Job ID = 1301384 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:54:57 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 : 20,210,628 reads read : 20,210,628 reads written : 20,210,628 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: 00:08:07 20210628 reads; of these: 20210628 (100.00%) were unpaired; of these: 3335404 (16.50%) aligned 0 times 9608035 (47.54%) aligned exactly 1 time 7267189 (35.96%) aligned >1 times 83.50% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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] 5718409 / 16875224 = 0.3389 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 20:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.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 20:09:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.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 20:09:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.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 20:09:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:32: 1000000 INFO @ Mon, 03 Jun 2019 20:09:34: 1000000 INFO @ Mon, 03 Jun 2019 20:09:34: 1000000 INFO @ Mon, 03 Jun 2019 20:09:39: 2000000 INFO @ Mon, 03 Jun 2019 20:09:41: 2000000 INFO @ Mon, 03 Jun 2019 20:09:42: 2000000 INFO @ Mon, 03 Jun 2019 20:09:45: 3000000 INFO @ Mon, 03 Jun 2019 20:09:48: 3000000 INFO @ Mon, 03 Jun 2019 20:09:50: 3000000 INFO @ Mon, 03 Jun 2019 20:09:52: 4000000 INFO @ Mon, 03 Jun 2019 20:09:56: 4000000 INFO @ Mon, 03 Jun 2019 20:09:58: 5000000 INFO @ Mon, 03 Jun 2019 20:09:58: 4000000 INFO @ Mon, 03 Jun 2019 20:10:04: 5000000 INFO @ Mon, 03 Jun 2019 20:10:05: 6000000 INFO @ Mon, 03 Jun 2019 20:10:06: 5000000 INFO @ Mon, 03 Jun 2019 20:10:11: 6000000 INFO @ Mon, 03 Jun 2019 20:10:11: 7000000 INFO @ Mon, 03 Jun 2019 20:10:14: 6000000 INFO @ Mon, 03 Jun 2019 20:10:18: 8000000 INFO @ Mon, 03 Jun 2019 20:10:18: 7000000 INFO @ Mon, 03 Jun 2019 20:10:23: 7000000 INFO @ Mon, 03 Jun 2019 20:10:24: 9000000 INFO @ Mon, 03 Jun 2019 20:10:26: 8000000 INFO @ Mon, 03 Jun 2019 20:10:31: 10000000 INFO @ Mon, 03 Jun 2019 20:10:31: 8000000 INFO @ Mon, 03 Jun 2019 20:10:33: 9000000 INFO @ Mon, 03 Jun 2019 20:10:38: 11000000 INFO @ Mon, 03 Jun 2019 20:10:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:10:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:10:39: #1 total tags in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:10:39: #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 20:10:39: #1 tags after filtering in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:10:39: #1 finished! INFO @ Mon, 03 Jun 2019 20:10:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:10:39: 9000000 INFO @ Mon, 03 Jun 2019 20:10:40: 10000000 INFO @ Mon, 03 Jun 2019 20:10:40: #2 number of paired peaks: 2446 INFO @ Mon, 03 Jun 2019 20:10:40: start model_add_line... INFO @ Mon, 03 Jun 2019 20:10:40: start X-correlation... INFO @ Mon, 03 Jun 2019 20:10:40: end of X-cor INFO @ Mon, 03 Jun 2019 20:10:40: #2 finished! INFO @ Mon, 03 Jun 2019 20:10:40: #2 predicted fragment length is 236 bps INFO @ Mon, 03 Jun 2019 20:10:40: #2 alternative fragment length(s) may be 236 bps INFO @ Mon, 03 Jun 2019 20:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10_model.r INFO @ Mon, 03 Jun 2019 20:10:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:10:47: 10000000 INFO @ Mon, 03 Jun 2019 20:10:47: 11000000 INFO @ Mon, 03 Jun 2019 20:10:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:10:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:10:48: #1 total tags in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:10:48: #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 20:10:49: #1 tags after filtering in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:10:49: #1 finished! INFO @ Mon, 03 Jun 2019 20:10:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:10:50: #2 number of paired peaks: 2446 INFO @ Mon, 03 Jun 2019 20:10:50: start model_add_line... INFO @ Mon, 03 Jun 2019 20:10:50: start X-correlation... INFO @ Mon, 03 Jun 2019 20:10:50: end of X-cor INFO @ Mon, 03 Jun 2019 20:10:50: #2 finished! INFO @ Mon, 03 Jun 2019 20:10:50: #2 predicted fragment length is 236 bps INFO @ Mon, 03 Jun 2019 20:10:50: #2 alternative fragment length(s) may be 236 bps INFO @ Mon, 03 Jun 2019 20:10:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20_model.r INFO @ Mon, 03 Jun 2019 20:10:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:10:55: 11000000 INFO @ Mon, 03 Jun 2019 20:10:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:10:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:10:56: #1 total tags in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:10:56: #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 20:10:56: #1 tags after filtering in treatment: 11156815 INFO @ Mon, 03 Jun 2019 20:10:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:10:56: #1 finished! INFO @ Mon, 03 Jun 2019 20:10:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:10:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:10:58: #2 number of paired peaks: 2446 INFO @ Mon, 03 Jun 2019 20:10:58: start model_add_line... INFO @ Mon, 03 Jun 2019 20:10:58: start X-correlation... INFO @ Mon, 03 Jun 2019 20:10:58: end of X-cor INFO @ Mon, 03 Jun 2019 20:10:58: #2 finished! INFO @ Mon, 03 Jun 2019 20:10:58: #2 predicted fragment length is 236 bps INFO @ Mon, 03 Jun 2019 20:10:58: #2 alternative fragment length(s) may be 236 bps INFO @ Mon, 03 Jun 2019 20:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05_model.r INFO @ Mon, 03 Jun 2019 20:10:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:11:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:11:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:11:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.10_summits.bed INFO @ Mon, 03 Jun 2019 20:11:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5436 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.20_summits.bed INFO @ Mon, 03 Jun 2019 20:11:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2534 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:11:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485213/SRX485213.05_summits.bed INFO @ Mon, 03 Jun 2019 20:11:54: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9600 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。