Job ID = 1294878 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:33:17 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 : 13,596,200 reads read : 13,596,200 reads written : 13,596,200 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: 00:05:06 13596200 reads; of these: 13596200 (100.00%) were unpaired; of these: 748884 (5.51%) aligned 0 times 9977608 (73.39%) aligned exactly 1 time 2869708 (21.11%) aligned >1 times 94.49% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 2852418 / 12847316 = 0.2220 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 10:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.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 10:47:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.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 10:47:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.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 10:47:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:35: 1000000 INFO @ Mon, 03 Jun 2019 10:47:37: 1000000 INFO @ Mon, 03 Jun 2019 10:47:38: 1000000 INFO @ Mon, 03 Jun 2019 10:47:43: 2000000 INFO @ Mon, 03 Jun 2019 10:47:47: 2000000 INFO @ Mon, 03 Jun 2019 10:47:48: 2000000 INFO @ Mon, 03 Jun 2019 10:47:51: 3000000 INFO @ Mon, 03 Jun 2019 10:47:56: 3000000 INFO @ Mon, 03 Jun 2019 10:47:58: 3000000 INFO @ Mon, 03 Jun 2019 10:47:59: 4000000 INFO @ Mon, 03 Jun 2019 10:48:06: 4000000 INFO @ Mon, 03 Jun 2019 10:48:07: 5000000 INFO @ Mon, 03 Jun 2019 10:48:08: 4000000 INFO @ Mon, 03 Jun 2019 10:48:15: 6000000 INFO @ Mon, 03 Jun 2019 10:48:16: 5000000 INFO @ Mon, 03 Jun 2019 10:48:18: 5000000 INFO @ Mon, 03 Jun 2019 10:48:23: 7000000 INFO @ Mon, 03 Jun 2019 10:48:25: 6000000 INFO @ Mon, 03 Jun 2019 10:48:28: 6000000 INFO @ Mon, 03 Jun 2019 10:48:30: 8000000 INFO @ Mon, 03 Jun 2019 10:48:34: 7000000 INFO @ Mon, 03 Jun 2019 10:48:38: 7000000 INFO @ Mon, 03 Jun 2019 10:48:38: 9000000 INFO @ Mon, 03 Jun 2019 10:48:43: 8000000 INFO @ Mon, 03 Jun 2019 10:48:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:48:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:48:46: #1 total tags in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:48:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:48:46: #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 10:48:46: #1 tags after filtering in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:48:46: #1 finished! INFO @ Mon, 03 Jun 2019 10:48:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:48:47: #2 number of paired peaks: 1917 INFO @ Mon, 03 Jun 2019 10:48:47: start model_add_line... INFO @ Mon, 03 Jun 2019 10:48:47: start X-correlation... INFO @ Mon, 03 Jun 2019 10:48:47: end of X-cor INFO @ Mon, 03 Jun 2019 10:48:47: #2 finished! INFO @ Mon, 03 Jun 2019 10:48:47: #2 predicted fragment length is 389 bps INFO @ Mon, 03 Jun 2019 10:48:47: #2 alternative fragment length(s) may be 389 bps INFO @ Mon, 03 Jun 2019 10:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05_model.r INFO @ Mon, 03 Jun 2019 10:48:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:48:48: 8000000 INFO @ Mon, 03 Jun 2019 10:48:52: 9000000 INFO @ Mon, 03 Jun 2019 10:48:58: 9000000 INFO @ Mon, 03 Jun 2019 10:49:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:49:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:49:02: #1 total tags in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:49:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:49:02: #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 10:49:02: #1 tags after filtering in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:49:02: #1 finished! INFO @ Mon, 03 Jun 2019 10:49:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:49:03: #2 number of paired peaks: 1917 INFO @ Mon, 03 Jun 2019 10:49:03: start model_add_line... INFO @ Mon, 03 Jun 2019 10:49:03: start X-correlation... INFO @ Mon, 03 Jun 2019 10:49:03: end of X-cor INFO @ Mon, 03 Jun 2019 10:49:03: #2 finished! INFO @ Mon, 03 Jun 2019 10:49:03: #2 predicted fragment length is 389 bps INFO @ Mon, 03 Jun 2019 10:49:03: #2 alternative fragment length(s) may be 389 bps INFO @ Mon, 03 Jun 2019 10:49:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10_model.r INFO @ Mon, 03 Jun 2019 10:49:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:49:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:49:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:49:07: #1 total tags in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:49:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:49:07: #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 10:49:07: #1 tags after filtering in treatment: 9994898 INFO @ Mon, 03 Jun 2019 10:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:49:07: #1 finished! INFO @ Mon, 03 Jun 2019 10:49:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:49:09: #2 number of paired peaks: 1917 INFO @ Mon, 03 Jun 2019 10:49:09: start model_add_line... INFO @ Mon, 03 Jun 2019 10:49:09: start X-correlation... INFO @ Mon, 03 Jun 2019 10:49:09: end of X-cor INFO @ Mon, 03 Jun 2019 10:49:09: #2 finished! INFO @ Mon, 03 Jun 2019 10:49:09: #2 predicted fragment length is 389 bps INFO @ Mon, 03 Jun 2019 10:49:09: #2 alternative fragment length(s) may be 389 bps INFO @ Mon, 03 Jun 2019 10:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20_model.r INFO @ Mon, 03 Jun 2019 10:49:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:49:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.05_summits.bed INFO @ Mon, 03 Jun 2019 10:49:38: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5640 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:49:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:49:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:49:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.10_summits.bed INFO @ Mon, 03 Jun 2019 10:49:54: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4360 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287957/SRX287957.20_summits.bed INFO @ Mon, 03 Jun 2019 10:50:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2979 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。