dec 22 13:07:29 2021 [INFO] + Completed! (CPU time: 1.96s; Real time: 6.04s)
Wed Dec 22 13:08:14 2021 [INFO] + Loading genome sequence...
Wed Dec 22 13:08:19 2021 [INFO] + Completed! (CPU time: 1.40s; Real time: 5.51s)
Segmentation fault (core dumped)
The following files were generated but NOT out.circ_report:
output_1_remain_R1.fastq
output_1_remain_R2.fastq
output_2_remain_R1.fastq
output_2_remain_R2.fastq
output_3_remain_R1.fastq
output_3_remain_R1.fastq.srt
output_3_remain_R2.fastq
output_3_remain_R2.fastq.srt
output.candidates.pam
What am I doing wrong here?
The text was updated successfully, but these errors were encountered: