Help with BlockingIOError: [Errno 35] Resource temporarily unavailable

[jestlin15]

Hi, I have about 190 (x2 because of paired end) fastq files to download. However, I have faced the below issue twice when downloading:

[ENA Attempt 1] Downloading ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_1.fastq.gz into /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz
Exception in thread Thread-141 (background):
Traceback (most recent call last):
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
self.run()
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 975, in run
self._target(self._args, **self._kwargs)
File "/Volumes/LaCie/sradownloader-3.11/sradownloader", line 142, in background
block = sock.recv(10241024)
^^^^^^^^^^^^^^^^^^^^
BlockingIOError: [Errno 35] Resource temporarily unavailable

When I check when the SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz was last modified, it showed that it has been more than 24 hours.

Would you suggest that I restarted the whole download again? Or wait it out?

The first time this occurred, after waiting for a whole day, restarted my computer and I redownloaded all the datasets as I was not sure which files were downloaded and which files were not.

Update: I restarted the downloads after clearing my internet history and cache. It seems to have gotten to attempt 3 but got stuck again:

[ENA] Downloading SRR3140303 into SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq
run_accession fastq_ftp
SRR3140303 ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_2.fastq.gz
[ENA Attempt 1] Downloading ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_1.fastq.gz into /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz
Exception in thread Thread-1 (background):
Traceback (most recent call last):
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
self.run()
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 975, in run
self._target(self._args, **self._kwargs)
File "/Volumes/LaCie/sradownloader-3.11/sradownloader", line 142, in background
block = sock.recv(10241024)
^^^^^^^^^^^^^^^^^^^^
BlockingIOError: [Errno 35] Resource temporarily unavailable
426 Failure writing network stream.
[ENA] Download failed for SRR3140303 - going around for another try
[ENA Attempt 2] Downloading ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_1.fastq.gz into /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz
Sleeping for 4 seconds before retrying
426 Failure writing network stream.
[ENA] Download failed for SRR3140303 - going around for another try
[ENA Attempt 3] Downloading ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/003/SRR3140303/SRR3140303_1.fastq.gz into /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140303_GSM2053449_N20_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz
Sleeping for 9 seconds before retrying
Exception in thread Thread-3 (background):
Traceback (most recent call last):
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
self.run()
File "/Users/j/miniconda3/lib/python3.11/threading.py", line 975, in run
self._target(self._args, **self._kwargs)
File "/Volumes/LaCie/sradownloader-3.11/sradownloader", line 142, in background
block = sock.recv(10241024)
^^^^^^^^^^^^^^^^^^^^
BlockingIOError: [Errno 35] Resource temporarily unavailable

2. In the scenario where it passes the BlockingIOError and goes to attempt5 and downloads from NCBI, is it possible to set for it to overwrite? I do not check the terminal all the time as it runs in the background hence when I leave it too long, it seems to just decide to not compress/overwrite.

[ENA Attempt 5] Downloading ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/000/SRR3140250/SRR3140250_1.fastq.gz into /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140250_GSM2053438_N8_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz
Sleeping for 25 seconds before retrying
426 Failure writing network stream.
WARNING: Failed to download via ENA: [ENA] Download repeatedly failed for SRR3140250 - giving up trying NCBI instead
[NCBI] Downloading SRR3140250 into SRR3140250_GSM2053438_N8_RNA-seq_Homo_sapiens_RNA-Seq
[NCBI Attempt 1] Running: fasterq-dump --split-files --include-technical --threads 1 --temp /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq --outfile SRR3140250_GSM2053438_N8_RNA-seq_Homo_sapiens_RNA-Seq.fastq --progress --outdir /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq SRR3140250
join :|-------------------------------------------------- 100%
concat :|-------------------------------------------------- 100%
spots read : 12,894,974
reads read : 25,789,948
reads written : 25,789,948
Compressing /Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140250_GSM2053438_N8_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq
/Volumes/LaCie/S100A10/Fastq_files/GSE77509/fastq/SRR3140250_GSM2053438_N8_RNA-seq_Homo_sapiens_RNA-Seq_1.fastq.gz already exists -- do you wish to overwrite (y or n)?

thank you.