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armbrustlab / SEAStAR

SEAStAR is a package of tools supporting the construction of complete analysis pipelines for next-generation (Illumina®, SOLiD™) sequencing data generated from environmental samples.
https://armbrustlab.ocean.washington.edu/tools/seastar/
GNU General Public License v3.0
13 stars 2 forks source link

make test fails when using cmake version 2.8.4 #5

Open aboffin opened 10 years ago

aboffin commented 10 years ago

Hi,

I installed the latest version of SEAStAR from github, the installation steps proceed okay, however, running make test gives the following error:

Running tests...
Test project /home/senthil/git_repos/SEAStAR
      Start 13: ref_select_runs
 1/24 Test #13: ref_select_runs .....................   Passed    0.00 sec
      Start 24: RDP_train_to_heirarchy_test_data
 2/24 Test #24: RDP_train_to_heirarchy_test_data ....   Passed    0.03 sec
      Start 23: fix_fasta_line_lengths_test_data
 3/24 Test #23: fix_fasta_line_lengths_test_data ....***Failed  Required regular expression not found.Regex=[8c8d7485d2e86c55e89b92cdbd15f9fc
]  0.00 sec
      Start 22: graph_ops_scaffolding_test_data
 4/24 Test #22: graph_ops_scaffolding_test_data .....***Failed  Required regular expression not found.Regex=[c07eb882a4ff3a3d00937ae261c41ea0
]  0.05 sec
      Start 21: csfasta2ntfasta_test_data
 5/24 Test #21: csfasta2ntfasta_test_data ...........***Failed  Required regular expression not found.Regex=[185357ad83ec46928edfcc225bcde638
]  0.05 sec
      Start 20: csfasta2fasta_paired_test_data
 6/24 Test #20: csfasta2fasta_paired_test_data ......***Failed  Required regular expression not found.Regex=[587dcdfa4b69f2422172235fb63faf2a
]  0.00 sec
      Start 19: csfasta2fasta_test_data
 7/24 Test #19: csfasta2fasta_test_data .............***Failed  Required regular expression not found.Regex=[b3138e9d395a2ac59e8861b617f8f184
]  0.00 sec
      Start 18: fastq2csfasta_test_data
 8/24 Test #18: fastq2csfasta_test_data .............***Failed  Required regular expression not found.Regex=[9d93279bbd578cbb88d74755d20ee357
]  0.01 sec
      Start 17: tetracalc_test_data
 9/24 Test #17: tetracalc_test_data .................   Passed    0.07 sec
      Start 16: tetracalc_runs
10/24 Test #16: tetracalc_runs ......................   Passed    0.00 sec
      Start 15: ref_select_test_data_no_cat
11/24 Test #15: ref_select_test_data_no_cat .........***Failed  Required regular expression not found.Regex=[39cfeb91807617ca50f2d8c25a8982f2
]  0.00 sec
      Start 14: ref_select_test_data
12/24 Test #14: ref_select_test_data ................***Failed  Required regular expression not found.Regex=[49c3c84716be3120716f48c7ae335906
]  0.00 sec
      Start  1: solid2fastq_runs
13/24 Test  #1: solid2fastq_runs ....................   Passed    0.00 sec
      Start 12: samplefastq_test_data
14/24 Test #12: samplefastq_test_data ...............***Failed  Required regular expression not found.Regex=[e1a7c29691a8542449dcf06c575c3e02
]  0.02 sec
      Start 11: samplefastq_runs
15/24 Test #11: samplefastq_runs ....................   Passed    0.00 sec
      Start 10: trimfastq_singlet_input_test_data
16/24 Test #10: trimfastq_singlet_input_test_data ...***Failed  Required regular expression not found.Regex=[df84824a396d016689ca7a0e35085a15
]  0.01 sec
      Start  9: trimfastq_2singlets_test_data
17/24 Test  #9: trimfastq_2singlets_test_data .......***Failed  Required regular expression not found.Regex=[487481a8b4156040d98295080d5064fa
]  0.01 sec
      Start  8: trimfastq_test_data
18/24 Test  #8: trimfastq_test_data .................***Failed  Required regular expression not found.Regex=[61eb67ca4b9458ef260e9fe19b4a09fb
]  0.01 sec
      Start  7: trimfastq_runs
19/24 Test  #7: trimfastq_runs ......................   Passed    0.00 sec
      Start  6: fastq_nodup_test_data
20/24 Test  #6: fastq_nodup_test_data ...............   Passed    1.83 sec
      Start  5: fastq_nodup_runs
21/24 Test  #5: fastq_nodup_runs ....................   Passed    0.00 sec
      Start  4: solid2fastq_nt_input_test_data
22/24 Test  #4: solid2fastq_nt_input_test_data ......   Passed    2.42 sec
      Start  3: solid2fastq_test_no_suffix
23/24 Test  #3: solid2fastq_test_no_suffix ..........   Passed    1.29 sec
      Start  2: solid2fastq_test_data
24/24 Test  #2: solid2fastq_test_data ...............   Passed    1.33 sec

50% tests passed, 12 tests failed out of 24

Total Test time (real) =   7.17 sec

The following tests FAILED:
     23 - fix_fasta_line_lengths_test_data (Failed)
     22 - graph_ops_scaffolding_test_data (Failed)
     21 - csfasta2ntfasta_test_data (Failed)
     20 - csfasta2fasta_paired_test_data (Failed)
     19 - csfasta2fasta_test_data (Failed)
     18 - fastq2csfasta_test_data (Failed)
     15 - ref_select_test_data_no_cat (Failed)
     14 - ref_select_test_data (Failed)
     12 - samplefastq_test_data (Failed)
     10 - trimfastq_singlet_input_test_data (Failed)
      9 - trimfastq_2singlets_test_data (Failed)
      8 - trimfastq_test_data (Failed)
Errors while running CTest
make: *** [test] Error 8
$ uname -a
Linux deepthought 2.6.37.6 #3 SMP Sat Apr 9 22:49:32 CDT 2011 x86_64 Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz GenuineIntel GNU/Linux

Can you please tell me what is wrong? I have the prerequisites installed (gcc, cmake, gawk, node.js) and they are in PATH.

Thank you,

Sen

vsivsi commented 10 years ago

Take a look at the file Testing/Temporary/LastTest.log and see if there is anything obviously wrong with the output of the trimfastq_test_data test. Most the rest are failing because they depend on the output of that one. If you'd like me to take a look, just throw that whole file in a gist and post a link to it here.

vsivsi commented 10 years ago

It should look like:

8/24 Testing: trimfastq_test_data
8/24 Test: trimfastq_test_data
Command: "/bin/bash" "-c" "/Users/user/SEASTAR/bin/trimfastq -z --prefix=lambda_tst.d90 -p 0.9 -l 34 -m 34 -e 3.0 --add_len --mates_file /Users/user/SEASTAR/output_test_data/lambda_reads_d /Users/user/SEASTAR/output_test_data/lambda_reads_d90; gunzip -c /Users/user/SEASTAR/output_test_data/lambda_reads_d90.{mates,read1,read2,single}.fastq.gz | openssl md5"
Directory: /Users/user/SEASTAR/src_trimfastq
"trimfastq_test_data" start time: Mar 21 22:28 PDT
Output:
----------------------------------------------------------

Warning! read1/read2 files were processed, but no corresponding input singlets were found.

Low complexity reads discarded: Read1: 117, Read2: 59, Singlets: 0 0

Matepairs: Before: 79270, After: 43080
Singlets: Before: 0 0 After: 29596 0
Read1 singlets: 16734, Read2 singlets: 12862, Original singlets: 0 0
Total Reads Processed: 158540, Reads retained: 115756
(stdin)= 61eb67ca4b9458ef260e9fe19b4a09fb
<end of output>
Test time =   1.28 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[61eb67ca4b9458ef260e9fe19b4a09fb
]
"trimfastq_test_data" end time: Mar 21 22:28 PDT
"trimfastq_test_data" time elapsed: 00:00:01
aboffin commented 10 years ago

Hi,

Thank you, here is the entire Testing/Temporary/LastTest.log:

Start testing: Mar 24 19:22 PDT
----------------------------------------------------------
13/24 Testing: ref_select_runs
13/24 Test: ref_select_runs
Command: "/home/sen/git_repos/SEAStAR/bin/ref_select" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_ref_select
"ref_select_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/ref_select version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"ref_select_runs" end time: Mar 24 19:22 PDT
"ref_select_runs" time elapsed: 00:00:00
----------------------------------------------------------

24/24 Testing: RDP_train_to_heirarchy_test_data
24/24 Test: RDP_train_to_heirarchy_test_data
Command: "/usr/bin/bash" "-c" "echo -e '0*Root*-1*0*norank\n1*Bacteria*0*1*domain\n2*Acidobacteria*1*2*phylum\n3*Holophagae*2*3*class\n4*Acanthopleuribacterales*3*4*order\n5*Acanthopleuribacteraceae*4*5*family\n6*Acanthopleuribacter*5*6*genus' | /home/sen/programs/node.js/bin/node /home/sen/git_repos/SEAStAR/bin/RDP_train_to_tree.js | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"RDP_train_to_heirarchy_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
126f51df16a689518a951e13f3983cf8
<end of output>
Test time =   0.03 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[126f51df16a689518a951e13f3983cf8
]
"RDP_train_to_heirarchy_test_data" end time: Mar 24 19:22 PDT
"RDP_train_to_heirarchy_test_data" time elapsed: 00:00:00
----------------------------------------------------------

23/24 Testing: fix_fasta_line_lengths_test_data
23/24 Test: fix_fasta_line_lengths_test_data
Command: "/usr/bin/bash" "-c" "/usr/bin/gawk --re-interval -v minlen=500 -v maxlen=4000 -v ll=80 -f /home/sen/git_repos/SEAStAR/bin/fix_fasta_line_lengths.awk /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_recon.fna | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_recon_fixed_ll.fna | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"fix_fasta_line_lengths_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[8c8d7485d2e86c55e89b92cdbd15f9fc
]
"fix_fasta_line_lengths_test_data" end time: Mar 24 19:22 PDT
"fix_fasta_line_lengths_test_data" time elapsed: 00:00:00
----------------------------------------------------------

22/24 Testing: graph_ops_scaffolding_test_data
22/24 Test: graph_ops_scaffolding_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/programs/node.js/bin/node /home/sen/git_repos/SEAStAR/bin/graph_ops.js /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm.json MST PLUCK PRUNE PUSH INSERT SCAFF DUMP '{"file":"/home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_scaffs.json"}' FASTA '{"scaff":true}' | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_scaffs.fna | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"graph_ops_scaffolding_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
Executing LOAD {"file":"/home/sen/git_repos/SEAStAR/output_test_data/lambda_asm.json"}
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.05 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[c07eb882a4ff3a3d00937ae261c41ea0
]
"graph_ops_scaffolding_test_data" end time: Mar 24 19:22 PDT
"graph_ops_scaffolding_test_data" time elapsed: 00:00:00
----------------------------------------------------------

21/24 Testing: csfasta2ntfasta_test_data
21/24 Test: csfasta2ntfasta_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/programs/node.js/bin/node /home/sen/git_repos/SEAStAR/bin/graph_ops.js /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm.json FASTA | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_recon.fna | /usr/bin/gawk -v numstarts=4 -f /home/sen/git_repos/SEAStAR/bin/csfasta2ntfasta.awk | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_recon_4starts.fasta | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"csfasta2ntfasta_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
Executing LOAD {"file":"/home/sen/git_repos/SEAStAR/output_test_data/lambda_asm.json"}
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.05 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[185357ad83ec46928edfcc225bcde638
]
"csfasta2ntfasta_test_data" end time: Mar 24 19:22 PDT
"csfasta2ntfasta_test_data" time elapsed: 00:00:00
----------------------------------------------------------

20/24 Testing: csfasta2fasta_paired_test_data
20/24 Test: csfasta2fasta_paired_test_data
Command: "/usr/bin/bash" "-c" "/usr/bin/gawk -f /home/sen/git_repos/SEAStAR/bin/csfasta2fasta.awk /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.csfasta /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.csfasta | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.mates.fasta | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"csfasta2fasta_paired_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[587dcdfa4b69f2422172235fb63faf2a
]
"csfasta2fasta_paired_test_data" end time: Mar 24 19:22 PDT
"csfasta2fasta_paired_test_data" time elapsed: 00:00:00
----------------------------------------------------------

19/24 Testing: csfasta2fasta_test_data
19/24 Test: csfasta2fasta_test_data
Command: "/usr/bin/bash" "-c" "/usr/bin/gawk -f /home/sen/git_repos/SEAStAR/bin/csfasta2fasta.awk /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.csfasta | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fasta | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"csfasta2fasta_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[b3138e9d395a2ac59e8861b617f8f184
]
"csfasta2fasta_test_data" end time: Mar 24 19:22 PDT
"csfasta2fasta_test_data" time elapsed: 00:00:00
----------------------------------------------------------

18/24 Testing: fastq2csfasta_test_data
18/24 Test: fastq2csfasta_test_data
Command: "/usr/bin/bash" "-c" "gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.fastq.gz | /usr/bin/gawk -f /home/sen/git_repos/SEAStAR/bin/fastq2csfasta.awk > /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.csfasta; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fastq.gz | /usr/bin/gawk -f /home/sen/git_repos/SEAStAR/bin/fastq2csfasta.awk | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.csfasta | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/scripts
"fastq2csfasta_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fastq.gz: No such file or directory
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.01 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[9d93279bbd578cbb88d74755d20ee357
]
"fastq2csfasta_test_data" end time: Mar 24 19:22 PDT
"fastq2csfasta_test_data" time elapsed: 00:00:00
----------------------------------------------------------

17/24 Testing: tetracalc_test_data
17/24 Test: tetracalc_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/tetracalc --merge_tar=0.99 --chunk=50000 /home/sen/git_repos/SEAStAR/test_data/NC_008209.1.fna /home/sen/git_repos/SEAStAR/test_data/NC_008044.1.fna /home/sen/git_repos/SEAStAR/test_data/NC_007205.1.fna | tee /home/sen/git_repos/SEAStAR/output_test_data/3_alphas_clustered.json | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_tetracalc
"tetracalc_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ab56ec052736ca5c2536028c63b50bf6
<end of output>
Test time =   0.07 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[ab56ec052736ca5c2536028c63b50bf6
]
"tetracalc_test_data" end time: Mar 24 19:22 PDT
"tetracalc_test_data" time elapsed: 00:00:00
----------------------------------------------------------

16/24 Testing: tetracalc_runs
16/24 Test: tetracalc_runs
Command: "/home/sen/git_repos/SEAStAR/bin/tetracalc" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_tetracalc
"tetracalc_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/tetracalc version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"tetracalc_runs" end time: Mar 24 19:22 PDT
"tetracalc_runs" time elapsed: 00:00:00
----------------------------------------------------------

15/24 Testing: ref_select_test_data_no_cat
15/24 Test: ref_select_test_data_no_cat
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/ref_select --per_base --mp_inserts -m --mp_mate_cnt=10 -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.single.fastq.gz -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.fastq.gz -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fastq.gz -q /home/sen/git_repos/SEAStAR/test_data/lambda_reads.read2.fastq.gz_lambda_asm.fasta.sam.gz /home/sen/git_repos/SEAStAR/test_data/lambda_reads.read1.fastq.gz_lambda_asm.fasta.sam.gz /home/sen/git_repos/SEAStAR/test_data/lambda_reads.single.fastq.gz_lambda_asm.fasta.sam.gz | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm_no_cat.json | sed 's/"SEASTAR_tool":[^}]*},//' | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_ref_select
"ref_select_test_data_no_cat" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ERROR: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.single.fastq.gz is not a valid FASTQ file!
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[39cfeb91807617ca50f2d8c25a8982f2
]
"ref_select_test_data_no_cat" end time: Mar 24 19:22 PDT
"ref_select_test_data_no_cat" time elapsed: 00:00:00
----------------------------------------------------------

14/24 Testing: ref_select_test_data
14/24 Test: ref_select_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/ref_select --per_base --mp_inserts -m --mp_mate_cnt=10 -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.single.fastq.gz -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.fastq.gz -r /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fastq.gz -q -c /home/sen/git_repos/SEAStAR/test_data/lambda_asm_catalog.txt.gz /home/sen/git_repos/SEAStAR/test_data/lambda_reads.read2.fastq.gz_lambda_asm.fasta.sam.gz /home/sen/git_repos/SEAStAR/test_data/lambda_reads.read1.fastq.gz_lambda_asm.fasta.sam.gz /home/sen/git_repos/SEAStAR/test_data/lambda_reads.single.fastq.gz_lambda_asm.fasta.sam.gz | tee /home/sen/git_repos/SEAStAR/output_test_data/lambda_asm.json | sed 's/"SEASTAR_tool":[^}]*},//' | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_ref_select
"ref_select_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ERROR: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.single.fastq.gz is not a valid FASTQ file!
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[49c3c84716be3120716f48c7ae335906
]
"ref_select_test_data" end time: Mar 24 19:22 PDT
"ref_select_test_data" time elapsed: 00:00:00
----------------------------------------------------------

1/24 Testing: solid2fastq_runs
1/24 Test: solid2fastq_runs
Command: "/home/sen/git_repos/SEAStAR/bin/solid2fastq" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_solid2fastq
"solid2fastq_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/solid2fastq version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"solid2fastq_runs" end time: Mar 24 19:22 PDT
"solid2fastq_runs" time elapsed: 00:00:00
----------------------------------------------------------

12/24 Testing: samplefastq_test_data
12/24 Test: samplefastq_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/samplefastq -f 0.1 -z /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90 /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_samp; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_samp.{read1,read2,single}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_samplefastq
"samplefastq_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
Error! No reads found in input files, or input(s) not found.
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_samp.read1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_samp.read2.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_samp.single.fastq.gz: No such file or directory
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.02 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[e1a7c29691a8542449dcf06c575c3e02
]
"samplefastq_test_data" end time: Mar 24 19:22 PDT
"samplefastq_test_data" time elapsed: 00:00:00
----------------------------------------------------------

11/24 Testing: samplefastq_runs
11/24 Test: samplefastq_runs
Command: "/home/sen/git_repos/SEAStAR/bin/samplefastq" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_samplefastq
"samplefastq_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/samplefastq version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"samplefastq_runs" end time: Mar 24 19:22 PDT
"samplefastq_runs" time elapsed: 00:00:00
----------------------------------------------------------

10/24 Testing: trimfastq_singlet_input_test_data
10/24 Test: trimfastq_singlet_input_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/trimfastq -z --prefix=lambda_tst.d70 -p 0.7 -l 34 -m 34 -e 3.0 --add_len /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2 /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70; (gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.{read1,read2}.fastq.gz; for f in /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.{single1,single2}.fastq.gz; do gunzip -c $f | /usr/bin/gawk 'NR %4 == 1 {cur=$0; next} {cur = cur $0} NR % 4 == 0 {x[i++] = cur} END {n = asort(x); for (j=1; j<=n; j++) {print x[j]}}'; done) | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_trimfastq
"trimfastq_singlet_input_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ERROR! No reads found in input files, or input(s) not found.
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.read1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.read2.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.single1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d70.single2.fastq.gz: No such file or directory
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.01 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[df84824a396d016689ca7a0e35085a15
]
"trimfastq_singlet_input_test_data" end time: Mar 24 19:22 PDT
"trimfastq_singlet_input_test_data" time elapsed: 00:00:00
----------------------------------------------------------

9/24 Testing: trimfastq_2singlets_test_data
9/24 Test: trimfastq_2singlets_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/trimfastq -z --prefix=lambda_tst.d50s2 -p 0.5 -s -l 34 -m 34 -e 3.0 --add_len /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2.{read1,read2,single1,single2}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_trimfastq
"trimfastq_2singlets_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ERROR! No reads found in input files, or input(s) not found.
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2.read1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2.read2.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2.single1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d50s2.single2.fastq.gz: No such file or directory
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.01 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[487481a8b4156040d98295080d5064fa
]
"trimfastq_2singlets_test_data" end time: Mar 24 19:22 PDT
"trimfastq_2singlets_test_data" time elapsed: 00:00:00
----------------------------------------------------------

8/24 Testing: trimfastq_test_data
8/24 Test: trimfastq_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/trimfastq -z --prefix=lambda_tst.d90 -p 0.9 -l 34 -m 34 -e 3.0 --add_len --mates_file /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.{mates,read1,read2,single}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_trimfastq
"trimfastq_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
ERROR! No reads found in input files, or input(s) not found.
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.mates.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read1.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.read2.fastq.gz: No such file or directory
gzip: /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d90.single.fastq.gz: No such file or directory
d41d8cd98f00b204e9800998ecf8427e
<end of output>
Test time =   0.01 sec
----------------------------------------------------------
Test Fail Reason:
Required regular expression not found.Regex=[61eb67ca4b9458ef260e9fe19b4a09fb
]
"trimfastq_test_data" end time: Mar 24 19:22 PDT
"trimfastq_test_data" time elapsed: 00:00:00
----------------------------------------------------------

7/24 Testing: trimfastq_runs
7/24 Test: trimfastq_runs
Command: "/home/sen/git_repos/SEAStAR/bin/trimfastq" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_trimfastq
"trimfastq_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/trimfastq version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"trimfastq_runs" end time: Mar 24 19:22 PDT
"trimfastq_runs" time elapsed: 00:00:00
----------------------------------------------------------

6/24 Testing: fastq_nodup_test_data
6/24 Test: fastq_nodup_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/fastq_nodup -z --prefix=lambda_tst.d -l 13 -d 2 -e 3 /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_d.{read1,read2}.fastq.gz | openssl md5 "
Directory: /home/sen/git_repos/SEAStAR/src_fastq_nodup
"fastq_nodup_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------

Matepairs: 80374  Rejected: 1104 (1.4%)
Singlets: 0 0  Rejected: 0 0 (-nan%)
c4c8331dd1ffbe372ffe326617854ade
<end of output>
Test time =   1.83 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[c4c8331dd1ffbe372ffe326617854ade
]
"fastq_nodup_test_data" end time: Mar 24 19:22 PDT
"fastq_nodup_test_data" time elapsed: 00:00:01
----------------------------------------------------------

5/24 Testing: fastq_nodup_runs
5/24 Test: fastq_nodup_runs
Command: "/home/sen/git_repos/SEAStAR/bin/fastq_nodup" "--version"
Directory: /home/sen/git_repos/SEAStAR/src_fastq_nodup
"fastq_nodup_runs" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------
/home/sen/git_repos/SEAStAR/bin/fastq_nodup version: v0.4.18
<end of output>
Test time =   0.00 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[version: v0.4.18
]
"fastq_nodup_runs" end time: Mar 24 19:22 PDT
"fastq_nodup_runs" time elapsed: 00:00:00
----------------------------------------------------------

4/24 Testing: solid2fastq_nt_input_test_data
4/24 Test: solid2fastq_nt_input_test_data
Command: "/usr/bin/bash" "-c" "gzip -dc /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads.read1.fastq.gz | /usr/bin/gawk -v EVERY=4 -v HEADSTART=@ -v F3=_F3 -v R3=_R3 'line == 4 {x=0; line=0} NR % 4 == 1 {cnt++;sub(/^[^:]+:/, HEADSTART);sub(/\/2$/, F3);sub(/\/1$/, R3)} cnt % EVERY == 0 {x=1} x == 1 {line++; next} {print}' | gzip >/home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_unsync_default_R3.fastq.gz; gzip -dc /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads.read2.fastq.gz | /usr/bin/gawk -v EVERY=3 -v HEADSTART=@ -v F3=_F3 -v R3=_R3 'line == 4 {x=0; line=0} NR % 4 == 1 {cnt++;sub(/^[^:]+:/, HEADSTART);sub(/\/1$/, R3);sub(/\/2$/, F3)} cnt % EVERY == 0 {x=1} x == 1 {line++; next} {print}' | gzip >/home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_unsync_default_F3.fastq.gz; /home/sen/git_repos/SEAStAR/bin/solid2fastq -b default -z --prefix=lambda_tst /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_unsync /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_sync; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_sync.{read1,read2,single}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_solid2fastq
"solid2fastq_nt_input_test_data" start time: Mar 24 19:22 PDT
Output:
----------------------------------------------------------

Matepairs: 40187, Matepaired Reads: 80374
F3 singlets: 13396, R3 singlets: 20094, Total singlets: 33490
Total Reads Processed: 113864
5c85d2f526c9cc9fb28068e6d33b9283
<end of output>
Test time =   2.42 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[5c85d2f526c9cc9fb28068e6d33b9283
]
"solid2fastq_nt_input_test_data" end time: Mar 24 19:23 PDT
"solid2fastq_nt_input_test_data" time elapsed: 00:00:02
----------------------------------------------------------

3/24 Testing: solid2fastq_test_no_suffix
3/24 Test: solid2fastq_test_no_suffix
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/solid2fastq -z --prefix=lambda_tst --no_suffix /home/sen/git_repos/SEAStAR/test_data/lambda_reads /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_no_suffix; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads_no_suffix.{read1,read2}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_solid2fastq
"solid2fastq_test_no_suffix" start time: Mar 24 19:23 PDT
Output:
----------------------------------------------------------

Matepairs: 80374, Matepaired Reads: 160748
F3 singlets: 0, R3 singlets: 0, Total singlets: 0
Total Reads Processed: 160748
791734e70eb0c93f6db4fa21daf2a263
<end of output>
Test time =   1.29 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[791734e70eb0c93f6db4fa21daf2a263
]
"solid2fastq_test_no_suffix" end time: Mar 24 19:23 PDT
"solid2fastq_test_no_suffix" time elapsed: 00:00:01
----------------------------------------------------------

2/24 Testing: solid2fastq_test_data
2/24 Test: solid2fastq_test_data
Command: "/usr/bin/bash" "-c" "/home/sen/git_repos/SEAStAR/bin/solid2fastq -z --prefix=lambda_tst /home/sen/git_repos/SEAStAR/test_data/lambda_reads /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads; gunzip -c /home/sen/git_repos/SEAStAR/output_test_data/lambda_reads.{read1,read2}.fastq.gz | openssl md5"
Directory: /home/sen/git_repos/SEAStAR/src_solid2fastq
"solid2fastq_test_data" start time: Mar 24 19:23 PDT
Output:
----------------------------------------------------------

Matepairs: 80374, Matepaired Reads: 160748
F3 singlets: 0, R3 singlets: 0, Total singlets: 0
Total Reads Processed: 160748
97925a0daa5e9d31a4b9c746cd0c1ba7
<end of output>
Test time =   1.33 sec
----------------------------------------------------------
Test Pass Reason:
Required regular expression found.Regex=[97925a0daa5e9d31a4b9c746cd0c1ba7
]
"solid2fastq_test_data" end time: Mar 24 19:23 PDT
"solid2fastq_test_data" time elapsed: 00:00:01
----------------------------------------------------------

End testing: Mar 24 19:23 PDT
vsivsi commented 10 years ago

Very strange... The tests appear to be failing because they aren't running in the correct order. Many of the tests require the output from a previous test as input, so they must run in succession to succeed. The log above shows the tests running in nearly reverse order. I've never seen this before. What version of cmake are you using?

vsivsi commented 10 years ago

Adding more information... I can confirm that the tests run correctly with cmake 2.8.12.2 (the current latest release). It looks like there was at least one version of cmake (2.8.4) where this was a known bug. See: http://public.kitware.com/Bug/view.php?id=11877

So if you are running cmake 2.8.4, the solution is easy: upgrade cmake to the latest version. If not, we'll need to dig in a bit further.

aboffin commented 10 years ago

Hi, Updating cmake from 2.8.4 to 2.8.12.2 solved the problem. All tests pass now, I am closing this issue.

Thanks for your help, Sen

~/git_repos/SEAStAR $ make test
Running tests...
Test project /home/sen/git_repos/SEAStAR
      Start  1: solid2fastq_runs
 1/24 Test  #1: solid2fastq_runs ....................   Passed    0.00 sec
      Start  2: solid2fastq_test_data
 2/24 Test  #2: solid2fastq_test_data ...............   Passed    1.27 sec
      Start  3: solid2fastq_test_no_suffix
 3/24 Test  #3: solid2fastq_test_no_suffix ..........   Passed    1.26 sec
      Start  4: solid2fastq_nt_input_test_data
 4/24 Test  #4: solid2fastq_nt_input_test_data ......   Passed    2.45 sec
      Start  5: fastq_nodup_runs
 5/24 Test  #5: fastq_nodup_runs ....................   Passed    0.00 sec
      Start  6: fastq_nodup_test_data
 6/24 Test  #6: fastq_nodup_test_data ...............   Passed    1.73 sec
      Start  7: trimfastq_runs
 7/24 Test  #7: trimfastq_runs ......................   Passed    0.00 sec
      Start  8: trimfastq_test_data
 8/24 Test  #8: trimfastq_test_data .................   Passed    1.36 sec
      Start  9: trimfastq_2singlets_test_data
 9/24 Test  #9: trimfastq_2singlets_test_data .......   Passed    1.03 sec
      Start 10: trimfastq_singlet_input_test_data
10/24 Test #10: trimfastq_singlet_input_test_data ...   Passed    1.03 sec
      Start 11: samplefastq_runs
11/24 Test #11: samplefastq_runs ....................   Passed    0.00 sec
      Start 12: samplefastq_test_data
12/24 Test #12: samplefastq_test_data ...............   Passed    0.13 sec
      Start 13: ref_select_runs
13/24 Test #13: ref_select_runs .....................   Passed    0.00 sec
      Start 14: ref_select_test_data
14/24 Test #14: ref_select_test_data ................   Passed    0.85 sec
      Start 15: ref_select_test_data_no_cat
15/24 Test #15: ref_select_test_data_no_cat .........   Passed    2.22 sec
      Start 16: tetracalc_runs
16/24 Test #16: tetracalc_runs ......................   Passed    0.00 sec
      Start 17: tetracalc_test_data
17/24 Test #17: tetracalc_test_data .................   Passed    0.07 sec
      Start 18: fastq2csfasta_test_data
18/24 Test #18: fastq2csfasta_test_data .............   Passed    1.94 sec
      Start 19: csfasta2fasta_test_data
19/24 Test #19: csfasta2fasta_test_data .............   Passed    0.87 sec
      Start 20: csfasta2fasta_paired_test_data
20/24 Test #20: csfasta2fasta_paired_test_data ......   Passed    1.69 sec
      Start 21: csfasta2ntfasta_test_data
21/24 Test #21: csfasta2ntfasta_test_data ...........   Passed    0.21 sec
      Start 22: graph_ops_scaffolding_test_data
22/24 Test #22: graph_ops_scaffolding_test_data .....   Passed    0.35 sec
      Start 23: fix_fasta_line_lengths_test_data
23/24 Test #23: fix_fasta_line_lengths_test_data ....   Passed    0.00 sec
      Start 24: RDP_train_to_heirarchy_test_data
24/24 Test #24: RDP_train_to_heirarchy_test_data ....   Passed    0.03 sec

100% tests passed, 0 tests failed out of 24

Total Test time (real) =  18.51 sec
vsivsi commented 10 years ago

I'm going to reopen this for now so it's visible to others until we release an update that checks for this case and fails in a more informative manner. Glad I could help.