Job ID = 4178379 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,963,054 reads read : 15,963,054 reads written : 15,963,054 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: 00:03:40 15963054 reads; of these: 15963054 (100.00%) were unpaired; of these: 2299944 (14.41%) aligned 0 times 11890109 (74.49%) aligned exactly 1 time 1773001 (11.11%) aligned >1 times 85.59% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 2510516 / 13663110 = 0.1837 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.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 12:32:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:14: 1000000 INFO @ Thu, 05 Dec 2019 12:32:22: 2000000 INFO @ Thu, 05 Dec 2019 12:32:31: 3000000 INFO @ Thu, 05 Dec 2019 12:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.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 12:32:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:39: 4000000 INFO @ Thu, 05 Dec 2019 12:32:44: 1000000 INFO @ Thu, 05 Dec 2019 12:32:47: 5000000 INFO @ Thu, 05 Dec 2019 12:32:51: 2000000 INFO @ Thu, 05 Dec 2019 12:32:55: 6000000 INFO @ Thu, 05 Dec 2019 12:32:59: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:33:03: 7000000 INFO @ Thu, 05 Dec 2019 12:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.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 12:33:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:07: 4000000 INFO @ Thu, 05 Dec 2019 12:33:12: 8000000 INFO @ Thu, 05 Dec 2019 12:33:13: 1000000 INFO @ Thu, 05 Dec 2019 12:33:15: 5000000 INFO @ Thu, 05 Dec 2019 12:33:20: 9000000 INFO @ Thu, 05 Dec 2019 12:33:20: 2000000 INFO @ Thu, 05 Dec 2019 12:33:23: 6000000 INFO @ Thu, 05 Dec 2019 12:33:27: 3000000 INFO @ Thu, 05 Dec 2019 12:33:28: 10000000 INFO @ Thu, 05 Dec 2019 12:33:31: 7000000 INFO @ Thu, 05 Dec 2019 12:33:35: 4000000 INFO @ Thu, 05 Dec 2019 12:33:36: 11000000 INFO @ Thu, 05 Dec 2019 12:33:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:38: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:38: #1 total tags in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:33:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:38: #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 12:33:38: #1 tags after filtering in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:39: #2 number of paired peaks: 952 WARNING @ Thu, 05 Dec 2019 12:33:39: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Thu, 05 Dec 2019 12:33:39: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:39: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:39: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:39: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:39: #2 predicted fragment length is 121 bps INFO @ Thu, 05 Dec 2019 12:33:39: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 05 Dec 2019 12:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05_model.r INFO @ Thu, 05 Dec 2019 12:33:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:39: 8000000 INFO @ Thu, 05 Dec 2019 12:33:43: 5000000 INFO @ Thu, 05 Dec 2019 12:33:48: 9000000 INFO @ Thu, 05 Dec 2019 12:33:50: 6000000 INFO @ Thu, 05 Dec 2019 12:33:56: 10000000 INFO @ Thu, 05 Dec 2019 12:33:57: 7000000 INFO @ Thu, 05 Dec 2019 12:34:04: 8000000 INFO @ Thu, 05 Dec 2019 12:34:05: 11000000 INFO @ Thu, 05 Dec 2019 12:34:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:07: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:07: #1 total tags in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:34:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:07: #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 12:34:07: #1 tags after filtering in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:08: #2 number of paired peaks: 952 WARNING @ Thu, 05 Dec 2019 12:34:08: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Thu, 05 Dec 2019 12:34:08: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:08: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:08: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:08: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:08: #2 predicted fragment length is 121 bps INFO @ Thu, 05 Dec 2019 12:34:08: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 05 Dec 2019 12:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10_model.r INFO @ Thu, 05 Dec 2019 12:34:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:11: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:12: 9000000 INFO @ Thu, 05 Dec 2019 12:34:19: 10000000 INFO @ Thu, 05 Dec 2019 12:34:26: 11000000 INFO @ Thu, 05 Dec 2019 12:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.05_summits.bed INFO @ Thu, 05 Dec 2019 12:34:27: Done! INFO @ Thu, 05 Dec 2019 12:34:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:27: #1 total tags in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:34:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5248 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:27: #1 tags after filtering in treatment: 11152594 INFO @ Thu, 05 Dec 2019 12:34:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:28: #2 number of paired peaks: 952 WARNING @ Thu, 05 Dec 2019 12:34:28: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Thu, 05 Dec 2019 12:34:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:29: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:29: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:29: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:29: #2 predicted fragment length is 121 bps INFO @ Thu, 05 Dec 2019 12:34:29: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 05 Dec 2019 12:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20_model.r INFO @ Thu, 05 Dec 2019 12:34:29: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.10_summits.bed INFO @ Thu, 05 Dec 2019 12:34:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3925 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:35:01: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107868/SRX4107868.20_summits.bed INFO @ Thu, 05 Dec 2019 12:35:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2449 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。