Job ID = 4178393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,333,763 reads read : 21,333,763 reads written : 21,333,763 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: 00:04:32 21333763 reads; of these: 21333763 (100.00%) were unpaired; of these: 1366504 (6.41%) aligned 0 times 17469065 (81.88%) aligned exactly 1 time 2498194 (11.71%) aligned >1 times 93.59% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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 12 files... [bam_rmdupse_core] 3591566 / 19967259 = 0.1799 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.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 12:33:54: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:54: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:04: 1000000 INFO @ Thu, 05 Dec 2019 12:34:14: 2000000 INFO @ Thu, 05 Dec 2019 12:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.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 12:34:23: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:23: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:23: 3000000 INFO @ Thu, 05 Dec 2019 12:34:31: 1000000 INFO @ Thu, 05 Dec 2019 12:34:33: 4000000 INFO @ Thu, 05 Dec 2019 12:34:38: 2000000 INFO @ Thu, 05 Dec 2019 12:34:44: 5000000 INFO @ Thu, 05 Dec 2019 12:34:48: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.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 12:34:53: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:53: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:55: 6000000 INFO @ Thu, 05 Dec 2019 12:34:56: 4000000 INFO @ Thu, 05 Dec 2019 12:35:02: 1000000 INFO @ Thu, 05 Dec 2019 12:35:04: 5000000 INFO @ Thu, 05 Dec 2019 12:35:05: 7000000 INFO @ Thu, 05 Dec 2019 12:35:10: 2000000 INFO @ Thu, 05 Dec 2019 12:35:11: 6000000 INFO @ Thu, 05 Dec 2019 12:35:15: 8000000 INFO @ Thu, 05 Dec 2019 12:35:18: 3000000 INFO @ Thu, 05 Dec 2019 12:35:19: 7000000 INFO @ Thu, 05 Dec 2019 12:35:25: 9000000 INFO @ Thu, 05 Dec 2019 12:35:26: 8000000 INFO @ Thu, 05 Dec 2019 12:35:26: 4000000 INFO @ Thu, 05 Dec 2019 12:35:34: 9000000 INFO @ Thu, 05 Dec 2019 12:35:35: 5000000 INFO @ Thu, 05 Dec 2019 12:35:35: 10000000 INFO @ Thu, 05 Dec 2019 12:35:41: 10000000 INFO @ Thu, 05 Dec 2019 12:35:43: 6000000 INFO @ Thu, 05 Dec 2019 12:35:45: 11000000 INFO @ Thu, 05 Dec 2019 12:35:49: 11000000 INFO @ Thu, 05 Dec 2019 12:35:51: 7000000 INFO @ Thu, 05 Dec 2019 12:35:55: 12000000 INFO @ Thu, 05 Dec 2019 12:35:56: 12000000 INFO @ Thu, 05 Dec 2019 12:36:00: 8000000 INFO @ Thu, 05 Dec 2019 12:36:04: 13000000 INFO @ Thu, 05 Dec 2019 12:36:05: 13000000 INFO @ Thu, 05 Dec 2019 12:36:08: 9000000 INFO @ Thu, 05 Dec 2019 12:36:12: 14000000 INFO @ Thu, 05 Dec 2019 12:36:16: 14000000 INFO @ Thu, 05 Dec 2019 12:36:16: 10000000 INFO @ Thu, 05 Dec 2019 12:36:19: 15000000 INFO @ Thu, 05 Dec 2019 12:36:24: 11000000 INFO @ Thu, 05 Dec 2019 12:36:26: 15000000 INFO @ Thu, 05 Dec 2019 12:36:27: 16000000 INFO @ Thu, 05 Dec 2019 12:36:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:29: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:29: #1 total tags in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:36:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:29: #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 12:36:30: #1 tags after filtering in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:30: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:30: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:31: #2 number of paired peaks: 596 WARNING @ Thu, 05 Dec 2019 12:36:31: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:31: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:31: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:31: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:31: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:31: #2 predicted fragment length is 125 bps INFO @ Thu, 05 Dec 2019 12:36:31: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 05 Dec 2019 12:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10_model.r INFO @ Thu, 05 Dec 2019 12:36:31: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:32: 12000000 INFO @ Thu, 05 Dec 2019 12:36:36: 16000000 INFO @ Thu, 05 Dec 2019 12:36:40: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:40: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:40: #1 total tags in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:36:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:40: #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 12:36:40: #1 tags after filtering in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:40: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:40: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:41: 13000000 INFO @ Thu, 05 Dec 2019 12:36:41: #2 number of paired peaks: 596 WARNING @ Thu, 05 Dec 2019 12:36:41: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:41: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:42: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:42: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:42: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:42: #2 predicted fragment length is 125 bps INFO @ Thu, 05 Dec 2019 12:36:42: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 05 Dec 2019 12:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05_model.r INFO @ Thu, 05 Dec 2019 12:36:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:48: 14000000 INFO @ Thu, 05 Dec 2019 12:36:56: 15000000 INFO @ Thu, 05 Dec 2019 12:37:04: 16000000 INFO @ Thu, 05 Dec 2019 12:37:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:07: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:07: #1 total tags in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:37:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:07: #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 12:37:07: #1 tags after filtering in treatment: 16375693 INFO @ Thu, 05 Dec 2019 12:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:09: #2 number of paired peaks: 596 WARNING @ Thu, 05 Dec 2019 12:37:09: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:09: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:09: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:09: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:09: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:09: #2 predicted fragment length is 125 bps INFO @ Thu, 05 Dec 2019 12:37:09: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 05 Dec 2019 12:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20_model.r INFO @ Thu, 05 Dec 2019 12:37:09: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:37:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.10_summits.bed INFO @ Thu, 05 Dec 2019 12:37:50: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4618 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:37:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.05_summits.bed INFO @ Thu, 05 Dec 2019 12:37:56: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6353 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:38:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107871/SRX4107871.20_summits.bed INFO @ Thu, 05 Dec 2019 12:38:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2861 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。