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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
84 stars 16 forks source link

Problems: did not produce the out files even the job was success #15

Closed luongphekidz07 closed 4 years ago

luongphekidz07 commented 4 years ago

Dear experts,

I would like to receive your help in running isescan,

I typed: isescan.py /scratch/lephuong07/isescan/E97.fasta /scratch/lephuong07/isescan/proteome /scratch/lephuong07/isescan/hmm

and I received the log files: ***Start_time: Tue Nov 12 11:13:19 KST 2019 isPredict begins at Tue Nov 12 11:13:21 2019

Begin to translate genome into proteome. /home/lephuong07/anaconda3/bin/FragGeneScan -s /scratch/lephuong07/isescan/E97.fasta -o /scratch/lephuong07/isescan/proteome/isescan/E97.fasta -w 0 -t illumina_5 -p 4 Using 4 threads. no. of seqs: 142 Clock time used (by 4 threads) = 0.21 mins prepare gff file.. Time elapsed: 0 hours 0 minutes and 4 seconds. Translating genome into proteome for /scratch/lephuong07/isescan/E97.fasta , return 0

Finish translating genome into proteome. Tue Nov 12 11:13:25 2019

Begin to phmmer search against proteome database. Tue Nov 12 11:13:25 2019 Finish phmmer searching /home/lephuong07/anaconda3/bin/pHMMs/clusters.single.faa against /scratch/lephuong07/isescan/proteome/isescan/E97.fasta.faa , output /scratch/lephuong07/isescan/hmm/isescan/clusters.single.faa.E97.fasta.faa

Finish phmmer searching against proteome database. Tue Nov 12 11:24:54 2019

Begin to profile HMM search against proteome database. Tue Nov 12 11:24:54 2019 Finish Profile HMM searching /home/lephuong07/anaconda3/bin/pHMMs/clusters.faa.hmm against /scratch/lephuong07/isescan/proteome/isescan/E97.fasta.faa , output /scratch/lephuong07/isescan/hmm/isescan/clusters.faa.hmm.E97.fasta.faa

Finish profile HMM searching against proteome database. Tue Nov 12 11:35:20 2019 pred begins at Tue Nov 12 11:35:20 2019

NODE_3_length_335243_cov_69.9765: no intersected hits found NODE_40_length_26361_cov_65.9784: no intersected hits found NODE_41_length_24724_cov_72.5998: 2 intersected hits found, do clustering to pick the representative hit for each cluster NODE_43_length_24389_cov_76.7189: no intersected hits found NODE_45_length_22361_cov_78.7038: no intersected hits found NODE_44_length_23258_cov_78.8783: 2 intersected hits found, do clustering to pick the representative hit for each cluster NODE_47_length_20085_cov_76.1527: no intersected hits found NODE_49_length_19174_cov_74.4346: no intersected hits found NODE_50_length_14775_cov_63.214: no intersected hits found NODE_53_length_11686_cov_75.764: no intersected hits found NODE_55_length_10058_cov_134.567: no intersected hits found NODE_57_length_8985_cov_67.552: no intersected hits found NODE_5_length_268228_cov_67.8102: no intersected hits found NODE_61_length_6239_cov_77.0816: no intersected hits found NODE_73_length_2583_cov_222.032: no intersected hits found NODE_74_length_2532_cov_282.28: no intersected hits found NODE_80_length_1888_cov_151.026: no intersected hits found NODE_85_length_1656_cov_1411.77: no intersected hits found NODE_87_length_1643_cov_121.001: no intersected hits found NODE_89_length_1457_cov_202.582: 2 intersected hits found, do clustering to pick the representative hit for each cluster NODE_8_length_191062_cov_77.8905: no intersected hits found NODE_90_length_1443_cov_274.112: no intersected hits found NODE_91_length_1433_cov_137.664: no intersected hits found NODE_92_length_1319_cov_70.8893: no intersected hits found NODE_93_length_1315_cov_52.3375: no intersected hits found NODE_95_length_1250_cov_351.89: no intersected hits found NODE_97_length_1232_cov_151.111: no intersected hits found NODE_68_length_3478_cov_239.767: no intersected hits found Finish removeOverlappedHits at Tue Nov 12 11:35:35 2019 Begin reading protein database at Tue Nov 12 11:35:35 2019 Finish reading protein database at Tue Nov 12 11:35:35 2019 End in pred Tue Nov 12 11:35:35 2019 Both complete and partial IS elements are reported. isPredict ends at Tue Nov 12 11:35:35 2019

Job_exited_code: 0 (Success)

***End_time: Tue Nov 12 11:35:35 KST 2019

but there no out files such as .fna.sum; .fna.raw; .fna.is.fna, etc

I am using the fasta file as the input file, is there any problem with this?

Thank you very much,

Yours sincerely, Le Phuong.

luongphekidz07 commented 4 years ago

Dear experts, I am sorry, I found the "prediction" folder in the working directory, I would like to close this issue, Thank you very much,