Job ID = 2590454 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,564,783 reads read : 29,129,566 reads written : 14,564,783 reads 0-length : 14,564,783 spots read : 14,581,524 reads read : 29,163,048 reads written : 14,581,524 reads 0-length : 14,581,524 2019-08-12T12:54:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,486,367 reads read : 28,972,734 reads written : 14,486,367 reads 0-length : 14,486,367 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: 00:11:36 43632674 reads; of these: 43632674 (100.00%) were unpaired; of these: 1000440 (2.29%) aligned 0 times 36674221 (84.05%) aligned exactly 1 time 5958013 (13.65%) aligned >1 times 97.71% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 10243784 / 42632234 = 0.2403 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 @ Mon, 12 Aug 2019 22:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:18:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:18:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:18:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:11: 1000000 INFO @ Mon, 12 Aug 2019 22:18:12: 1000000 INFO @ Mon, 12 Aug 2019 22:18:15: 1000000 INFO @ Mon, 12 Aug 2019 22:18:19: 2000000 INFO @ Mon, 12 Aug 2019 22:18:19: 2000000 INFO @ Mon, 12 Aug 2019 22:18:23: 2000000 INFO @ Mon, 12 Aug 2019 22:18:25: 3000000 INFO @ Mon, 12 Aug 2019 22:18:26: 3000000 INFO @ Mon, 12 Aug 2019 22:18:32: 3000000 INFO @ Mon, 12 Aug 2019 22:18:32: 4000000 INFO @ Mon, 12 Aug 2019 22:18:34: 4000000 INFO @ Mon, 12 Aug 2019 22:18:39: 5000000 INFO @ Mon, 12 Aug 2019 22:18:40: 4000000 INFO @ Mon, 12 Aug 2019 22:18:42: 5000000 INFO @ Mon, 12 Aug 2019 22:18:46: 6000000 INFO @ Mon, 12 Aug 2019 22:18:49: 6000000 INFO @ Mon, 12 Aug 2019 22:18:49: 5000000 INFO @ Mon, 12 Aug 2019 22:18:53: 7000000 INFO @ Mon, 12 Aug 2019 22:18:56: 7000000 INFO @ Mon, 12 Aug 2019 22:18:58: 6000000 INFO @ Mon, 12 Aug 2019 22:18:59: 8000000 INFO @ Mon, 12 Aug 2019 22:19:04: 8000000 INFO @ Mon, 12 Aug 2019 22:19:06: 9000000 INFO @ Mon, 12 Aug 2019 22:19:06: 7000000 INFO @ Mon, 12 Aug 2019 22:19:11: 9000000 INFO @ Mon, 12 Aug 2019 22:19:13: 10000000 INFO @ Mon, 12 Aug 2019 22:19:15: 8000000 INFO @ Mon, 12 Aug 2019 22:19:19: 10000000 INFO @ Mon, 12 Aug 2019 22:19:20: 11000000 INFO @ Mon, 12 Aug 2019 22:19:24: 9000000 INFO @ Mon, 12 Aug 2019 22:19:26: 11000000 INFO @ Mon, 12 Aug 2019 22:19:26: 12000000 INFO @ Mon, 12 Aug 2019 22:19:32: 10000000 INFO @ Mon, 12 Aug 2019 22:19:33: 13000000 INFO @ Mon, 12 Aug 2019 22:19:34: 12000000 INFO @ Mon, 12 Aug 2019 22:19:40: 14000000 INFO @ Mon, 12 Aug 2019 22:19:41: 13000000 INFO @ Mon, 12 Aug 2019 22:19:41: 11000000 INFO @ Mon, 12 Aug 2019 22:19:47: 15000000 INFO @ Mon, 12 Aug 2019 22:19:48: 14000000 INFO @ Mon, 12 Aug 2019 22:19:50: 12000000 INFO @ Mon, 12 Aug 2019 22:19:53: 16000000 INFO @ Mon, 12 Aug 2019 22:19:56: 15000000 INFO @ Mon, 12 Aug 2019 22:19:58: 13000000 INFO @ Mon, 12 Aug 2019 22:20:00: 17000000 INFO @ Mon, 12 Aug 2019 22:20:03: 16000000 INFO @ Mon, 12 Aug 2019 22:20:07: 18000000 INFO @ Mon, 12 Aug 2019 22:20:07: 14000000 INFO @ Mon, 12 Aug 2019 22:20:11: 17000000 INFO @ Mon, 12 Aug 2019 22:20:14: 19000000 INFO @ Mon, 12 Aug 2019 22:20:16: 15000000 INFO @ Mon, 12 Aug 2019 22:20:18: 18000000 INFO @ Mon, 12 Aug 2019 22:20:21: 20000000 INFO @ Mon, 12 Aug 2019 22:20:25: 16000000 INFO @ Mon, 12 Aug 2019 22:20:26: 19000000 INFO @ Mon, 12 Aug 2019 22:20:28: 21000000 INFO @ Mon, 12 Aug 2019 22:20:33: 20000000 INFO @ Mon, 12 Aug 2019 22:20:35: 17000000 INFO @ Mon, 12 Aug 2019 22:20:35: 22000000 INFO @ Mon, 12 Aug 2019 22:20:41: 21000000 INFO @ Mon, 12 Aug 2019 22:20:41: 23000000 INFO @ Mon, 12 Aug 2019 22:20:44: 18000000 INFO @ Mon, 12 Aug 2019 22:20:48: 24000000 INFO @ Mon, 12 Aug 2019 22:20:49: 22000000 INFO @ Mon, 12 Aug 2019 22:20:53: 19000000 INFO @ Mon, 12 Aug 2019 22:20:55: 25000000 INFO @ Mon, 12 Aug 2019 22:20:56: 23000000 INFO @ Mon, 12 Aug 2019 22:21:02: 20000000 INFO @ Mon, 12 Aug 2019 22:21:02: 26000000 INFO @ Mon, 12 Aug 2019 22:21:04: 24000000 INFO @ Mon, 12 Aug 2019 22:21:09: 27000000 INFO @ Mon, 12 Aug 2019 22:21:11: 21000000 INFO @ Mon, 12 Aug 2019 22:21:11: 25000000 INFO @ Mon, 12 Aug 2019 22:21:16: 28000000 INFO @ Mon, 12 Aug 2019 22:21:19: 26000000 INFO @ Mon, 12 Aug 2019 22:21:20: 22000000 INFO @ Mon, 12 Aug 2019 22:21:23: 29000000 INFO @ Mon, 12 Aug 2019 22:21:26: 27000000 INFO @ Mon, 12 Aug 2019 22:21:29: 30000000 INFO @ Mon, 12 Aug 2019 22:21:30: 23000000 INFO @ Mon, 12 Aug 2019 22:21:34: 28000000 INFO @ Mon, 12 Aug 2019 22:21:36: 31000000 INFO @ Mon, 12 Aug 2019 22:21:39: 24000000 INFO @ Mon, 12 Aug 2019 22:21:42: 29000000 INFO @ Mon, 12 Aug 2019 22:21:43: 32000000 INFO @ Mon, 12 Aug 2019 22:21:46: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:46: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:46: #1 total tags in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:21:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:21:47: #1 tags after filtering in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:47: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:49: 25000000 INFO @ Mon, 12 Aug 2019 22:21:49: 30000000 INFO @ Mon, 12 Aug 2019 22:21:50: #2 number of paired peaks: 1778 INFO @ Mon, 12 Aug 2019 22:21:50: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:50: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:50: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:50: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:50: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:21:50: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:21:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10_model.r INFO @ Mon, 12 Aug 2019 22:21:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:56: 31000000 INFO @ Mon, 12 Aug 2019 22:21:58: 26000000 INFO @ Mon, 12 Aug 2019 22:22:04: 32000000 INFO @ Mon, 12 Aug 2019 22:22:07: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:07: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:07: #1 total tags in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:22:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:22:07: 27000000 INFO @ Mon, 12 Aug 2019 22:22:08: #1 tags after filtering in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:08: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:11: #2 number of paired peaks: 1778 INFO @ Mon, 12 Aug 2019 22:22:11: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:11: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:11: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:11: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:11: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:22:11: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05_model.r INFO @ Mon, 12 Aug 2019 22:22:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:17: 28000000 INFO @ Mon, 12 Aug 2019 22:22:26: 29000000 INFO @ Mon, 12 Aug 2019 22:22:34: 30000000 INFO @ Mon, 12 Aug 2019 22:22:43: 31000000 INFO @ Mon, 12 Aug 2019 22:22:51: 32000000 INFO @ Mon, 12 Aug 2019 22:22:55: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:55: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:55: #1 total tags in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:22:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:22:56: #1 tags after filtering in treatment: 32388450 INFO @ Mon, 12 Aug 2019 22:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:56: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:59: #2 number of paired peaks: 1778 INFO @ Mon, 12 Aug 2019 22:22:59: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:59: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:59: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:59: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:59: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:22:59: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20_model.r INFO @ Mon, 12 Aug 2019 22:22:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:23:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:23:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.10_summits.bed INFO @ Mon, 12 Aug 2019 22:23:48: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8458 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.05_summits.bed INFO @ Mon, 12 Aug 2019 22:24:12: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (12341 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:24:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981686/SRX3981686.20_summits.bed INFO @ Mon, 12 Aug 2019 22:24:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4383 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。