Job ID = 1294888 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:40:39 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 : 15,295,346 reads read : 15,295,346 reads written : 15,295,346 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: 00:04:27 15295346 reads; of these: 15295346 (100.00%) were unpaired; of these: 1195612 (7.82%) aligned 0 times 13032848 (85.21%) aligned exactly 1 time 1066886 (6.98%) aligned >1 times 92.18% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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 8 files... [bam_rmdupse_core] 1501863 / 14099734 = 0.1065 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 10:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.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 10:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.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 10:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.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 10:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:51:48: 1000000 INFO @ Mon, 03 Jun 2019 10:51:49: 1000000 INFO @ Mon, 03 Jun 2019 10:51:50: 1000000 INFO @ Mon, 03 Jun 2019 10:51:56: 2000000 INFO @ Mon, 03 Jun 2019 10:51:56: 2000000 INFO @ Mon, 03 Jun 2019 10:51:58: 2000000 INFO @ Mon, 03 Jun 2019 10:52:03: 3000000 INFO @ Mon, 03 Jun 2019 10:52:03: 3000000 INFO @ Mon, 03 Jun 2019 10:52:07: 3000000 INFO @ Mon, 03 Jun 2019 10:52:11: 4000000 INFO @ Mon, 03 Jun 2019 10:52:11: 4000000 INFO @ Mon, 03 Jun 2019 10:52:15: 4000000 INFO @ Mon, 03 Jun 2019 10:52:18: 5000000 INFO @ Mon, 03 Jun 2019 10:52:18: 5000000 INFO @ Mon, 03 Jun 2019 10:52:23: 5000000 INFO @ Mon, 03 Jun 2019 10:52:26: 6000000 INFO @ Mon, 03 Jun 2019 10:52:26: 6000000 INFO @ Mon, 03 Jun 2019 10:52:32: 6000000 INFO @ Mon, 03 Jun 2019 10:52:33: 7000000 INFO @ Mon, 03 Jun 2019 10:52:33: 7000000 INFO @ Mon, 03 Jun 2019 10:52:40: 8000000 INFO @ Mon, 03 Jun 2019 10:52:40: 7000000 INFO @ Mon, 03 Jun 2019 10:52:40: 8000000 INFO @ Mon, 03 Jun 2019 10:52:47: 9000000 INFO @ Mon, 03 Jun 2019 10:52:48: 9000000 INFO @ Mon, 03 Jun 2019 10:52:48: 8000000 INFO @ Mon, 03 Jun 2019 10:52:55: 10000000 INFO @ Mon, 03 Jun 2019 10:52:55: 10000000 INFO @ Mon, 03 Jun 2019 10:52:57: 9000000 INFO @ Mon, 03 Jun 2019 10:53:02: 11000000 INFO @ Mon, 03 Jun 2019 10:53:03: 11000000 INFO @ Mon, 03 Jun 2019 10:53:05: 10000000 INFO @ Mon, 03 Jun 2019 10:53:10: 12000000 INFO @ Mon, 03 Jun 2019 10:53:10: 12000000 INFO @ Mon, 03 Jun 2019 10:53:13: 11000000 INFO @ Mon, 03 Jun 2019 10:53:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:53:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:53:14: #1 total tags in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:53:14: #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 10:53:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:53:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:53:14: #1 total tags in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:53:14: #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 10:53:14: #1 tags after filtering in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:53:14: #1 finished! INFO @ Mon, 03 Jun 2019 10:53:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:53:15: #1 tags after filtering in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:53:15: #1 finished! INFO @ Mon, 03 Jun 2019 10:53:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:53:16: #2 number of paired peaks: 2199 INFO @ Mon, 03 Jun 2019 10:53:16: start model_add_line... INFO @ Mon, 03 Jun 2019 10:53:16: start X-correlation... INFO @ Mon, 03 Jun 2019 10:53:16: end of X-cor INFO @ Mon, 03 Jun 2019 10:53:16: #2 finished! INFO @ Mon, 03 Jun 2019 10:53:16: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 10:53:16: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 10:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05_model.r INFO @ Mon, 03 Jun 2019 10:53:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:53:16: #2 number of paired peaks: 2199 INFO @ Mon, 03 Jun 2019 10:53:16: start model_add_line... INFO @ Mon, 03 Jun 2019 10:53:16: start X-correlation... INFO @ Mon, 03 Jun 2019 10:53:16: end of X-cor INFO @ Mon, 03 Jun 2019 10:53:16: #2 finished! INFO @ Mon, 03 Jun 2019 10:53:16: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 10:53:16: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 10:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10_model.r INFO @ Mon, 03 Jun 2019 10:53:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:53:21: 12000000 INFO @ Mon, 03 Jun 2019 10:53:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:53:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:53:26: #1 total tags in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:53:26: #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 10:53:27: #1 tags after filtering in treatment: 12597871 INFO @ Mon, 03 Jun 2019 10:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:53:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:53:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:53:28: #2 number of paired peaks: 2199 INFO @ Mon, 03 Jun 2019 10:53:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:53:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:53:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:53:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:53:28: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 10:53:28: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 10:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20_model.r INFO @ Mon, 03 Jun 2019 10:53:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.10_summits.bed INFO @ Mon, 03 Jun 2019 10:54:15: Done! INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05_peaks.xls pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4571 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.05_summits.bed INFO @ Mon, 03 Jun 2019 10:54:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7782 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287965/SRX287965.20_summits.bed INFO @ Mon, 03 Jun 2019 10:54:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1842 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。