Job ID = 1291785 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:32:52 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 ) 2019-06-02T07:32:52 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 : 17,976,698 reads read : 35,953,396 reads written : 17,976,698 reads 0-length : 17,976,698 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: 00:07:03 17976698 reads; of these: 17976698 (100.00%) were unpaired; of these: 1750243 (9.74%) aligned 0 times 14359639 (79.88%) aligned exactly 1 time 1866816 (10.38%) aligned >1 times 90.26% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3542532 / 16226455 = 0.2183 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 @ Sun, 02 Jun 2019 16:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:41: 1000000 INFO @ Sun, 02 Jun 2019 16:46:44: 1000000 INFO @ Sun, 02 Jun 2019 16:46:44: 1000000 INFO @ Sun, 02 Jun 2019 16:46:49: 2000000 INFO @ Sun, 02 Jun 2019 16:46:55: 2000000 INFO @ Sun, 02 Jun 2019 16:46:55: 2000000 INFO @ Sun, 02 Jun 2019 16:46:58: 3000000 INFO @ Sun, 02 Jun 2019 16:47:05: 3000000 INFO @ Sun, 02 Jun 2019 16:47:05: 3000000 INFO @ Sun, 02 Jun 2019 16:47:06: 4000000 INFO @ Sun, 02 Jun 2019 16:47:14: 5000000 INFO @ Sun, 02 Jun 2019 16:47:15: 4000000 INFO @ Sun, 02 Jun 2019 16:47:15: 4000000 INFO @ Sun, 02 Jun 2019 16:47:23: 6000000 INFO @ Sun, 02 Jun 2019 16:47:24: 5000000 INFO @ Sun, 02 Jun 2019 16:47:25: 5000000 INFO @ Sun, 02 Jun 2019 16:47:31: 7000000 INFO @ Sun, 02 Jun 2019 16:47:34: 6000000 INFO @ Sun, 02 Jun 2019 16:47:35: 6000000 INFO @ Sun, 02 Jun 2019 16:47:39: 8000000 INFO @ Sun, 02 Jun 2019 16:47:44: 7000000 INFO @ Sun, 02 Jun 2019 16:47:45: 7000000 INFO @ Sun, 02 Jun 2019 16:47:48: 9000000 INFO @ Sun, 02 Jun 2019 16:47:54: 8000000 INFO @ Sun, 02 Jun 2019 16:47:55: 8000000 INFO @ Sun, 02 Jun 2019 16:47:56: 10000000 INFO @ Sun, 02 Jun 2019 16:48:04: 9000000 INFO @ Sun, 02 Jun 2019 16:48:04: 11000000 INFO @ Sun, 02 Jun 2019 16:48:05: 9000000 INFO @ Sun, 02 Jun 2019 16:48:12: 12000000 INFO @ Sun, 02 Jun 2019 16:48:14: 10000000 INFO @ Sun, 02 Jun 2019 16:48:15: 10000000 INFO @ Sun, 02 Jun 2019 16:48:18: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:18: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:18: #1 total tags in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:18: #1 tags after filtering in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:18: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:20: #2 number of paired peaks: 1664 INFO @ Sun, 02 Jun 2019 16:48:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:20: #2 predicted fragment length is 244 bps INFO @ Sun, 02 Jun 2019 16:48:20: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sun, 02 Jun 2019 16:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20_model.r INFO @ Sun, 02 Jun 2019 16:48:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:24: 11000000 INFO @ Sun, 02 Jun 2019 16:48:25: 11000000 INFO @ Sun, 02 Jun 2019 16:48:34: 12000000 INFO @ Sun, 02 Jun 2019 16:48:35: 12000000 INFO @ Sun, 02 Jun 2019 16:48:40: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:40: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:40: #1 total tags in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:41: #1 tags after filtering in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:41: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:41: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:41: #1 total tags in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:42: #1 tags after filtering in treatment: 12683923 INFO @ Sun, 02 Jun 2019 16:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:42: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:42: #2 number of paired peaks: 1664 INFO @ Sun, 02 Jun 2019 16:48:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:42: #2 predicted fragment length is 244 bps INFO @ Sun, 02 Jun 2019 16:48:42: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sun, 02 Jun 2019 16:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10_model.r INFO @ Sun, 02 Jun 2019 16:48:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:43: #2 number of paired peaks: 1664 INFO @ Sun, 02 Jun 2019 16:48:43: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:43: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:43: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:43: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:43: #2 predicted fragment length is 244 bps INFO @ Sun, 02 Jun 2019 16:48:43: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sun, 02 Jun 2019 16:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05_model.r INFO @ Sun, 02 Jun 2019 16:48:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:49:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.20_summits.bed INFO @ Sun, 02 Jun 2019 16:49:19: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2033 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.10_summits.bed INFO @ Sun, 02 Jun 2019 16:49:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3990 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543055/SRX2543055.05_summits.bed INFO @ Sun, 02 Jun 2019 16:49:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6228 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。