Job ID = 1292415 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,998,110 reads read : 9,996,220 reads written : 4,998,110 reads 0-length : 4,998,110 spots read : 4,879,899 reads read : 9,759,798 reads written : 4,879,899 reads 0-length : 4,879,899 spots read : 4,984,542 reads read : 9,969,084 reads written : 4,984,542 reads 0-length : 4,984,542 spots read : 4,828,879 reads read : 9,657,758 reads written : 4,828,879 reads 0-length : 4,828,879 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: 00:07:31 19691430 reads; of these: 19691430 (100.00%) were unpaired; of these: 272116 (1.38%) aligned 0 times 17227549 (87.49%) aligned exactly 1 time 2191765 (11.13%) aligned >1 times 98.62% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 3674720 / 19419314 = 0.1892 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 @ Sun, 02 Jun 2019 18:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.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 @ Sun, 02 Jun 2019 18:46:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:46:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.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 @ Sun, 02 Jun 2019 18:46:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:46:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.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 @ Sun, 02 Jun 2019 18:46:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:46:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:46:47: 1000000 INFO @ Sun, 02 Jun 2019 18:46:49: 1000000 INFO @ Sun, 02 Jun 2019 18:46:49: 1000000 INFO @ Sun, 02 Jun 2019 18:46:56: 2000000 INFO @ Sun, 02 Jun 2019 18:46:59: 2000000 INFO @ Sun, 02 Jun 2019 18:46:59: 2000000 INFO @ Sun, 02 Jun 2019 18:47:04: 3000000 INFO @ Sun, 02 Jun 2019 18:47:08: 3000000 INFO @ Sun, 02 Jun 2019 18:47:08: 3000000 INFO @ Sun, 02 Jun 2019 18:47:12: 4000000 INFO @ Sun, 02 Jun 2019 18:47:17: 4000000 INFO @ Sun, 02 Jun 2019 18:47:18: 4000000 INFO @ Sun, 02 Jun 2019 18:47:21: 5000000 INFO @ Sun, 02 Jun 2019 18:47:27: 5000000 INFO @ Sun, 02 Jun 2019 18:47:28: 5000000 INFO @ Sun, 02 Jun 2019 18:47:29: 6000000 INFO @ Sun, 02 Jun 2019 18:47:36: 6000000 INFO @ Sun, 02 Jun 2019 18:47:37: 7000000 INFO @ Sun, 02 Jun 2019 18:47:37: 6000000 INFO @ Sun, 02 Jun 2019 18:47:45: 7000000 INFO @ Sun, 02 Jun 2019 18:47:45: 8000000 INFO @ Sun, 02 Jun 2019 18:47:47: 7000000 INFO @ Sun, 02 Jun 2019 18:47:53: 9000000 INFO @ Sun, 02 Jun 2019 18:47:54: 8000000 INFO @ Sun, 02 Jun 2019 18:47:57: 8000000 INFO @ Sun, 02 Jun 2019 18:48:01: 10000000 INFO @ Sun, 02 Jun 2019 18:48:03: 9000000 INFO @ Sun, 02 Jun 2019 18:48:06: 9000000 INFO @ Sun, 02 Jun 2019 18:48:10: 11000000 INFO @ Sun, 02 Jun 2019 18:48:13: 10000000 INFO @ Sun, 02 Jun 2019 18:48:15: 10000000 INFO @ Sun, 02 Jun 2019 18:48:18: 12000000 INFO @ Sun, 02 Jun 2019 18:48:22: 11000000 INFO @ Sun, 02 Jun 2019 18:48:25: 11000000 INFO @ Sun, 02 Jun 2019 18:48:26: 13000000 INFO @ Sun, 02 Jun 2019 18:48:31: 12000000 INFO @ Sun, 02 Jun 2019 18:48:34: 12000000 INFO @ Sun, 02 Jun 2019 18:48:34: 14000000 INFO @ Sun, 02 Jun 2019 18:48:40: 13000000 INFO @ Sun, 02 Jun 2019 18:48:42: 15000000 INFO @ Sun, 02 Jun 2019 18:48:43: 13000000 INFO @ Sun, 02 Jun 2019 18:48:48: #1 tag size is determined as 73 bps INFO @ Sun, 02 Jun 2019 18:48:48: #1 tag size = 73 INFO @ Sun, 02 Jun 2019 18:48:48: #1 total tags in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:48:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:48:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:48:49: #1 tags after filtering in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:48:49: #1 finished! INFO @ Sun, 02 Jun 2019 18:48:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:48:49: 14000000 INFO @ Sun, 02 Jun 2019 18:48:50: #2 number of paired peaks: 594 WARNING @ Sun, 02 Jun 2019 18:48:50: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 02 Jun 2019 18:48:50: start model_add_line... INFO @ Sun, 02 Jun 2019 18:48:50: start X-correlation... INFO @ Sun, 02 Jun 2019 18:48:50: end of X-cor INFO @ Sun, 02 Jun 2019 18:48:50: #2 finished! INFO @ Sun, 02 Jun 2019 18:48:50: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:48:50: #2 alternative fragment length(s) may be 3,105 bps INFO @ Sun, 02 Jun 2019 18:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20_model.r WARNING @ Sun, 02 Jun 2019 18:48:50: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:48:50: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Sun, 02 Jun 2019 18:48:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:48:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:48:52: 14000000 INFO @ Sun, 02 Jun 2019 18:48:58: 15000000 INFO @ Sun, 02 Jun 2019 18:49:02: 15000000 INFO @ Sun, 02 Jun 2019 18:49:05: #1 tag size is determined as 73 bps INFO @ Sun, 02 Jun 2019 18:49:05: #1 tag size = 73 INFO @ Sun, 02 Jun 2019 18:49:05: #1 total tags in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:49:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:49:05: #1 tags after filtering in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:49:05: #1 finished! INFO @ Sun, 02 Jun 2019 18:49:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:49:06: #2 number of paired peaks: 594 WARNING @ Sun, 02 Jun 2019 18:49:06: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 02 Jun 2019 18:49:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:49:07: start X-correlation... INFO @ Sun, 02 Jun 2019 18:49:07: end of X-cor INFO @ Sun, 02 Jun 2019 18:49:07: #2 finished! INFO @ Sun, 02 Jun 2019 18:49:07: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:49:07: #2 alternative fragment length(s) may be 3,105 bps INFO @ Sun, 02 Jun 2019 18:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10_model.r WARNING @ Sun, 02 Jun 2019 18:49:07: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:49:07: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Sun, 02 Jun 2019 18:49:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:49:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:49:08: #1 tag size is determined as 73 bps INFO @ Sun, 02 Jun 2019 18:49:08: #1 tag size = 73 INFO @ Sun, 02 Jun 2019 18:49:08: #1 total tags in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:49:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:49:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:49:09: #1 tags after filtering in treatment: 15744594 INFO @ Sun, 02 Jun 2019 18:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:49:09: #1 finished! INFO @ Sun, 02 Jun 2019 18:49:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:49:10: #2 number of paired peaks: 594 WARNING @ Sun, 02 Jun 2019 18:49:10: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 02 Jun 2019 18:49:10: start model_add_line... INFO @ Sun, 02 Jun 2019 18:49:10: start X-correlation... INFO @ Sun, 02 Jun 2019 18:49:10: end of X-cor INFO @ Sun, 02 Jun 2019 18:49:10: #2 finished! INFO @ Sun, 02 Jun 2019 18:49:10: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:49:10: #2 alternative fragment length(s) may be 3,105 bps INFO @ Sun, 02 Jun 2019 18:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05_model.r WARNING @ Sun, 02 Jun 2019 18:49:10: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:49:10: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Sun, 02 Jun 2019 18:49:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:49:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:49:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:49:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.20_summits.bed INFO @ Sun, 02 Jun 2019 18:49:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:49:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.10_summits.bed INFO @ Sun, 02 Jun 2019 18:50:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3173 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194200/SRX4194200.05_summits.bed INFO @ Sun, 02 Jun 2019 18:50:11: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (9009 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。