Job ID = 4178562 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:03:54 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 ) 2019-12-05T04:03:54 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 : 13,916,804 reads read : 27,833,608 reads written : 13,916,804 reads 0-length : 13,916,804 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:06 13916804 reads; of these: 13916804 (100.00%) were unpaired; of these: 1833376 (13.17%) aligned 0 times 9557893 (68.68%) aligned exactly 1 time 2525535 (18.15%) aligned >1 times 86.83% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 5786938 / 12083428 = 0.4789 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.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 @ Thu, 05 Dec 2019 13:16:49: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:16:49: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:16:57: 1000000 INFO @ Thu, 05 Dec 2019 13:17:05: 2000000 INFO @ Thu, 05 Dec 2019 13:17:13: 3000000 INFO @ Thu, 05 Dec 2019 13:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.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 @ Thu, 05 Dec 2019 13:17:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:17:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:17:21: 4000000 INFO @ Thu, 05 Dec 2019 13:17:27: 1000000 INFO @ Thu, 05 Dec 2019 13:17:30: 5000000 INFO @ Thu, 05 Dec 2019 13:17:37: 2000000 INFO @ Thu, 05 Dec 2019 13:17:38: 6000000 INFO @ Thu, 05 Dec 2019 13:17:41: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:17:41: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:17:41: #1 total tags in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:17:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:17:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:17:41: #1 tags after filtering in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:17:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:17:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:17:41: #2 number of paired peaks: 563 WARNING @ Thu, 05 Dec 2019 13:17:41: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Thu, 05 Dec 2019 13:17:41: start model_add_line... INFO @ Thu, 05 Dec 2019 13:17:42: start X-correlation... INFO @ Thu, 05 Dec 2019 13:17:42: end of X-cor INFO @ Thu, 05 Dec 2019 13:17:42: #2 finished! INFO @ Thu, 05 Dec 2019 13:17:42: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 13:17:42: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 13:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05_model.r INFO @ Thu, 05 Dec 2019 13:17:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:17:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.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 @ Thu, 05 Dec 2019 13:17:46: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:17:46: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:17:47: 3000000 INFO @ Thu, 05 Dec 2019 13:17:57: 1000000 INFO @ Thu, 05 Dec 2019 13:17:58: 4000000 INFO @ Thu, 05 Dec 2019 13:18:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:18:07: 2000000 INFO @ Thu, 05 Dec 2019 13:18:08: 5000000 INFO @ Thu, 05 Dec 2019 13:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.05_summits.bed INFO @ Thu, 05 Dec 2019 13:18:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1922 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:18:18: 3000000 INFO @ Thu, 05 Dec 2019 13:18:19: 6000000 INFO @ Thu, 05 Dec 2019 13:18:22: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:18:22: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:18:22: #1 total tags in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:18:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:18:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:18:22: #1 tags after filtering in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:18:22: #1 finished! INFO @ Thu, 05 Dec 2019 13:18:22: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:18:22: #2 number of paired peaks: 563 WARNING @ Thu, 05 Dec 2019 13:18:22: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Thu, 05 Dec 2019 13:18:22: start model_add_line... INFO @ Thu, 05 Dec 2019 13:18:22: start X-correlation... INFO @ Thu, 05 Dec 2019 13:18:22: end of X-cor INFO @ Thu, 05 Dec 2019 13:18:22: #2 finished! INFO @ Thu, 05 Dec 2019 13:18:22: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 13:18:22: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 13:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10_model.r INFO @ Thu, 05 Dec 2019 13:18:22: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:18:28: 4000000 INFO @ Thu, 05 Dec 2019 13:18:39: 5000000 INFO @ Thu, 05 Dec 2019 13:18:43: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:18:50: 6000000 INFO @ Thu, 05 Dec 2019 13:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:18:53: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:18:53: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:18:53: #1 total tags in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:18:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:18:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:18:53: #1 tags after filtering in treatment: 6296490 INFO @ Thu, 05 Dec 2019 13:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:18:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:18:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:18:54: #2 number of paired peaks: 563 WARNING @ Thu, 05 Dec 2019 13:18:54: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Thu, 05 Dec 2019 13:18:54: start model_add_line... INFO @ Thu, 05 Dec 2019 13:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.10_summits.bed INFO @ Thu, 05 Dec 2019 13:18:54: Done! INFO @ Thu, 05 Dec 2019 13:18:54: start X-correlation... INFO @ Thu, 05 Dec 2019 13:18:54: end of X-cor INFO @ Thu, 05 Dec 2019 13:18:54: #2 finished! INFO @ Thu, 05 Dec 2019 13:18:54: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 13:18:54: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 13:18:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20_model.r INFO @ Thu, 05 Dec 2019 13:18:54: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:18:54: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1210 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:19:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827834/SRX5827834.20_summits.bed INFO @ Thu, 05 Dec 2019 13:19:29: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (729 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。