Job ID = 1294799 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:11:53 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 ) 1900-01-00T00:00:00 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 ) 2019-06-03T01:11:53 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 : 18,826,306 reads read : 18,826,306 reads written : 18,826,306 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: 00:07:32 18826306 reads; of these: 18826306 (100.00%) were unpaired; of these: 897643 (4.77%) aligned 0 times 13281362 (70.55%) aligned exactly 1 time 4647301 (24.69%) aligned >1 times 95.23% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 1789877 / 17928663 = 0.0998 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 10:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.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 10:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.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 10:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.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 10:28:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:39: 1000000 INFO @ Mon, 03 Jun 2019 10:28:39: 1000000 INFO @ Mon, 03 Jun 2019 10:28:41: 1000000 INFO @ Mon, 03 Jun 2019 10:28:45: 2000000 INFO @ Mon, 03 Jun 2019 10:28:47: 2000000 INFO @ Mon, 03 Jun 2019 10:28:50: 2000000 INFO @ Mon, 03 Jun 2019 10:28:52: 3000000 INFO @ Mon, 03 Jun 2019 10:28:55: 3000000 INFO @ Mon, 03 Jun 2019 10:28:58: 3000000 INFO @ Mon, 03 Jun 2019 10:28:59: 4000000 INFO @ Mon, 03 Jun 2019 10:29:03: 4000000 INFO @ Mon, 03 Jun 2019 10:29:06: 5000000 INFO @ Mon, 03 Jun 2019 10:29:07: 4000000 INFO @ Mon, 03 Jun 2019 10:29:10: 5000000 INFO @ Mon, 03 Jun 2019 10:29:13: 6000000 INFO @ Mon, 03 Jun 2019 10:29:16: 5000000 INFO @ Mon, 03 Jun 2019 10:29:19: 6000000 INFO @ Mon, 03 Jun 2019 10:29:20: 7000000 INFO @ Mon, 03 Jun 2019 10:29:25: 6000000 INFO @ Mon, 03 Jun 2019 10:29:27: 7000000 INFO @ Mon, 03 Jun 2019 10:29:28: 8000000 INFO @ Mon, 03 Jun 2019 10:29:35: 8000000 INFO @ Mon, 03 Jun 2019 10:29:35: 7000000 INFO @ Mon, 03 Jun 2019 10:29:37: 9000000 INFO @ Mon, 03 Jun 2019 10:29:43: 9000000 INFO @ Mon, 03 Jun 2019 10:29:44: 8000000 INFO @ Mon, 03 Jun 2019 10:29:46: 10000000 INFO @ Mon, 03 Jun 2019 10:29:52: 10000000 INFO @ Mon, 03 Jun 2019 10:29:54: 9000000 INFO @ Mon, 03 Jun 2019 10:29:54: 11000000 INFO @ Mon, 03 Jun 2019 10:29:59: 11000000 INFO @ Mon, 03 Jun 2019 10:30:01: 12000000 INFO @ Mon, 03 Jun 2019 10:30:03: 10000000 INFO @ Mon, 03 Jun 2019 10:30:07: 12000000 INFO @ Mon, 03 Jun 2019 10:30:09: 13000000 INFO @ Mon, 03 Jun 2019 10:30:12: 11000000 INFO @ Mon, 03 Jun 2019 10:30:15: 13000000 INFO @ Mon, 03 Jun 2019 10:30:17: 14000000 INFO @ Mon, 03 Jun 2019 10:30:21: 12000000 INFO @ Mon, 03 Jun 2019 10:30:23: 14000000 INFO @ Mon, 03 Jun 2019 10:30:24: 15000000 INFO @ Mon, 03 Jun 2019 10:30:30: 13000000 INFO @ Mon, 03 Jun 2019 10:30:30: 15000000 INFO @ Mon, 03 Jun 2019 10:30:32: 16000000 INFO @ Mon, 03 Jun 2019 10:30:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:30:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:30:33: #1 total tags in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:30:33: #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 10:30:33: #1 tags after filtering in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:30:33: #1 finished! INFO @ Mon, 03 Jun 2019 10:30:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:30:35: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 10:30:35: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 10:30:35: start model_add_line... INFO @ Mon, 03 Jun 2019 10:30:35: start X-correlation... INFO @ Mon, 03 Jun 2019 10:30:35: end of X-cor INFO @ Mon, 03 Jun 2019 10:30:35: #2 finished! INFO @ Mon, 03 Jun 2019 10:30:35: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 10:30:35: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 10:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05_model.r INFO @ Mon, 03 Jun 2019 10:30:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:30:38: 16000000 INFO @ Mon, 03 Jun 2019 10:30:38: 14000000 INFO @ Mon, 03 Jun 2019 10:30:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:30:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:30:39: #1 total tags in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:30:39: #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 10:30:40: #1 tags after filtering in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:30:40: #1 finished! INFO @ Mon, 03 Jun 2019 10:30:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:30:41: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 10:30:41: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 10:30:41: start model_add_line... INFO @ Mon, 03 Jun 2019 10:30:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:30:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:30:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:30:41: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 10:30:41: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 10:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10_model.r INFO @ Mon, 03 Jun 2019 10:30:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:30:47: 15000000 INFO @ Mon, 03 Jun 2019 10:30:55: 16000000 INFO @ Mon, 03 Jun 2019 10:30:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:30:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:30:56: #1 total tags in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:30:56: #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 10:30:57: #1 tags after filtering in treatment: 16138786 INFO @ Mon, 03 Jun 2019 10:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:30:57: #1 finished! INFO @ Mon, 03 Jun 2019 10:30:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:30:58: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 10:30:58: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 10:30:58: start model_add_line... INFO @ Mon, 03 Jun 2019 10:30:58: start X-correlation... INFO @ Mon, 03 Jun 2019 10:30:58: end of X-cor INFO @ Mon, 03 Jun 2019 10:30:58: #2 finished! INFO @ Mon, 03 Jun 2019 10:30:58: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 10:30:58: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 10:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20_model.r INFO @ Mon, 03 Jun 2019 10:30:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:31:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:31:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.05_summits.bed INFO @ Mon, 03 Jun 2019 10:31:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6214 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:31:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.10_summits.bed INFO @ Mon, 03 Jun 2019 10:31:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4350 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287887/SRX287887.20_summits.bed INFO @ Mon, 03 Jun 2019 10:32:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2260 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。