rsync error going to /volume2/web/gitrepos/urol-e5/

[sr320]

Running

rsync -avz ../timeseries_molecular \
--exclude='*.sam' \
--exclude='tmp*' \
--exclude='*gz_C_to_T.fastq' \
--exclude='*gz_G_to_A.fastq' \
--exclude='Non_CpG_context*' \
--exclude='.*' --exclude='*/.*' \
sr320@gannet.fish.washington.edu:/volume2/web/gitrepos/urol-e5/

get

....
timeseries_molecular/M-multi-species/data/rna_metadata.csv
timeseries_molecular/M-multi-species/data/lipidomics/
timeseries_molecular/M-multi-species/data/lipidomics/2025-02-05_Roberts_Test_Coral.xlsx
timeseries_molecular/M-multi-species/data/lipidomics/2025-02-05_Roberts_Test_Coral_BCA.xlsx
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/data/metabolomics": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/01-geneID": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/02-phys-PC1": Operation not permitted (1)
rsync: mkstemp "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/02.20-F-Ptua-RNAseq-alignment-HiSat2/POC-259-TP2/.POC-259-TP2_hisat2.stats.abat1v" failed: Permission denied (13)
rsync: mkstemp "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/02.20-F-Ptua-RNAseq-alignment-HiSat2/POC-259-TP2/.e2t.ctab.H2C6Ev" failed: Permission denied (13)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/03-test-lipidomics": Operation not permitted (1)
timeseries_molecular/M-multi-species/data/lipidomics/2025-02-20_Roberts_QuantLipidData.xlsx
timeseries_molecular/M-multi-species/data/lipidomics/NWMRC_SampleForm_Roberts_Jan2025.xlsx
....
rsync: mkstemp "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/.alignment_details.tsv.HHl7DG" failed: Permission denied (13)
rsync: mkstemp "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/.known_miRNAs.gff3.C45hfT" failed: Permission denied (13)
rsync: mkstemp "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/.known_miRNAs_unaligned.fasta.DLmaZL" failed: Permission denied (13)
....

[kubu4]

Okay, I changed permissions (775). See if that fixes it?

[sr320]

getting

...
timeseries_molecular/E-Peve/output/02.20-E-Peve-RNAseq-alignment-HiSat2/POR-83-TP4/
timeseries_molecular/E-Peve/output/02.20-E-Peve-RNAseq-alignment-HiSat2/multiqc_data/
timeseries_molecular/E-Peve/output/03-Peve-bismark/
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/04.3-Peve-bismark-array": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/04.3-Peve-bismark-array/multiqc_data": Operation not permitted (1)
timeseries_molecular/E-Peve/output/04.3-Peve-bismark-array/
timeseries_molecular/E-Peve/output/04.3-Peve-bismark-array/multiqc_data/
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/05-Peve-energy-GO": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/06-Peve-epimods-blast": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/figures": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/12-Peve-lncRNA-discovery": Operation not permitted (1)
timeseries_molecular/E-Peve/output/05-Peve-energy-GO/
timeseries_molecular/E-Peve/output/06-Peve-epimods-blast/
timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/
timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/
timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/figures/
timeseries_molecular/E-Peve/output/12-Peve-lncRNA-discovery/
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/13-Peve-lncRNA-matrix": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/03-Ptua-epimods-blast_files": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/03-Ptua-epimods-blast_files/libs": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/03-Ptua-epimods-blast_files/libs/bootstrap": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/03-Ptua-epimods-blast_files/libs/clipboard": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/03-Ptua-epimods-blast_files/libs/quarto-html": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/04-Ptua-sRNA-discovery-ShortStack_files": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/code/04-Ptua-sRNA-discovery-ShortStack_files/figure-gfm": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data/rnaseq-raw-fastqs": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data/rnaseq-raw-fastqs/multiqc_data": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data/wgbs-raw-fastqs": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data/wgbs-raw-fastqs/multiqc_data": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/00.10-F-Ptua-sRNAseq-reads-FastQC-MultiQC": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/00.10-F-Ptua-sRNAseq-reads-FastQC-MultiQC/raw-fastqc-sRNA": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/00.10-F-Ptua-sRNAseq-reads-FastQC-MultiQC/raw-fastqc-sRNA/multiqc_data": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/01.00-F-Ptua-RNAseq-trimming-fastp-FastQC-MultiQC": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/01.00-F-Ptua-RNAseq-trimming-fastp-FastQC-MultiQC/multiqc_data": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/01.00-F-Ptua-WGBS-trimming-fastp-FastQC-MultiQC": Operation not permitted (1)
timeseries_molecular/E-Peve/output/12-Peve-lncRNA-discovery/POR-69-TP1.sorted.bam
deflate on token returned 0 (904 bytes left)
rsync error: error in rsync protocol data stream (code 12) at token.c(481) [sender=3.2.7]
sr320@n3435:/mmfs1/gscratch/scrubbed/sr320/github/timeseries_molecular$ 

[kubu4]

What happens if you remove the -z flag and re-run?

[sr320]

still throwing errors

...
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/03-test-lipidomics": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/09-metabolomics-WGCNA": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/output/10-format-miRNA-counts": Operation not permitted (1)
rsync: failed to set times on "/volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/scripts": Operation not permitted (1)
timeseries_molecular/M-multi-species/data/lipidomics/
timeseries_molecular/M-multi-species/data/metabolomics/
timeseries_molecular/M-multi-species/output/
timeseries_molecular/M-multi-species/output/01-geneID/
timeseries_molecular/M-multi-species/output/02-phys-PC1/
timeseries_molecular/M-multi-species/output/03-test-lipidomics/
timeseries_molecular/M-multi-species/output/09-metabolomics-WGCNA/
timeseries_molecular/M-multi-species/output/10-format-miRNA-counts/
timeseries_molecular/M-multi-species/scripts/

sent 308,290 bytes  received 72,312 bytes  84,578.22 bytes/sec
total size is 515,003,461,260  speedup is 1,353,128.63
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1338) [sender=3.2.7]
sr320@n3435:/mmfs1/gscratch/scrubbed/sr320/github/timeseries_molecular$ 

[kubu4]

This is better, as we're no longer getting this error: deflate on token returned 0 (904 bytes left) rsync error: error in rsync protocol data stream (code 12) at token.c(481) [sender=3.2.7]

The other errors are related to setting times (obviously), but may not impact actual file transfer.

When you have a sec, can you confirm whether or not files that were supposed to get sync'd actually got sync'd?

E.g. Do the contents of /volume2/web/gitrepos/urol-e5/timeseries_molecular/M-multi-species/scripts match on Klone and on Gannet?