However, I got this error (only the tail end of the error is printed):
inflating: SRR5676841_R1_fastqc/fastqc.fo
Finished fastqc to infer read length on: Tue 07/16/2024 at: 22:46:12
Completed data processing on: Tue 07/16/2024 at: 22:46:12
[E::hts_open_format] Failed to open file "SRR2126053_R1.fastq.gz" : No such file or directory
Traceback (most recent call last):
File "/root/PolyAMiner-Bulk/PolyA-miner.py", line 486, in
main()
File "/root/PolyAMiner-Bulk/PolyA-miner.py", line 272, in main
if ExtractPolyASites4Bulk1.extractPolyA():
File "/root/PolyAMiner-Bulk/lib/ExtractPolyAsites4Bulk.py", line 507, in extractPolyA
self._extractSoftClippedReads()
File "/root/PolyAMiner-Bulk/lib/ExtractPolyAsites4Bulk.py", line 69, in _extractSoftClippedReads
bamfile = pysam.AlignmentFile(BAM_FILE, 'rb')
File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file SRR2126053_R1.fastq.gz: No such file or directory
I noticed that the alignment steps in PolyA-miner.py are commented out. Is fastq mode unavailable?
Hello, does the PolyAMiner-bulk code work on FASTQ files? I ran the following command interactively within a docker container:
python3 PolyA-miner.py -mode fastq \ -fasta /root/PolyAMiner-Bulk/ReferenceFiles/GRCh38.primary_assembly.genome.fa \ -gtf /root/PolyAMiner-Bulk/ReferenceFiles/gencode.v33.primary_assembly.annotation.gtf \ -index /root/PolyAMiner-Bulk/fastq_test/GRCh38_noalt_as -verboseLogging \ -p 4 -a 0.65 -outPrefix 3UTROnly -expNovel 1 -s 0 \ -o /root/PolyAMiner-Bulk/fastq_test/results_fastq \ -d /root/PolyAMiner-Bulk/fastq_test/hu_fastq \ -c1 SRR2126053_R1.fastq.gz,\ SRR2126053_R2.fastq.gz,\ SRR2126106_R1.fastq.gz,\ SRR2126106_R2.fastq.gz,\ SRR2126247_R1.fastq.gz,\ SRR2126247_R2.fastq.gz \ -c2 SRR5676841_R1.fastq.gz,\ SRR5676841_R2.fastq.gz,\ SRR5676900_R1.fastq.gz,\ SRR5676900_R2.fastq.gz,\ SRR5676931_R1.fastq.gz,\ SRR5676931_R2.fastq.gz \ -verboseLogging -ignore UTR5,CDS,Intron,UN -apriori_annotations -modelOrganism human \ -visualizeTopNum 0 -visualizeCondition1Name Control -visualizeCondition2Name Treatment \ -noDEGAnalyzer
However, I got this error (only the tail end of the error is printed):
inflating: SRR5676841_R1_fastqc/fastqc.fo
Finished fastqc to infer read length on: Tue 07/16/2024 at: 22:46:12
Completed data processing on: Tue 07/16/2024 at: 22:46:12
[E::hts_open_format] Failed to open file "SRR2126053_R1.fastq.gz" : No such file or directory Traceback (most recent call last): File "/root/PolyAMiner-Bulk/PolyA-miner.py", line 486, in
main()
File "/root/PolyAMiner-Bulk/PolyA-miner.py", line 272, in main
if ExtractPolyASites4Bulk1.extractPolyA():
File "/root/PolyAMiner-Bulk/lib/ExtractPolyAsites4Bulk.py", line 507, in extractPolyA self._extractSoftClippedReads() File "/root/PolyAMiner-Bulk/lib/ExtractPolyAsites4Bulk.py", line 69, in _extractSoftClippedReads bamfile = pysam.AlignmentFile(BAM_FILE, 'rb') File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open FileNotFoundError: [Errno 2] could not open alignment file
SRR2126053_R1.fastq.gz: No such file or directoryI noticed that the alignment steps in PolyA-miner.py are commented out. Is fastq mode unavailable?
Thanks, Christy