Job ID = 1294961 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:01:26 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 : 15,554,135 reads read : 15,554,135 reads written : 15,554,135 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: 00:05:28 15554135 reads; of these: 15554135 (100.00%) were unpaired; of these: 973251 (6.26%) aligned 0 times 11640288 (74.84%) aligned exactly 1 time 2940596 (18.91%) aligned >1 times 93.74% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 1412445 / 14580884 = 0.0969 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 11:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.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 11:12:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.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 11:12:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.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 11:12:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:57: 1000000 INFO @ Mon, 03 Jun 2019 11:12:57: 1000000 INFO @ Mon, 03 Jun 2019 11:12:59: 1000000 INFO @ Mon, 03 Jun 2019 11:13:04: 2000000 INFO @ Mon, 03 Jun 2019 11:13:05: 2000000 INFO @ Mon, 03 Jun 2019 11:13:08: 2000000 INFO @ Mon, 03 Jun 2019 11:13:11: 3000000 INFO @ Mon, 03 Jun 2019 11:13:12: 3000000 INFO @ Mon, 03 Jun 2019 11:13:17: 3000000 INFO @ Mon, 03 Jun 2019 11:13:18: 4000000 INFO @ Mon, 03 Jun 2019 11:13:20: 4000000 INFO @ Mon, 03 Jun 2019 11:13:24: 5000000 INFO @ Mon, 03 Jun 2019 11:13:25: 4000000 INFO @ Mon, 03 Jun 2019 11:13:27: 5000000 INFO @ Mon, 03 Jun 2019 11:13:33: 6000000 INFO @ Mon, 03 Jun 2019 11:13:35: 6000000 INFO @ Mon, 03 Jun 2019 11:13:35: 5000000 INFO @ Mon, 03 Jun 2019 11:13:42: 7000000 INFO @ Mon, 03 Jun 2019 11:13:44: 7000000 INFO @ Mon, 03 Jun 2019 11:13:45: 6000000 INFO @ Mon, 03 Jun 2019 11:13:50: 8000000 INFO @ Mon, 03 Jun 2019 11:13:52: 8000000 INFO @ Mon, 03 Jun 2019 11:13:54: 7000000 INFO @ Mon, 03 Jun 2019 11:13:57: 9000000 INFO @ Mon, 03 Jun 2019 11:13:59: 9000000 INFO @ Mon, 03 Jun 2019 11:14:03: 8000000 INFO @ Mon, 03 Jun 2019 11:14:04: 10000000 INFO @ Mon, 03 Jun 2019 11:14:06: 10000000 INFO @ Mon, 03 Jun 2019 11:14:11: 9000000 INFO @ Mon, 03 Jun 2019 11:14:12: 11000000 INFO @ Mon, 03 Jun 2019 11:14:13: 11000000 INFO @ Mon, 03 Jun 2019 11:14:19: 12000000 INFO @ Mon, 03 Jun 2019 11:14:21: 10000000 INFO @ Mon, 03 Jun 2019 11:14:22: 12000000 INFO @ Mon, 03 Jun 2019 11:14:27: 13000000 INFO @ Mon, 03 Jun 2019 11:14:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:28: #1 total tags in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:28: #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 11:14:28: #1 tags after filtering in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:28: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:30: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 11:14:30: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:30: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:30: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:30: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:30: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 11:14:30: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 11:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10_model.r INFO @ Mon, 03 Jun 2019 11:14:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:31: 11000000 INFO @ Mon, 03 Jun 2019 11:14:32: 13000000 INFO @ Mon, 03 Jun 2019 11:14:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:34: #1 total tags in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:34: #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 11:14:34: #1 tags after filtering in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:34: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:36: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 11:14:36: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:36: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:36: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:36: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:36: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 11:14:36: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 11:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05_model.r INFO @ Mon, 03 Jun 2019 11:14:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:40: 12000000 INFO @ Mon, 03 Jun 2019 11:14:49: 13000000 INFO @ Mon, 03 Jun 2019 11:14:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:50: #1 total tags in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:50: #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 11:14:50: #1 tags after filtering in treatment: 13168439 INFO @ Mon, 03 Jun 2019 11:14:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:52: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 11:14:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:52: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 11:14:52: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 11:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20_model.r INFO @ Mon, 03 Jun 2019 11:14:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:15:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.10_summits.bed INFO @ Mon, 03 Jun 2019 11:15:27: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4663 records, 4 fields): 346 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.05_summits.bed INFO @ Mon, 03 Jun 2019 11:15:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6366 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288022/SRX288022.20_summits.bed INFO @ Mon, 03 Jun 2019 11:15:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3096 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。