Job ID = 1307096 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:14:00 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T13:26:44 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 ) 2019-06-03T13:26:44 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 ) 2019-06-03T13:26:44 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 : 52,969,278 reads read : 52,969,278 reads written : 52,969,278 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:12:39 52969278 reads; of these: 52969278 (100.00%) were unpaired; of these: 7442221 (14.05%) aligned 0 times 41559908 (78.46%) aligned exactly 1 time 3967149 (7.49%) aligned >1 times 85.95% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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] 18348581 / 45527057 = 0.4030 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, 03 Jun 2019 22:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.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, 03 Jun 2019 22:54:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.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, 03 Jun 2019 22:54:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.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, 03 Jun 2019 22:54:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:42: 1000000 INFO @ Mon, 03 Jun 2019 22:54:43: 1000000 INFO @ Mon, 03 Jun 2019 22:54:44: 1000000 INFO @ Mon, 03 Jun 2019 22:54:51: 2000000 INFO @ Mon, 03 Jun 2019 22:54:51: 2000000 INFO @ Mon, 03 Jun 2019 22:54:53: 2000000 INFO @ Mon, 03 Jun 2019 22:54:59: 3000000 INFO @ Mon, 03 Jun 2019 22:54:59: 3000000 INFO @ Mon, 03 Jun 2019 22:55:02: 3000000 INFO @ Mon, 03 Jun 2019 22:55:07: 4000000 INFO @ Mon, 03 Jun 2019 22:55:07: 4000000 INFO @ Mon, 03 Jun 2019 22:55:12: 4000000 INFO @ Mon, 03 Jun 2019 22:55:15: 5000000 INFO @ Mon, 03 Jun 2019 22:55:15: 5000000 INFO @ Mon, 03 Jun 2019 22:55:21: 5000000 INFO @ Mon, 03 Jun 2019 22:55:23: 6000000 INFO @ Mon, 03 Jun 2019 22:55:23: 6000000 INFO @ Mon, 03 Jun 2019 22:55:30: 6000000 INFO @ Mon, 03 Jun 2019 22:55:32: 7000000 INFO @ Mon, 03 Jun 2019 22:55:32: 7000000 INFO @ Mon, 03 Jun 2019 22:55:40: 7000000 INFO @ Mon, 03 Jun 2019 22:55:40: 8000000 INFO @ Mon, 03 Jun 2019 22:55:40: 8000000 INFO @ Mon, 03 Jun 2019 22:55:49: 9000000 INFO @ Mon, 03 Jun 2019 22:55:49: 9000000 INFO @ Mon, 03 Jun 2019 22:55:50: 8000000 INFO @ Mon, 03 Jun 2019 22:55:57: 10000000 INFO @ Mon, 03 Jun 2019 22:55:58: 10000000 INFO @ Mon, 03 Jun 2019 22:56:01: 9000000 INFO @ Mon, 03 Jun 2019 22:56:06: 11000000 INFO @ Mon, 03 Jun 2019 22:56:07: 11000000 INFO @ Mon, 03 Jun 2019 22:56:11: 10000000 INFO @ Mon, 03 Jun 2019 22:56:14: 12000000 INFO @ Mon, 03 Jun 2019 22:56:15: 12000000 INFO @ Mon, 03 Jun 2019 22:56:22: 13000000 INFO @ Mon, 03 Jun 2019 22:56:22: 11000000 INFO @ Mon, 03 Jun 2019 22:56:23: 13000000 INFO @ Mon, 03 Jun 2019 22:56:31: 14000000 INFO @ Mon, 03 Jun 2019 22:56:32: 14000000 INFO @ Mon, 03 Jun 2019 22:56:32: 12000000 INFO @ Mon, 03 Jun 2019 22:56:39: 15000000 INFO @ Mon, 03 Jun 2019 22:56:40: 15000000 INFO @ Mon, 03 Jun 2019 22:56:41: 13000000 INFO @ Mon, 03 Jun 2019 22:56:46: 16000000 INFO @ Mon, 03 Jun 2019 22:56:47: 16000000 INFO @ Mon, 03 Jun 2019 22:56:51: 14000000 INFO @ Mon, 03 Jun 2019 22:56:54: 17000000 INFO @ Mon, 03 Jun 2019 22:56:55: 17000000 INFO @ Mon, 03 Jun 2019 22:57:01: 15000000 INFO @ Mon, 03 Jun 2019 22:57:02: 18000000 INFO @ Mon, 03 Jun 2019 22:57:04: 18000000 INFO @ Mon, 03 Jun 2019 22:57:10: 16000000 INFO @ Mon, 03 Jun 2019 22:57:10: 19000000 INFO @ Mon, 03 Jun 2019 22:57:12: 19000000 INFO @ Mon, 03 Jun 2019 22:57:18: 20000000 INFO @ Mon, 03 Jun 2019 22:57:19: 17000000 INFO @ Mon, 03 Jun 2019 22:57:20: 20000000 INFO @ Mon, 03 Jun 2019 22:57:27: 21000000 INFO @ Mon, 03 Jun 2019 22:57:28: 21000000 INFO @ Mon, 03 Jun 2019 22:57:30: 18000000 INFO @ Mon, 03 Jun 2019 22:57:35: 22000000 INFO @ Mon, 03 Jun 2019 22:57:36: 22000000 INFO @ Mon, 03 Jun 2019 22:57:40: 19000000 INFO @ Mon, 03 Jun 2019 22:57:43: 23000000 INFO @ Mon, 03 Jun 2019 22:57:44: 23000000 INFO @ Mon, 03 Jun 2019 22:57:49: 20000000 INFO @ Mon, 03 Jun 2019 22:57:51: 24000000 INFO @ Mon, 03 Jun 2019 22:57:52: 24000000 INFO @ Mon, 03 Jun 2019 22:57:58: 21000000 INFO @ Mon, 03 Jun 2019 22:57:59: 25000000 INFO @ Mon, 03 Jun 2019 22:58:00: 25000000 INFO @ Mon, 03 Jun 2019 22:58:06: 26000000 INFO @ Mon, 03 Jun 2019 22:58:08: 26000000 INFO @ Mon, 03 Jun 2019 22:58:08: 22000000 INFO @ Mon, 03 Jun 2019 22:58:14: 27000000 INFO @ Mon, 03 Jun 2019 22:58:16: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 22:58:16: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 22:58:16: #1 total tags in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:16: 27000000 INFO @ Mon, 03 Jun 2019 22:58:16: #1 tags after filtering in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:16: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:17: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 22:58:17: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 22:58:17: #1 total tags in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:18: 23000000 INFO @ Mon, 03 Jun 2019 22:58:18: #1 tags after filtering in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:18: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:19: #2 number of paired peaks: 1780 INFO @ Mon, 03 Jun 2019 22:58:19: start model_add_line... INFO @ Mon, 03 Jun 2019 22:58:19: start X-correlation... INFO @ Mon, 03 Jun 2019 22:58:19: end of X-cor INFO @ Mon, 03 Jun 2019 22:58:19: #2 finished! INFO @ Mon, 03 Jun 2019 22:58:19: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:58:19: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10_model.r INFO @ Mon, 03 Jun 2019 22:58:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:58:21: #2 number of paired peaks: 1780 INFO @ Mon, 03 Jun 2019 22:58:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:58:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:58:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:58:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:58:21: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:58:21: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:58:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05_model.r INFO @ Mon, 03 Jun 2019 22:58:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:58:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:58:27: 24000000 INFO @ Mon, 03 Jun 2019 22:58:36: 25000000 INFO @ Mon, 03 Jun 2019 22:58:45: 26000000 INFO @ Mon, 03 Jun 2019 22:58:54: 27000000 INFO @ Mon, 03 Jun 2019 22:58:56: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 22:58:56: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 22:58:56: #1 total tags in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:57: #1 tags after filtering in treatment: 27178476 INFO @ Mon, 03 Jun 2019 22:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:57: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:59: #2 number of paired peaks: 1780 INFO @ Mon, 03 Jun 2019 22:58:59: start model_add_line... INFO @ Mon, 03 Jun 2019 22:59:00: start X-correlation... INFO @ Mon, 03 Jun 2019 22:59:00: end of X-cor INFO @ Mon, 03 Jun 2019 22:59:00: #2 finished! INFO @ Mon, 03 Jun 2019 22:59:00: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:59:00: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20_model.r INFO @ Mon, 03 Jun 2019 22:59:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:59:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:59:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.10_summits.bed INFO @ Mon, 03 Jun 2019 23:00:05: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9922 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.05_summits.bed INFO @ Mon, 03 Jun 2019 23:00:07: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (12823 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:00:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX512269/SRX512269.20_summits.bed INFO @ Mon, 03 Jun 2019 23:00:46: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7755 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。