Job ID = 1307246 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:12:23 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 ) 2019-06-03T13:12:23 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 : 22,418,323 reads read : 22,418,323 reads written : 22,418,323 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: 00:07:22 22418323 reads; of these: 22418323 (100.00%) were unpaired; of these: 2073910 (9.25%) aligned 0 times 15410548 (68.74%) aligned exactly 1 time 4933865 (22.01%) aligned >1 times 90.75% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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 12 files... [bam_rmdupse_core] 9275957 / 20344413 = 0.4559 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 22:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.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 22:26:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.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 22:26:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.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 22:26:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:43: 1000000 INFO @ Mon, 03 Jun 2019 22:26:44: 1000000 INFO @ Mon, 03 Jun 2019 22:26:46: 1000000 INFO @ Mon, 03 Jun 2019 22:26:50: 2000000 INFO @ Mon, 03 Jun 2019 22:26:52: 2000000 INFO @ Mon, 03 Jun 2019 22:26:56: 2000000 INFO @ Mon, 03 Jun 2019 22:26:58: 3000000 INFO @ Mon, 03 Jun 2019 22:27:00: 3000000 INFO @ Mon, 03 Jun 2019 22:27:05: 4000000 INFO @ Mon, 03 Jun 2019 22:27:06: 3000000 INFO @ Mon, 03 Jun 2019 22:27:09: 4000000 INFO @ Mon, 03 Jun 2019 22:27:12: 5000000 INFO @ Mon, 03 Jun 2019 22:27:16: 4000000 INFO @ Mon, 03 Jun 2019 22:27:17: 5000000 INFO @ Mon, 03 Jun 2019 22:27:20: 6000000 INFO @ Mon, 03 Jun 2019 22:27:25: 6000000 INFO @ Mon, 03 Jun 2019 22:27:26: 5000000 INFO @ Mon, 03 Jun 2019 22:27:28: 7000000 INFO @ Mon, 03 Jun 2019 22:27:33: 7000000 INFO @ Mon, 03 Jun 2019 22:27:35: 8000000 INFO @ Mon, 03 Jun 2019 22:27:35: 6000000 INFO @ Mon, 03 Jun 2019 22:27:42: 8000000 INFO @ Mon, 03 Jun 2019 22:27:43: 9000000 INFO @ Mon, 03 Jun 2019 22:27:45: 7000000 INFO @ Mon, 03 Jun 2019 22:27:50: 9000000 INFO @ Mon, 03 Jun 2019 22:27:50: 10000000 INFO @ Mon, 03 Jun 2019 22:27:55: 8000000 INFO @ Mon, 03 Jun 2019 22:27:57: 11000000 INFO @ Mon, 03 Jun 2019 22:27:58: 10000000 INFO @ Mon, 03 Jun 2019 22:27:58: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 22:27:58: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 22:27:58: #1 total tags in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:27:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:27:58: #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 22:27:58: #1 tags after filtering in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:27:58: #1 finished! INFO @ Mon, 03 Jun 2019 22:27:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:27:59: #2 number of paired peaks: 1599 INFO @ Mon, 03 Jun 2019 22:27:59: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:00: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:00: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:00: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:00: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:00: #2 alternative fragment length(s) may be 3,118 bps INFO @ Mon, 03 Jun 2019 22:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20_model.r INFO @ Mon, 03 Jun 2019 22:28:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:28:05: 9000000 INFO @ Mon, 03 Jun 2019 22:28:06: 11000000 INFO @ Mon, 03 Jun 2019 22:28:06: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 22:28:06: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 22:28:06: #1 total tags in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:06: #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 22:28:07: #1 tags after filtering in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:07: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:08: #2 number of paired peaks: 1599 INFO @ Mon, 03 Jun 2019 22:28:08: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:08: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:08: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:08: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:08: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:08: #2 alternative fragment length(s) may be 3,118 bps INFO @ Mon, 03 Jun 2019 22:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05_model.r INFO @ Mon, 03 Jun 2019 22:28:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:28:15: 10000000 INFO @ Mon, 03 Jun 2019 22:28:24: 11000000 INFO @ Mon, 03 Jun 2019 22:28:25: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 22:28:25: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 22:28:25: #1 total tags in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:28:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:25: #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 22:28:25: #1 tags after filtering in treatment: 11068456 INFO @ Mon, 03 Jun 2019 22:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:25: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:26: #2 number of paired peaks: 1599 INFO @ Mon, 03 Jun 2019 22:28:26: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:26: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:26: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:26: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:26: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:26: #2 alternative fragment length(s) may be 3,118 bps INFO @ Mon, 03 Jun 2019 22:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10_model.r INFO @ Mon, 03 Jun 2019 22:28:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:28:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.20_summits.bed INFO @ Mon, 03 Jun 2019 22:28:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1315 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.05_summits.bed INFO @ Mon, 03 Jun 2019 22:28:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6202 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX529166/SRX529166.10_summits.bed INFO @ Mon, 03 Jun 2019 22:29:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3010 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。