Job ID = 4178397 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,402,523 reads read : 19,402,523 reads written : 19,402,523 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:11 19402523 reads; of these: 19402523 (100.00%) were unpaired; of these: 970162 (5.00%) aligned 0 times 15644716 (80.63%) aligned exactly 1 time 2787645 (14.37%) aligned >1 times 95.00% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 2551358 / 18432361 = 0.1384 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.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 @ Thu, 05 Dec 2019 12:34:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:52: 1000000 INFO @ Thu, 05 Dec 2019 12:35:00: 2000000 INFO @ Thu, 05 Dec 2019 12:35:09: 3000000 INFO @ Thu, 05 Dec 2019 12:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.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 @ Thu, 05 Dec 2019 12:35:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:24: 4000000 INFO @ Thu, 05 Dec 2019 12:35:31: 1000000 INFO @ Thu, 05 Dec 2019 12:35:35: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:35:44: 2000000 INFO @ Thu, 05 Dec 2019 12:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.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 @ Thu, 05 Dec 2019 12:35:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:48: 6000000 INFO @ Thu, 05 Dec 2019 12:35:58: 3000000 INFO @ Thu, 05 Dec 2019 12:36:00: 1000000 INFO @ Thu, 05 Dec 2019 12:36:01: 7000000 INFO @ Thu, 05 Dec 2019 12:36:12: 8000000 INFO @ Thu, 05 Dec 2019 12:36:12: 4000000 INFO @ Thu, 05 Dec 2019 12:36:13: 2000000 INFO @ Thu, 05 Dec 2019 12:36:21: 9000000 INFO @ Thu, 05 Dec 2019 12:36:23: 5000000 INFO @ Thu, 05 Dec 2019 12:36:24: 3000000 INFO @ Thu, 05 Dec 2019 12:36:30: 10000000 INFO @ Thu, 05 Dec 2019 12:36:33: 6000000 INFO @ Thu, 05 Dec 2019 12:36:34: 4000000 INFO @ Thu, 05 Dec 2019 12:36:39: 11000000 INFO @ Thu, 05 Dec 2019 12:36:43: 7000000 INFO @ Thu, 05 Dec 2019 12:36:46: 5000000 INFO @ Thu, 05 Dec 2019 12:36:47: 12000000 INFO @ Thu, 05 Dec 2019 12:36:53: 8000000 INFO @ Thu, 05 Dec 2019 12:36:56: 13000000 INFO @ Thu, 05 Dec 2019 12:36:57: 6000000 INFO @ Thu, 05 Dec 2019 12:37:04: 9000000 INFO @ Thu, 05 Dec 2019 12:37:05: 14000000 INFO @ Thu, 05 Dec 2019 12:37:08: 7000000 INFO @ Thu, 05 Dec 2019 12:37:13: 15000000 INFO @ Thu, 05 Dec 2019 12:37:14: 10000000 INFO @ Thu, 05 Dec 2019 12:37:19: 8000000 INFO @ Thu, 05 Dec 2019 12:37:21: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:21: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:21: #1 total tags in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:37:21: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:37:21: #1 tags after filtering in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:21: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:21: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:23: #2 number of paired peaks: 277 WARNING @ Thu, 05 Dec 2019 12:37:23: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:23: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:23: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:23: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:23: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:23: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 12:37:23: #2 alternative fragment length(s) may be 4,78 bps INFO @ Thu, 05 Dec 2019 12:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05_model.r WARNING @ Thu, 05 Dec 2019 12:37:23: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:37:23: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Thu, 05 Dec 2019 12:37:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:37:23: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:37:25: 11000000 INFO @ Thu, 05 Dec 2019 12:37:30: 9000000 INFO @ Thu, 05 Dec 2019 12:37:34: 12000000 INFO @ Thu, 05 Dec 2019 12:37:41: 10000000 INFO @ Thu, 05 Dec 2019 12:37:44: 13000000 INFO @ Thu, 05 Dec 2019 12:37:51: 11000000 INFO @ Thu, 05 Dec 2019 12:37:54: 14000000 INFO @ Thu, 05 Dec 2019 12:38:02: 12000000 INFO @ Thu, 05 Dec 2019 12:38:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:38:04: 15000000 INFO @ Thu, 05 Dec 2019 12:38:12: 13000000 INFO @ Thu, 05 Dec 2019 12:38:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:38:13: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:38:13: #1 total tags in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:38:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:38:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:38:13: #1 tags after filtering in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:38:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:38:13: #1 finished! INFO @ Thu, 05 Dec 2019 12:38:13: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:38:14: #2 number of paired peaks: 277 WARNING @ Thu, 05 Dec 2019 12:38:14: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Thu, 05 Dec 2019 12:38:14: start model_add_line... INFO @ Thu, 05 Dec 2019 12:38:15: start X-correlation... INFO @ Thu, 05 Dec 2019 12:38:15: end of X-cor INFO @ Thu, 05 Dec 2019 12:38:15: #2 finished! INFO @ Thu, 05 Dec 2019 12:38:15: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 12:38:15: #2 alternative fragment length(s) may be 4,78 bps INFO @ Thu, 05 Dec 2019 12:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10_model.r WARNING @ Thu, 05 Dec 2019 12:38:15: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:38:15: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Thu, 05 Dec 2019 12:38:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:38:15: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:38:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:38:22: 14000000 INFO @ Thu, 05 Dec 2019 12:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.05_summits.bed INFO @ Thu, 05 Dec 2019 12:38:23: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7037 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:38:32: 15000000 INFO @ Thu, 05 Dec 2019 12:38:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:38:41: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:38:41: #1 total tags in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:38:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:38:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:38:41: #1 tags after filtering in treatment: 15881003 INFO @ Thu, 05 Dec 2019 12:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:38:41: #1 finished! INFO @ Thu, 05 Dec 2019 12:38:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:38:43: #2 number of paired peaks: 277 WARNING @ Thu, 05 Dec 2019 12:38:43: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Thu, 05 Dec 2019 12:38:43: start model_add_line... INFO @ Thu, 05 Dec 2019 12:38:43: start X-correlation... INFO @ Thu, 05 Dec 2019 12:38:43: end of X-cor INFO @ Thu, 05 Dec 2019 12:38:43: #2 finished! INFO @ Thu, 05 Dec 2019 12:38:43: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 12:38:43: #2 alternative fragment length(s) may be 4,78 bps INFO @ Thu, 05 Dec 2019 12:38:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20_model.r WARNING @ Thu, 05 Dec 2019 12:38:43: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:38:43: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Thu, 05 Dec 2019 12:38:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:38:43: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:38:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:38:55: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.10_summits.bed INFO @ Thu, 05 Dec 2019 12:39:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3889 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:39:24: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107875/SRX4107875.20_summits.bed INFO @ Thu, 05 Dec 2019 12:39:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1479 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。