which: no docker in (/usr/local/current/singularity/sylabs/3.10.3/bin:/usr/local/slurm/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/X11R6/bin:/usr/local/jdk/bin:/usr/bin:/usr/local/mysql/bin:/home/hillts/.local/bin:/home/hillts/bin:/data/NCBR/projects/NCBR-298/Finder:/opt/ibutils/bin)
FATAL:   Image file already exists: "finder_1.1.0.sif" - will not overwrite
INFO:    Downloading library image to tmp cache: /tmp/sbuild-tmp-cache-4038968435
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
2022/11/04 16:46:49  info unpack layer: sha256:ea362f368469f909a95f9a6e54ebe0121ce0a8e3c30583dd9c5fb35b14544dec
2022/11/04 16:46:50  info unpack layer: sha256:bfe81b807c6b9f8c38072f918a42f1f95172563435f1055cd539a1da618b4140
2022/11/04 16:46:50  info unpack layer: sha256:de997a1bb165673c49246454d17ce5cbf614e5e28d43e7abe54165f5e842a240
2022/11/04 16:46:50  warn rootless{usr/lib/x86_64-linux-gnu/gstreamer1.0/gstreamer-1.0/gst-ptp-helper} ignoring (usually) harmless EPERM on setxattr "security.capability"
2022/11/04 16:46:51  info unpack layer: sha256:94ce60f09fb6e736f7e72e7658aaad65ba604097aea318521182907c8ab64b7e
2022/11/04 16:46:51  info unpack layer: sha256:3fdcfdd945808736b96a2c69536235ca075df16d65fe7d47f81f04ae4a9e65ea
2022/11/04 16:46:55  info unpack layer: sha256:31f6a82ab6ff006489fea24f7b2e3e3c08c9179558d9a2044f7a29fee08308fd
2022/11/04 16:46:55  info unpack layer: sha256:acfb0592e029e8773d7dc671eb6e72d6439428ba667aaedfee11af925291f1f2
2022/11/04 16:47:04  info unpack layer: sha256:055356419c4073b0b084d20005361fb3d3392f3ea1dae0504339ec43f9ee0c54
2022/11/04 16:47:04  info unpack layer: sha256:365406f0c6abb593e001d963833e8a6daac5052bc903301b51f1732d031ab879
2022/11/04 16:47:07  info unpack layer: sha256:7c048dbf572113eaa55cc1d198f1d3f926a11dbd2f3886ad2610da3f53c1b2f8
2022/11/04 16:47:07  info unpack layer: sha256:842d1be4787199b67ccbc10001d8784ba7c5065c9fdc58e849b456775d0acfad
2022/11/04 16:47:07  info unpack layer: sha256:f6e9c8e786332a91de53e356f21a8845dc121cc38b87629be97fbdf58cbb7ce2
2022/11/04 16:47:07  info unpack layer: sha256:1c26120ba13404e98d751e2ecbd5252a0f7502b12e5d63c552d46af2abe70e6b
2022/11/04 16:47:08  info unpack layer: sha256:a362609fe4c5ecb9cb38ff3446323cfe81790bf24fb383379f57499edee1bf10
2022/11/04 16:47:08  info unpack layer: sha256:ef895ea8230a063344eeda7fee24caca6e17985c0237f18f49811c01d31baee6
2022/11/04 16:47:08  info unpack layer: sha256:41e486411c60a0123b2fe89db94b976f7e3d5af2ff21602151a4bd683e4b03a6
2022/11/04 16:47:09  info unpack layer: sha256:ae311db4e0262055bfb4b01c59ba9658e67bae79a4943bc6f4322a375ff23db3
2022/11/04 16:47:09  info unpack layer: sha256:830baa40b54429d61ad9fbe3626abb2d88367190060700a852c719e7bf2aa7dc
2022/11/04 16:47:09  info unpack layer: sha256:7ce39dba5cfd81d390a8776b975b0164a26e57019b7723d9c42b85d32f32ded0
2022/11/04 16:47:10  info unpack layer: sha256:74e7f5db2ec79255cec6cb9c105859394fb6c17af212f0013be2fc93a0149612
2022/11/04 16:47:10  info unpack layer: sha256:65faf05e83c259297ce6b85dafefa6a514005212f25f4ae650c2683909af4b77
2022/11/04 16:47:10  info unpack layer: sha256:4f6b65b09dda0bc1302d7a77a7772890fd911ca8fa3d76bdd8701468eca8ee97
2022/11/04 16:47:10  info unpack layer: sha256:e7e65e909d80b9dce81060252a2134ce6ea07759dbbae5281ca5ce5c44d4f33c
2022/11/04 16:47:10  info unpack layer: sha256:01adc54e440ba7749fc17fbe05b69b2a066a6d89660717d2c79bfc38056434dc
2022/11/04 16:47:10  info unpack layer: sha256:092b19dfd5856b024a41672d46011e1d3ff24084c95001448804046b801afeba
2022/11/04 16:47:10  info unpack layer: sha256:0b18efc1cec7046c50198ab755eeaddd1e83024d6ba504655d2bf6e2e894841f
2022/11/04 16:47:11  info unpack layer: sha256:2e60c9f4ae43aa3c2c11533a08c5c6cc0f78ff6ae0669b88c7c86edbd98ff435
2022/11/04 16:47:16  info unpack layer: sha256:5c037c954847406ec894ed6ecda7fad94230b82908bfe4021cacacbd380063d9
2022/11/04 16:47:17  info unpack layer: sha256:c374a4c8613b75bde4c6c03da8accea8af31fd8900e82c9377c1f427517932f5
2022/11/04 16:47:17  info unpack layer: sha256:5062ab97aa7d3113ef8af171a751d5b2a04b12a6f56f48b8de6f8431e56ca881
2022/11/04 16:47:17  info unpack layer: sha256:7271da9b5c5b79f52427723381387be39948b7dffc580cc5eee2484682e58727
2022/11/04 16:47:18  info unpack layer: sha256:e51eea9696ee99711420e6c72419010360336b90e8b00431dc467838dad77b08
2022/11/04 16:47:18  warn rootless{root/.cpanm/work/1644448849.9/Scalar-List-Utils-1.60/blib/lib/List/Util/XS.pm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:18  warn rootless{root/.cpanm/work/1644448849.9/Scalar-List-Utils-1.60/blib/lib/List/Util.pm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:18  warn rootless{root/.cpanm/work/1644448849.9/Scalar-List-Utils-1.60/blib/lib/Scalar/Util.pm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:18  warn rootless{root/.cpanm/work/1644448849.9/Scalar-List-Utils-1.60/blib/lib/Sub/Util.pm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:18  info unpack layer: sha256:0ba23c39d4fe0fc776dbbf3be37024cad713ec7f7f7b445532961e75484e8732
2022/11/04 16:47:18  info unpack layer: sha256:4fd9760de66583c0092ae74c66142d41c36b9da7c9f4fc34f6b599234925db9a
2022/11/04 16:47:18  info unpack layer: sha256:15b115092a02dc0861169eeb25e1bb0c2e02a766f396970b75f836ce06a713aa
2022/11/04 16:47:18  info unpack layer: sha256:0b327e15a8298c31c119d6e7bacd8c91abba5af367054ff67c7c64a7a89a9b9b
2022/11/04 16:47:18  info unpack layer: sha256:b56e4520a380b6e58fac6a224d113bc52c72d04bff0bcc65286cf562798d8be8
2022/11/04 16:47:18  info unpack layer: sha256:115d86b5f8c487e4f96ef6308b2e2ec0decde38d34a279bd2f47d6cb4848f81c
2022/11/04 16:47:18  info unpack layer: sha256:29b8050312c6e29055a929cc94c07ed75f6559a7f31d9f5e67aaa738cc0848cd
2022/11/04 16:47:18  info unpack layer: sha256:5011b70eb0e0bd75272e0e352b39d69cb87ae07362ba0e34d2257e01b3cd7147
2022/11/04 16:47:18  info unpack layer: sha256:2b657240e63489bf4cb9d2d8c55ad5dd48770bd96991a5bbd688a51556a8984f
2022/11/04 16:47:18  info unpack layer: sha256:df8c91e5f89d77f03c3366c9c8913a890fbd0eddccd5f96031839abc34001f7c
2022/11/04 16:47:18  info unpack layer: sha256:2a62e96cb27a0ab2fe76ce0278f86edfcb2cfb40a3e554da87a2407ce8e46a42
2022/11/04 16:47:19  info unpack layer: sha256:2db08b88a669a35970aaf219471279c81ba7b924e75aaaafb70f8ab37d563be3
2022/11/04 16:47:19  info unpack layer: sha256:59b336eefaec5bfbcd1faa3d031cc0615372afaa667a747892870cd9af6279b6
2022/11/04 16:47:19  info unpack layer: sha256:4c449c229731d519f94fc4b9ef4558ddb7c6fcbae966b64ed4f5917fe003793b
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2bed_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2bed_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2bed_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2starch_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2starch_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bam2starch_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bedextract} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bedmap} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/bedops} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/closest-features} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/convert2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gff2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gff2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gtf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gtf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gvf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/gvf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/psl2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/psl2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/rmsk2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/rmsk2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/sam2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/sam2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/sort-bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starch-diff} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starchcat} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starchcluster_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starchcluster_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starchcluster_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/starchstrip} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/unstarch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/update-sort-bed-migrate-candidates} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/update-sort-bed-slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/update-sort-bed-starch-slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/vcf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/vcf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/wig2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  warn rootless{softwares/bedops/bin/wig2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/04 16:47:19  info unpack layer: sha256:e10efda06116428ab3a34796d65d5d81dda0b4a093f4d02b0ccdf563b707e0eb
2022/11/04 16:47:20  info unpack layer: sha256:8822507d45a69cc6e31c37c68428c943b3235dd035f2c899b1421c1bafc3f2a9
2022/11/04 16:47:26  info unpack layer: sha256:4f2bf2260f1e4c5cd348a79c05fd5af5d2740e45e30bba362b09c48de5a17496
2022/11/04 16:47:27  info unpack layer: sha256:9b5c4f827e10fb2bd67ac2e911bbe1c1e4ee247d6fb38552287bd35c6905241d
2022/11/04 16:47:30  info unpack layer: sha256:5b0f41e4c132aac447dfcc4bf72468fc1ca6b48d5a60ad03efb9db82092f6042
2022/11/04 16:47:30  info unpack layer: sha256:ad10175f9b591d92e474e3f11c038974ce710a0a04701c34e7b71708fde17dcb
2022/11/04 16:47:31  info unpack layer: sha256:e84f1ba634b03460a58a24621d3e0c426ee680405831383e303bfc8d3285fa58
2022/11/04 16:47:31  info unpack layer: sha256:612adca843f9e05fff59aba912411016046abf6912c48071755cc525c9373ae4
2022/11/04 16:47:31  info unpack layer: sha256:a7f63483ca08818a89e097d02c99e4a2068f569c7c58a43e8aa0b3aa5680120a
2022/11/04 16:47:31  info unpack layer: sha256:4653e19d0f327f247839d79f7b72e8b08765bd7f98aeb166ad548ec2092e8561
2022/11/04 16:47:33  info unpack layer: sha256:e42914e789575c71344172f78246dc0433a7ad67ec004b1073f31594b2355b1d
INFO:    Creating SIF file...
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_round2_SJ.out.tab: No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final_Log.final.out': No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_round3_SJ.out.tab: No such file or directory
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_round2_SJ.out.tab: No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final_Log.final.out': No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_round3_SJ.out.tab: No such file or directory
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_round1_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_round2_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_round2_SJ.out.tab: No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final_Log.final.out': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final_Unmapped.out.mate1': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final_Unmapped.out.mate2': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final_Log.final.out': No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_round3_SJ.out.tab: No such file or directory
cat: /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_round3_SJ.out.tab: No such file or directory
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final.sortedByCoord.out.bam.
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final.sortedByCoord.out.bam.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final.sortedByCoord.out.bam.
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final.sortedByCoord.out.bam.
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final.sortedByCoord.out.bam.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final.sortedByCoord.out.bam.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final.sortedByCoord.out.bam.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final.sortedByCoord.out.bam.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final.sortedByCoord.out.bam.
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197914_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_final.sortedByCoord.out.bam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197915_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422201_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844295_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422202_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR8422200_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR5197913_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844300_for_psiclass.sam".
[main_samview] fail to read the header from "/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/alignments/SRR9844296_for_psiclass.sam".
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_0.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_1.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_2.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_3.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_4.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_5.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_6.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_7.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_8.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_9.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_10.gtf': No such file or directory
mv: cannot stat '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_vote.gtf': No such file or directory
Traceback (most recent call last):
  File "/softwares/FINDER/Finder/finder", line 688, in <module>
    main()
  File "/softwares/FINDER/Finder/finder", line 649, in main
    orchestrateGeneModelPrediction( options, logger_proxy, logging_mutex )
  File "/softwares/FINDER/Finder/finder", line 461, in orchestrateGeneModelPrediction
    findTranscriptsInEachSampleNotReportedInCombinedAnnotations( options, logger_proxy, logging_mutex )
  File "/softwares/FINDER/Finder/scripts/findTranscriptsInEachSampleNotReportedInCombinedAnnotations.py", line 17, in findTranscriptsInEachSampleNotReportedInCombinedAnnotations
    combined_transcript_info = readAllTranscriptsFromGTFFileInParallel( [combined_gtf_filename, "combined", "combined"] )[0]
  File "/softwares/FINDER/Finder/scripts/fileReadWriteOperations.py", line 290, in readAllTranscriptsFromGTFFileInParallel
    fhr = open( gtf_filename, "r" )
FileNotFoundError: [Errno 2] No such file or directory: '/data/NCBR/projects/NCBR-298/Finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/combined.gtf'