Job ID = 1290612 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,069,535 reads read : 10,069,535 reads written : 10,069,535 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:06 10069535 reads; of these: 10069535 (100.00%) were unpaired; of these: 91655 (0.91%) aligned 0 times 8722543 (86.62%) aligned exactly 1 time 1255337 (12.47%) aligned >1 times 99.09% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1128388 / 9977880 = 0.1131 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 @ Sat, 01 Jun 2019 21:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 01 Jun 2019 21:50:20: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:20: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 01 Jun 2019 21:50:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 01 Jun 2019 21:50:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:31: 1000000 INFO @ Sat, 01 Jun 2019 21:50:31: 1000000 INFO @ Sat, 01 Jun 2019 21:50:32: 1000000 INFO @ Sat, 01 Jun 2019 21:50:42: 2000000 INFO @ Sat, 01 Jun 2019 21:50:42: 2000000 INFO @ Sat, 01 Jun 2019 21:50:43: 2000000 INFO @ Sat, 01 Jun 2019 21:50:52: 3000000 INFO @ Sat, 01 Jun 2019 21:50:53: 3000000 INFO @ Sat, 01 Jun 2019 21:50:53: 3000000 INFO @ Sat, 01 Jun 2019 21:51:02: 4000000 INFO @ Sat, 01 Jun 2019 21:51:03: 4000000 INFO @ Sat, 01 Jun 2019 21:51:04: 4000000 INFO @ Sat, 01 Jun 2019 21:51:12: 5000000 INFO @ Sat, 01 Jun 2019 21:51:12: 5000000 INFO @ Sat, 01 Jun 2019 21:51:14: 5000000 INFO @ Sat, 01 Jun 2019 21:51:22: 6000000 INFO @ Sat, 01 Jun 2019 21:51:22: 6000000 INFO @ Sat, 01 Jun 2019 21:51:24: 6000000 INFO @ Sat, 01 Jun 2019 21:51:32: 7000000 INFO @ Sat, 01 Jun 2019 21:51:32: 7000000 INFO @ Sat, 01 Jun 2019 21:51:34: 7000000 INFO @ Sat, 01 Jun 2019 21:51:42: 8000000 INFO @ Sat, 01 Jun 2019 21:51:42: 8000000 INFO @ Sat, 01 Jun 2019 21:51:44: 8000000 INFO @ Sat, 01 Jun 2019 21:51:51: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:51: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:51: #1 total tags in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:51: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:51: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:51: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:51: #1 total tags in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:51: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:51: #1 tags after filtering in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:51: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:51: #1 tags after filtering in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:51: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #2 number of paired peaks: 179 WARNING @ Sat, 01 Jun 2019 21:51:52: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:52: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:52: #2 number of paired peaks: 179 WARNING @ Sat, 01 Jun 2019 21:51:52: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:52: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:52: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:52: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:52: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:52: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2 alternative fragment length(s) may be 3,49,165,464,516,598 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20_model.r WARNING @ Sat, 01 Jun 2019 21:51:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:52: #2 You may need to consider one of the other alternative d(s): 3,49,165,464,516,598 WARNING @ Sat, 01 Jun 2019 21:51:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:52: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:52: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:52: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:52: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:52: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2 alternative fragment length(s) may be 3,49,165,464,516,598 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10_model.r WARNING @ Sat, 01 Jun 2019 21:51:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:52: #2 You may need to consider one of the other alternative d(s): 3,49,165,464,516,598 WARNING @ Sat, 01 Jun 2019 21:51:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:52: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:53: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:53: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:53: #1 total tags in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:53: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:53: #1 tags after filtering in treatment: 8849492 INFO @ Sat, 01 Jun 2019 21:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:53: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:53: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:54: #2 number of paired peaks: 179 WARNING @ Sat, 01 Jun 2019 21:51:54: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:54: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:54: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:54: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:54: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:54: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:51:54: #2 alternative fragment length(s) may be 3,49,165,464,516,598 bps INFO @ Sat, 01 Jun 2019 21:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05_model.r WARNING @ Sat, 01 Jun 2019 21:51:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:54: #2 You may need to consider one of the other alternative d(s): 3,49,165,464,516,598 WARNING @ Sat, 01 Jun 2019 21:51:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:54: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:20: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.20_summits.bed INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:32: Done! INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350750/SRX2350750.05_summits.bed INFO @ Sat, 01 Jun 2019 21:52:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。