ValueError: could not convert string to float

[SL1993]

Hi, I tried SJARACNe(v. 0.2.1) with my own expression matrix prepared by Network reconstruction pipeline from NetBID2. Everything looked fine until it threw this error in Create an enhanced consensus network part:

File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/bin/create_consensus_network.py", line 209, in create_enhanced_consensus_network exp_values2 = exp_symbol_values2[1:].astype(float) ValueError: could not convert string to float: 'RPL10'

In which 'RPL10' is a genesymbol.

The error resulted in a truncated consensus_networkncol.txt file, which apparently contained only part of network data.

Code and ouput is listed below.

sjaracne local -e ./test/input/input.exp -g ./test/input/tf.txt -n 2 -o ./test/output/SJARACNE_tf_out.final -pc 1.0

INFO:root:test/output/SJARACNE_tf_out.final/sjaracne_workflow.yml INFO:root:exp_file: class: File path: /home/user01/work/TF/test/input/input.exp probe_file: class: File path: /home/user01/work/TF/test/input/tf.txt p_value_consensus: 1.0 p_value_bootstrap: 1e-07 depth: 40 aracne_config_dir: class: Directory path: /home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/config bootstrap_num: 2 final_out_dir_name: SJARACNE_tf_out.final3 INFO:root:cwltool --parallel --outdir ./test/output/SJARACNE_tf_out.final /home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl test/output/SJARACNE_tf_out.final/sjaracne_workflow.yml INFO /home/user01/.conda/envs/py376/bin/cwltool 3.1.20220628170238 INFO Resolved '/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl' to 'file:///home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl' INFO [workflow ] starting step validate_files INFO [workflow ] start INFO [step validate_files] start INFO [workflow ] starting step ch_ending_exp INFO [step ch_ending_exp] start INFO [workflow ] starting step create_adjmat_names INFO [step create_adjmat_names] start INFO [workflow ] starting step ch_ending_probe INFO [step ch_ending_probe] start INFO [workflow ] starting step create_seeds INFO [step create_seeds] start INFO [job validate_files] /tmp/t70am_xd$ QC_input.py \ -e \ input.exp \ -g \ tf.txt INFO [job ch_ending_exp] /tmp/duo1yet9$ ch_line_ending.py \ -i \ input.exp INFO [job ch_ending_probe] /tmp/gvzv619s$ ch_line_ending.py \ -i \ tf.txt Unix line ending. No need to convert Unix line ending. No need to convert INFO [step create_seeds] completed success INFO [step create_adjmat_names] completed success INFO [job ch_ending_probe] completed success INFO [step ch_ending_probe] completed success INFO [job ch_ending_exp] completed success INFO [step ch_ending_exp] completed success INFO [workflow ] starting step bootstrap INFO [step bootstrap] start INFO [step bootstrap] start INFO [job bootstrap] /tmp/omfn6w8x$ sjaracne.exe \ -i \ /tmp/znbymlqn/stg839d274f-f440-4d80-9760-ff7437272384/input.exp \ -l \ /tmp/znbymlqn/stgdd1763b7-4abb-4450-ac9e-d52f3785d9c1/tf.txt \ -s \ /tmp/znbymlqn/stgdd1763b7-4abb-4450-ac9e-d52f3785d9c1/tf.txt \ -p \ 1e-07 \ -e \ 0 \ -a \ adaptive_partitioning \ -r \ 1 \ -H \ /tmp/znbymlqn/stg167fb5f1-5fe6-44e0-a222-28f89c4905db/config \ -N \ 40 \ -o \ TF_run_001.adj \ -S \ 1 INFO [job bootstrap_2] /tmp/4pzzy3tu$ sjaracne.exe \ -i \ /tmp/dhfpex2z/stg36ff59ea-6b99-4a8b-9dce-312ee18d8abe/input.exp \ -l \ /tmp/dhfpex2z/stg291b2ea6-7b1e-4b82-aef9-3cc80d86b4ae/tf.txt \ -s \ /tmp/dhfpex2z/stg291b2ea6-7b1e-4b82-aef9-3cc80d86b4ae/tf.txt \ -p \ 1e-07 \ -e \ 0 \ -a \ adaptive_partitioning \ -r \ 1 \ -H \ /tmp/dhfpex2z/stgcf32d1a8-ebd0-4275-9d53-89b75752c169/config \ -N \ 40 \ -o \ TF_run_002.adj \ -S \ 2 Displaying parameters

[PARA] Input file: /tmp/znbymlqn/stg839d274f-f440-4d80-9760-ff7437272384/input.exp [PARA] Output file: TF_run_001.adj [PARA] MI P-value: 1e-07 [PARA] DPI tolerance: 0 [PARA] Subset of probes to reconstruct: /tmp/znbymlqn/stgdd1763b7-4abb-4450-ac9e-d52f3785d9c1/tf.txt (1904) [PARA] TF annotation list: /tmp/znbymlqn/stgdd1763b7-4abb-4450-ac9e-d52f3785d9c1/tf.txt (1904) [PARA] Npar limit: 40

[READ] 0 Description lines bypassed. [READ] P-value columns not found. Displaying parameters

[PARA] Input file: /tmp/dhfpex2z/stg36ff59ea-6b99-4a8b-9dce-312ee18d8abe/input.exp [PARA] Output file: TF_run_002.adj [PARA] MI P-value: 1e-07 [PARA] DPI tolerance: 0 [PARA] Subset of probes to reconstruct: /tmp/dhfpex2z/stg291b2ea6-7b1e-4b82-aef9-3cc80d86b4ae/tf.txt (1904) [PARA] TF annotation list: /tmp/dhfpex2z/stg291b2ea6-7b1e-4b82-aef9-3cc80d86b4ae/tf.txt (1904) [PARA] Npar limit: 40

[READ] 0 Description lines bypassed. [READ] P-value columns not found. INFO:root:Number of genes in expression matrix: 17870 INFO:root:Number of hub genes in probe file: 1904 INFO [job validate_files] Max memory used: 10MiB INFO [job validate_files] completed success INFO [step validate_files] completed success Marker No: 17870 (17870 active), Array No: 504 MI threshold determined for p=1e-07: 0.0466551 Marker No: 17870 (17870 active), Array No: 504 MI threshold determined for p=1e-07: 0.0466551 10%, time: 269 10%, time: 271 20%, time: 536 20%, time: 541 30%, time: 802 30%, time: 810 40%, time: 1070 40%, time: 1079 50%, time: 1338 50%, time: 1350 60%, time: 1607 60%, time: 1620 70%, time: 1878 70%, time: 1894 80%, time: 2149 80%, time: 2167 90%, time: 2419 90%, time: 2440 Gene: 1904 Time: 2681 [NETWORK] Applying DPI ... Gene: 1904 Time: 2703 [NETWORK] Applying DPI ... DPI running time is: 65 Writing matrix: TF_run_001.adj Maximum observed npar: 6 INFO [job bootstrap] Max memory used: 56MiB INFO [job bootstrap] completed success DPI running time is: 70 Writing matrix: TF_run_002.adj Maximum observed npar: 7 INFO [job bootstrap_2] Max memory used: 55MiB INFO [job bootstrap_2] completed success INFO [step bootstrap] completed success INFO [workflow ] starting step copy_to_dir INFO [step copy_to_dir] start INFO [step copy_to_dir] completed success INFO [workflow ] starting step consensus INFO [step consensus] start INFO [job consensus] /tmp/zumrko8m$ create_consensus_network.py \ -a \ /tmp/e77t3_ny/stg4146412a-620d-464f-a257-850774127920/SJARACNE_tf_out.final \ -p \ 1.0 \ -e \ /tmp/e77t3_ny/stgda616f26-f6ff-4324-a681-aef2f1a329f3/input.exp \ -o \ SJARACNE_tf_out.final INFO:root:Create an initial consensus network ... INFO:root:Done INFO:root:Create an enhanced consensus network ... Traceback (most recent call last): File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/bin/create_consensus_network.py", line 251, in main() File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/bin/create_consensus_network.py", line 35, in main create_enhanced_consensus_network(args.exp_mat, network, args.out_dir, args.subnet) File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/bin/create_consensus_network.py", line 209, in create_enhanced_consensus_network exp_values2 = exp_symbol_values2[1:].astype(float) ValueError: could not convert string to float: 'RPL10' INFO [job consensus] Max memory used: 150MiB WARNING [job consensus] exited with status: 1 WARNING [job consensus] completed permanentFail WARNING [step consensus] completed permanentFail INFO [workflow ] completed permanentFail { "out_dir": { "location": "file:///home/user01/work/TF/test/output/SJARACNE_tf_out.final/consensus_networkncol.txt", "basename": "consensus_networkncol.txt", "class": "File", "checksum": "sha1$0d567f2e690e217b4aaf4095dfb7bdd2dac934c4", "size": 12339, "path": "/home/user01/work/TF/test/output/SJARACNE_tf_out.final/consensus_networkncol.txt" } } WARNING Final process status is permanentFail Traceback (most recent call last): File "/home/user01/.conda/envs/py376/bin/sjaracne", line 33, in sys.exit(load_entry_point('SJARACNe==0.2.1', 'console_scripts', 'sjaracne')()) File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/sjaracne.py", line 99, in main run_shell_command_call(cmd) File "/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/sjaracne.py", line 110, in run_shell_command_call subprocess.check_call(cmd_to_exec) File "/home/user01/.conda/envs/py376/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cwltool', '--parallel', '--outdir', './test/output/SJARACNE_tf_out.final', '/home/user01/.conda/envs/py376/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl', 'test/output/SJARACNE_tf_out.final/sjaracne_workflow.yml']' returned non-zero exit status 1.

After checking Input.exp file, i found SJARACNe recognized another gene , "MRPL10"(a mitochondrial ribosomal protein), as an isoform of "RPL10", which it isn't, and tranformed isoformId "MRPL10" to "RPL10", leaving duplicated isoformIds.

Is there any solution for this error?

BTW, is it necessary to set a random seed for a reproducible result, how to set it in linux command line?

Thanks.

[karlie002]

Hi ! I just met the same error message as you posted ' [READ] P-value columns not found. ' . Does this message matters when running sjaracne local ??