64]: 12760 nodes, 9679 edges, r 1 Converged after 64 iterations num_edges: 4463 num_nodes: 12760 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23573 Broken pipe cat ${FILE} 23574 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23580 Broken pipe cat ${FILE} 23581 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23586 Broken pipe cat ${FILE} 23587 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23592 Broken pipe cat ${FILE} 23593 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23598 Broken pipe cat ${FILE} 23599 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23604 Broken pipe cat ${FILE} 23605 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23610 Broken pipe cat ${FILE} 23611 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23616 Broken pipe cat ${FILE} 23617 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23622 Broken pipe cat ${FILE} 23623 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23628 Broken pipe cat ${FILE} 23629 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23634 Broken pipe cat ${FILE} 23635 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23640 Broken pipe cat ${FILE} 23641 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23646 Broken pipe cat ${FILE} 23647 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23652 Broken pipe cat ${FILE} 23653 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23658 Broken pipe cat ${FILE} 23659 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23664 Broken pipe cat ${FILE} 23665 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23670 Broken pipe cat ${FILE} 23671 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23676 Broken pipe cat ${FILE} 23677 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23682 Broken pipe cat ${FILE} 23683 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23688 Broken pipe cat ${FILE} 23689 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23694 Broken pipe cat ${FILE} 23695 Aborted (core dumped) | ${CNVER_FOLDER}/bwtie_concise_to_binary 1 Using window_size 200, num_bins 50 make_gc_map: make_gc_map.c:324: main: Assertion `bin=0' failed. /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 171: 23722 Done cat $f 23723 Aborted (core dumped) | ${CNVER_FOLDER}/make_gc_map ${FASTA_FILES_FOLDER}/${CONTIG}.fa ${CONTIG}.masks - ${CONTIG} 200 50 /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 171: 23782 Aborted (core dumped) ${CNVER_FOLDER}/make_donor_graph ${REFERENCE_GRAPH_FOLDER}/${CONTIG}.graph ${DONOR_EDGES_FOLDER}/links.${CONTIG} ${AUX_DATA_FOLDER}/${CONTIG}.scov ${AUX_DATA_FOLDER}/${CONTIG}.masks /dev/null ${AUX_DATA_FOLDER}/${CONTIG}.gc > ${CONTIG}.problem 2> ${CONTIG}.graphinfo AA 0 line 1 of input - bad value of a parameter in the problem line