make test errors

[marctormo]

Hi,

I'm trying to install signalAlign but I get some errors after make test ( I already copied motif.py and run make in externalTools):

OK (56 tests)

ok test_pysam (main.signalAlignLibTests) ... ERROR test_zymo_reads (main.SignalAlignAlignmentTest) ... FAIL test_pUC_r9_reads_5mer (main.SignalAlignAlignmentTest) ... FAIL test_pUC_r9_reads_6mer (main.SignalAlignAlignmentTest) ... FAIL test_Ecoli1D_reads_5mer (main.SignalAlignAlignmentTest) ... FAIL test_EM (main.signalAlign_EM_test) ... ok

====================================================================== ERROR: test_pysam (main.signalAlignLibTests)

Traceback (most recent call last): File "./testSignalAlign", line 55, in test_pysam query=single_read) File "/gpfs42/robbyfs/homes/aplic/noarch/build_custom/signalAlign/bin/signalAlignLib.py", line 306, in exonerated_bwa query_start, query_end, reference_start, reference_end, cigar_string = parse_cigar(aln[11], int(aln[9])) IndexError: list index out of range

====================================================================== FAIL: test_zymo_reads (main.SignalAlignAlignmentTest)

Traceback (most recent call last): File "./testSignalAlign", line 121, in test_zymo_reads reference=ZYMO_REFERENCE, kmer_length=6, extra_args="--2d ") File "./testSignalAlign", line 97, in check_alignments should=len(glob.glob(true_alignments + "*.tsv")))) AssertionError: Didn't make all alignments got 0 should be 6

====================================================================== FAIL: test_pUC_r9_reads_5mer (main.SignalAlignAlignmentTest)

Traceback (most recent call last): File "./testSignalAlign", line 139, in test_pUC_r9_reads_5mer extra_args="-T=../models/testModelR9_5mer_acegot_template.model " File "./testSignalAlign", line 97, in check_alignments should=len(glob.glob(true_alignments + "*.tsv")))) AssertionError: Didn't make all alignments got 0 should be 10

====================================================================== FAIL: test_pUC_r9_reads_6mer (main.SignalAlignAlignmentTest)

Traceback (most recent call last): File "./testSignalAlign", line 160, in test_pUC_r9_reads_6mer kmer_length=6, extra_args="--2d ") File "./testSignalAlign", line 97, in check_alignments should=len(glob.glob(true_alignments + "*.tsv")))) AssertionError: Didn't make all alignments got 0 should be 10

====================================================================== FAIL: test_Ecoli1D_reads_5mer (main.SignalAlignAlignmentTest)

Traceback (most recent call last): File "./testSignalAlign", line 151, in test_Ecoli1D_reads_5mer extra_args="-T=../models/testModelR9p4_5mer_acegt_template.model ") File "./testSignalAlign", line 97, in check_alignments should=len(glob.glob(true_alignments + "*.tsv")))) AssertionError: Didn't make all alignments got 0 should be 3

---

Ran 7 tests in 97.314s

FAILED (failures=4, errors=1) #cd ././sonLib/bin && ./sonLibTests

Do you know what I'm doing wrong?

Many thanks, Marc