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wtsi-npg / baton

iRODS client programs and API
http://wtsi-npg.github.io/baton
GNU General Public License v2.0
19 stars 19 forks source link

baton-get may trigger errors in a pipeline #273

Open kjsanger opened 1 year ago

kjsanger commented 1 year ago

E.g.

$ jq -n '{coll: "/testZone/home/irods", obj: "15440_1#0.bam"}' | baton-get --raw | samtools view | tail
[E::bgzf_read_block] Invalid BGZF header at offset 97296
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
samtools view: error reading file "-"
samtools view: error closing "-": -1
read.9000       16      test_ref9       892     40      100M    *       0       0       TAACAAGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACT        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9001       16      test_ref9       893     40      100M    *       0       0       AACAAGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTA        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9002       16      test_ref9       894     40      100M    *       0       0       ACAAGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTAC        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9003       16      test_ref9       895     40      100M    *       0       0       CAAGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACT        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9004       16      test_ref9       896     40      100M    *       0       0       AAGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTA        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9005       16      test_ref9       897     40      100M    *       0       0       AGTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTAC        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9006       16      test_ref9       898     40      100M    *       0       0       GTACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTACG        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9007       16      test_ref9       899     40      100M    *       0       0       TACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTACGT        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9008       16      test_ref9       900     40      100M    *       0       0       ACCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTACGTC        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
read.9009       16      test_ref9       901     40      100M    *       0       0       CCAACGCTTTCGCCCTGTTTCAAGACGACTAGTAGGATAACCCAGTACTTCTCGTAGCTGGCGGACATGTCTGTGTTCGTTTGGTTTGACTACTACGTCC        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Yet tears (using the same iRODS API calls) does not. It's also triggered by e.g. tee