Job ID = 2007645 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,675,114 reads read : 1,675,114 reads written : 1,675,114 2019-07-05T07:06:10 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 1,611,775 reads read : 1,611,775 reads written : 1,611,775 spots read : 1,651,832 reads read : 1,651,832 reads written : 1,651,832 spots read : 1,671,942 reads read : 1,671,942 reads written : 1,671,942 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529790.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529791.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529792.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529793.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:04 6610663 reads; of these: 6610663 (100.00%) were unpaired; of these: 323439 (4.89%) aligned 0 times 5168838 (78.19%) aligned exactly 1 time 1118386 (16.92%) aligned >1 times 95.11% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6221908 / 6287224 = 0.9896 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 16:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 16:17:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:17:05: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 16:17:05: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 16:17:05: #1 total tags in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:05: #1 tags after filtering in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:05: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:17:05: #2 number of paired peaks: 298 WARNING @ Fri, 05 Jul 2019 16:17:05: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:05: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:05: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:05: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:05: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:05: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 16:17:05: #2 alternative fragment length(s) may be 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 bps INFO @ Fri, 05 Jul 2019 16:17:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05_model.r WARNING @ Fri, 05 Jul 2019 16:17:05: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:05: #2 You may need to consider one of the other alternative d(s): 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 WARNING @ Fri, 05 Jul 2019 16:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 16:17:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:17:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.05_summits.bed INFO @ Fri, 05 Jul 2019 16:17:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:17:06: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 16:17:06: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 16:17:06: #1 total tags in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:06: #1 tags after filtering in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:06: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:17:06: #2 number of paired peaks: 298 WARNING @ Fri, 05 Jul 2019 16:17:06: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:06: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:06: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:06: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:06: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 16:17:06: #2 alternative fragment length(s) may be 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 bps INFO @ Fri, 05 Jul 2019 16:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10_model.r WARNING @ Fri, 05 Jul 2019 16:17:06: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:06: #2 You may need to consider one of the other alternative d(s): 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 WARNING @ Fri, 05 Jul 2019 16:17:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 16:17:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:17:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:17:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.10_summits.bed INFO @ Fri, 05 Jul 2019 16:17:06: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:17:07: #1 tag size is determined as 146 bps INFO @ Fri, 05 Jul 2019 16:17:07: #1 tag size = 146 INFO @ Fri, 05 Jul 2019 16:17:07: #1 total tags in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:17:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:17:07: #1 tags after filtering in treatment: 65316 INFO @ Fri, 05 Jul 2019 16:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:17:07: #1 finished! INFO @ Fri, 05 Jul 2019 16:17:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:17:07: #2 number of paired peaks: 298 WARNING @ Fri, 05 Jul 2019 16:17:07: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 05 Jul 2019 16:17:07: start model_add_line... INFO @ Fri, 05 Jul 2019 16:17:07: start X-correlation... INFO @ Fri, 05 Jul 2019 16:17:07: end of X-cor INFO @ Fri, 05 Jul 2019 16:17:07: #2 finished! INFO @ Fri, 05 Jul 2019 16:17:07: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 16:17:07: #2 alternative fragment length(s) may be 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 bps INFO @ Fri, 05 Jul 2019 16:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20_model.r WARNING @ Fri, 05 Jul 2019 16:17:07: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:17:07: #2 You may need to consider one of the other alternative d(s): 12,38,66,87,111,139,165,205,248,278,305,332,385,418,434,467,499,525,566,596,598 WARNING @ Fri, 05 Jul 2019 16:17:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:17:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:17:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548243/ERX2548243.20_summits.bed INFO @ Fri, 05 Jul 2019 16:17:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling