Job ID = 2001615 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,668,541 reads read : 26,668,541 reads written : 26,668,541 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:11 26668541 reads; of these: 26668541 (100.00%) were unpaired; of these: 705960 (2.65%) aligned 0 times 19898669 (74.61%) aligned exactly 1 time 6063912 (22.74%) aligned >1 times 97.35% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1906234 / 25962581 = 0.0734 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 @ Fri, 05 Jul 2019 06:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:34:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:34:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:34:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:34:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:34:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:34:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:34:23: 1000000 INFO @ Fri, 05 Jul 2019 06:34:24: 1000000 INFO @ Fri, 05 Jul 2019 06:34:24: 1000000 INFO @ Fri, 05 Jul 2019 06:34:30: 2000000 INFO @ Fri, 05 Jul 2019 06:34:31: 2000000 INFO @ Fri, 05 Jul 2019 06:34:31: 2000000 INFO @ Fri, 05 Jul 2019 06:34:36: 3000000 INFO @ Fri, 05 Jul 2019 06:34:38: 3000000 INFO @ Fri, 05 Jul 2019 06:34:39: 3000000 INFO @ Fri, 05 Jul 2019 06:34:44: 4000000 INFO @ Fri, 05 Jul 2019 06:34:45: 4000000 INFO @ Fri, 05 Jul 2019 06:34:48: 4000000 INFO @ Fri, 05 Jul 2019 06:34:51: 5000000 INFO @ Fri, 05 Jul 2019 06:34:52: 5000000 INFO @ Fri, 05 Jul 2019 06:34:55: 5000000 INFO @ Fri, 05 Jul 2019 06:34:58: 6000000 INFO @ Fri, 05 Jul 2019 06:34:59: 6000000 INFO @ Fri, 05 Jul 2019 06:35:03: 6000000 INFO @ Fri, 05 Jul 2019 06:35:05: 7000000 INFO @ Fri, 05 Jul 2019 06:35:06: 7000000 INFO @ Fri, 05 Jul 2019 06:35:10: 7000000 INFO @ Fri, 05 Jul 2019 06:35:12: 8000000 INFO @ Fri, 05 Jul 2019 06:35:13: 8000000 INFO @ Fri, 05 Jul 2019 06:35:18: 8000000 INFO @ Fri, 05 Jul 2019 06:35:19: 9000000 INFO @ Fri, 05 Jul 2019 06:35:20: 9000000 INFO @ Fri, 05 Jul 2019 06:35:25: 9000000 INFO @ Fri, 05 Jul 2019 06:35:27: 10000000 INFO @ Fri, 05 Jul 2019 06:35:27: 10000000 INFO @ Fri, 05 Jul 2019 06:35:33: 10000000 INFO @ Fri, 05 Jul 2019 06:35:34: 11000000 INFO @ Fri, 05 Jul 2019 06:35:34: 11000000 INFO @ Fri, 05 Jul 2019 06:35:41: 11000000 INFO @ Fri, 05 Jul 2019 06:35:41: 12000000 INFO @ Fri, 05 Jul 2019 06:35:41: 12000000 INFO @ Fri, 05 Jul 2019 06:35:48: 13000000 INFO @ Fri, 05 Jul 2019 06:35:48: 12000000 INFO @ Fri, 05 Jul 2019 06:35:48: 13000000 INFO @ Fri, 05 Jul 2019 06:35:55: 14000000 INFO @ Fri, 05 Jul 2019 06:35:55: 14000000 INFO @ Fri, 05 Jul 2019 06:35:56: 13000000 INFO @ Fri, 05 Jul 2019 06:36:02: 15000000 INFO @ Fri, 05 Jul 2019 06:36:02: 15000000 INFO @ Fri, 05 Jul 2019 06:36:03: 14000000 INFO @ Fri, 05 Jul 2019 06:36:09: 16000000 INFO @ Fri, 05 Jul 2019 06:36:09: 16000000 INFO @ Fri, 05 Jul 2019 06:36:11: 15000000 INFO @ Fri, 05 Jul 2019 06:36:16: 17000000 INFO @ Fri, 05 Jul 2019 06:36:16: 17000000 INFO @ Fri, 05 Jul 2019 06:36:18: 16000000 INFO @ Fri, 05 Jul 2019 06:36:23: 18000000 INFO @ Fri, 05 Jul 2019 06:36:23: 18000000 INFO @ Fri, 05 Jul 2019 06:36:26: 17000000 INFO @ Fri, 05 Jul 2019 06:36:30: 19000000 INFO @ Fri, 05 Jul 2019 06:36:30: 19000000 INFO @ Fri, 05 Jul 2019 06:36:33: 18000000 INFO @ Fri, 05 Jul 2019 06:36:36: 20000000 INFO @ Fri, 05 Jul 2019 06:36:37: 20000000 INFO @ Fri, 05 Jul 2019 06:36:41: 19000000 INFO @ Fri, 05 Jul 2019 06:36:43: 21000000 INFO @ Fri, 05 Jul 2019 06:36:44: 21000000 INFO @ Fri, 05 Jul 2019 06:36:49: 20000000 INFO @ Fri, 05 Jul 2019 06:36:50: 22000000 INFO @ Fri, 05 Jul 2019 06:36:51: 22000000 INFO @ Fri, 05 Jul 2019 06:36:56: 21000000 INFO @ Fri, 05 Jul 2019 06:36:57: 23000000 INFO @ Fri, 05 Jul 2019 06:36:58: 23000000 INFO @ Fri, 05 Jul 2019 06:37:04: 22000000 INFO @ Fri, 05 Jul 2019 06:37:04: 24000000 INFO @ Fri, 05 Jul 2019 06:37:04: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:37:04: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:37:04: #1 total tags in treatment: 24056347 INFO @ Fri, 05 Jul 2019 06:37:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:37:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:37:05: #1 tags after filtering in treatment: 24056180 INFO @ Fri, 05 Jul 2019 06:37:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:37:05: #1 finished! INFO @ Fri, 05 Jul 2019 06:37:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:37:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:37:05: 24000000 INFO @ Fri, 05 Jul 2019 06:37:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:37:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:37:05: #1 total tags in treatment: 24056347 INFO @ Fri, 05 Jul 2019 06:37:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:37:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:37:06: #1 tags after filtering in treatment: 24056180 INFO @ Fri, 05 Jul 2019 06:37:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:37:06: #1 finished! INFO @ Fri, 05 Jul 2019 06:37:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:37:10: #2 number of paired peaks: 68376 INFO @ Fri, 05 Jul 2019 06:37:10: start model_add_line... INFO @ Fri, 05 Jul 2019 06:37:11: start X-correlation... INFO @ Fri, 05 Jul 2019 06:37:11: end of X-cor INFO @ Fri, 05 Jul 2019 06:37:11: #2 finished! INFO @ Fri, 05 Jul 2019 06:37:11: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 06:37:11: #2 alternative fragment length(s) may be 0,140,299,515 bps INFO @ Fri, 05 Jul 2019 06:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20_model.r INFO @ Fri, 05 Jul 2019 06:37:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:37:11: 23000000 INFO @ Fri, 05 Jul 2019 06:37:12: #2 number of paired peaks: 68376 INFO @ Fri, 05 Jul 2019 06:37:12: start model_add_line... INFO @ Fri, 05 Jul 2019 06:37:12: start X-correlation... INFO @ Fri, 05 Jul 2019 06:37:12: end of X-cor INFO @ Fri, 05 Jul 2019 06:37:12: #2 finished! INFO @ Fri, 05 Jul 2019 06:37:12: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 06:37:12: #2 alternative fragment length(s) may be 0,140,299,515 bps INFO @ Fri, 05 Jul 2019 06:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05_model.r INFO @ Fri, 05 Jul 2019 06:37:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:37:19: 24000000 INFO @ Fri, 05 Jul 2019 06:37:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:37:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:37:19: #1 total tags in treatment: 24056347 INFO @ Fri, 05 Jul 2019 06:37:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:37:20: #1 tags after filtering in treatment: 24056180 INFO @ Fri, 05 Jul 2019 06:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:37:20: #1 finished! INFO @ Fri, 05 Jul 2019 06:37:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:37:25: #2 number of paired peaks: 68376 INFO @ Fri, 05 Jul 2019 06:37:25: start model_add_line... INFO @ Fri, 05 Jul 2019 06:37:25: start X-correlation... INFO @ Fri, 05 Jul 2019 06:37:25: end of X-cor INFO @ Fri, 05 Jul 2019 06:37:25: #2 finished! INFO @ Fri, 05 Jul 2019 06:37:25: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 06:37:25: #2 alternative fragment length(s) may be 0,140,299,515 bps INFO @ Fri, 05 Jul 2019 06:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10_model.r INFO @ Fri, 05 Jul 2019 06:37:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:38:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:38:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:38:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.20_summits.bed INFO @ Fri, 05 Jul 2019 06:39:09: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.05_summits.bed INFO @ Fri, 05 Jul 2019 06:39:11: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (5410 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101938/ERX101938.10_summits.bed INFO @ Fri, 05 Jul 2019 06:39:21: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (1286 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。