Job ID = 1303236 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:18:30 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 ) 2019-06-03T11:18:30 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 ) 2019-06-03T11:23:43 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 : 24,717,305 reads read : 24,717,305 reads written : 24,717,305 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: 00:06:47 24717305 reads; of these: 24717305 (100.00%) were unpaired; of these: 3902087 (15.79%) aligned 0 times 18550102 (75.05%) aligned exactly 1 time 2265116 (9.16%) aligned >1 times 84.21% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 14365488 / 20815218 = 0.6901 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 20:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.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 20:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.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 20:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.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 20:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:40:49: 1000000 INFO @ Mon, 03 Jun 2019 20:40:50: 1000000 INFO @ Mon, 03 Jun 2019 20:40:52: 1000000 INFO @ Mon, 03 Jun 2019 20:40:56: 2000000 INFO @ Mon, 03 Jun 2019 20:40:58: 2000000 INFO @ Mon, 03 Jun 2019 20:41:01: 2000000 INFO @ Mon, 03 Jun 2019 20:41:03: 3000000 INFO @ Mon, 03 Jun 2019 20:41:05: 3000000 INFO @ Mon, 03 Jun 2019 20:41:10: 4000000 INFO @ Mon, 03 Jun 2019 20:41:10: 3000000 INFO @ Mon, 03 Jun 2019 20:41:13: 4000000 INFO @ Mon, 03 Jun 2019 20:41:17: 5000000 INFO @ Mon, 03 Jun 2019 20:41:20: 4000000 INFO @ Mon, 03 Jun 2019 20:41:20: 5000000 INFO @ Mon, 03 Jun 2019 20:41:24: 6000000 INFO @ Mon, 03 Jun 2019 20:41:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:27: #1 total tags in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:27: #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 20:41:27: #1 tags after filtering in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:27: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:28: 6000000 INFO @ Mon, 03 Jun 2019 20:41:28: #2 number of paired peaks: 6013 INFO @ Mon, 03 Jun 2019 20:41:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:28: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 20:41:28: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 20:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10_model.r INFO @ Mon, 03 Jun 2019 20:41:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:29: 5000000 INFO @ Mon, 03 Jun 2019 20:41:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:31: #1 total tags in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:31: #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 20:41:31: #1 tags after filtering in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:31: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:32: #2 number of paired peaks: 6013 INFO @ Mon, 03 Jun 2019 20:41:32: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:33: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:33: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:33: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:33: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 20:41:33: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 20:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05_model.r INFO @ Mon, 03 Jun 2019 20:41:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:38: 6000000 INFO @ Mon, 03 Jun 2019 20:41:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:42: #1 total tags in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:42: #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 20:41:42: #1 tags after filtering in treatment: 6449730 INFO @ Mon, 03 Jun 2019 20:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:42: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:43: #2 number of paired peaks: 6013 INFO @ Mon, 03 Jun 2019 20:41:43: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:43: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:43: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:43: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:43: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 20:41:43: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 20:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20_model.r INFO @ Mon, 03 Jun 2019 20:41:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:41:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:42:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.10_summits.bed INFO @ Mon, 03 Jun 2019 20:42:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4610 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.05_summits.bed INFO @ Mon, 03 Jun 2019 20:42:05: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9254 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:42:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933901/SRX4933901.20_summits.bed INFO @ Mon, 03 Jun 2019 20:42:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1805 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。