Some reference data download link nolonger work, pending investigation.

[hsun3163]

(py3.11) [sunh14@lc03e22 ~]$ cd /sc/arion/projects/CommonMind/roussp01a/snmulti_QTL/working (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_hg_reference --cwd ../input/reference_data & [1] 189132 (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_gene_annotation --cwd ../input/reference_data & [2] 189133 (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_ercc_reference --cwd ../input/reference_data & [3] 189134 (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_dbsnp --cwd ../input/reference_data &INFO: Running download_hg_reference: INFO: Running download_ercc_reference: GRCh38_ful...lus_decoy_hla.fa: <urlopen error [Errno 101] Network is unreachable>: INFO: Running download_gene_annotation: ERROR: download_hg_reference (id=88880766584b8229) returns an error. Homo_sapie...8.103.chr.gtf.gz: 0%| | 0/49087092 [00:00<?, ?it/s] ERCC92.zip: 0%| | 0/28717 [00:00<?, ?it/s] INFO: download_ercc_reference is completed.
INFO: download_ercc_reference output: /sc/arion/projects/CommonMind/roussp01a/snmulti_QTL/input/reference_data/ERCC92.gtf /sc/arion/projects/CommonMind/roussp01a/snmulti_QTL/input/reference_data/ERCC92.fa Homo_sapie...8.103.chr.gtf.gz: 0%|▏ | 49152/49087092 [00:00<03:33, 229662.93it/s]INFO: Workflow download_ercc_reference (ID=w297010867a7f15c9) is executed successfully with 1 completed step.

[4] 189193 Homo_sapie...8.103.chr.gtf.gz: 0%|▍ | 172032/49087092 [00:00<01:56, 421643.95it/s] [3]- Done sos run pipeline/reference_data.ipynb download_ercc_reference --cwd ../input/reference_data Homo_sapie...8.103.chr.gtf.gz: 1%|█ | 360448/49087092 [00:00<01:39, 490429.95it/s]ERROR: [download_hg_reference]: [0]:

RuntimeError Traceback (most recent call last) script_8878139621259498696 in ----> download('ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa\n\n', dest_dir = cwd)

RuntimeError: Failed to download {urls[0]} Homo_sapie...8.103.chr.gtf.gz: 1%|█▏ | 425984/49087092 [00:00<01:35, 507455.58it/s]INFO: Running download_dbsnp: 00-All.vcf.gz: <urlopen error [Errno 101] Network is unreachable>: 00-All.vcf.gz.tbi: <urlopen error [Errno 101] Network is unreachable>: ERROR: download_dbsnp (id=eb7f9a9839feca92) returns an error. Homo_sapie...8.103.chr.gtf.gz: 2%|██▊ | 1007616/49087092 [00:02<01:30, 532953.87it/s]ERROR: [download_dbsnp]: [0]:

RuntimeError Traceback (most recent call last) script_8177488568793545762 in ----> download('ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz\nftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz.tbi\n\n', dest_dir = cwd)

RuntimeError: Failed to download ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz (2 out of 2) Homo_sapie...8.103.chr.gtf.gz: 31%|█████████████████████████████████████████▉ | 15007744/49087092 [00:28<01:05, 518354.50it/s]