Job ID = 1295034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:19:12 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 : 22,815,880 reads read : 22,815,880 reads written : 22,815,880 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 22815880 reads; of these: 22815880 (100.00%) were unpaired; of these: 752483 (3.30%) aligned 0 times 16857565 (73.89%) aligned exactly 1 time 5205832 (22.82%) aligned >1 times 96.70% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 5361778 / 22063397 = 0.2430 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 11:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.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 11:47:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:47:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.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 11:47:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:47:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.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 11:47:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:47:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:47:16: 1000000 INFO @ Mon, 03 Jun 2019 11:47:17: 1000000 INFO @ Mon, 03 Jun 2019 11:47:20: 1000000 INFO @ Mon, 03 Jun 2019 11:47:27: 2000000 INFO @ Mon, 03 Jun 2019 11:47:28: 2000000 INFO @ Mon, 03 Jun 2019 11:47:31: 2000000 INFO @ Mon, 03 Jun 2019 11:47:38: 3000000 INFO @ Mon, 03 Jun 2019 11:47:38: 3000000 INFO @ Mon, 03 Jun 2019 11:47:43: 3000000 INFO @ Mon, 03 Jun 2019 11:47:48: 4000000 INFO @ Mon, 03 Jun 2019 11:47:49: 4000000 INFO @ Mon, 03 Jun 2019 11:47:55: 4000000 INFO @ Mon, 03 Jun 2019 11:47:59: 5000000 INFO @ Mon, 03 Jun 2019 11:47:59: 5000000 INFO @ Mon, 03 Jun 2019 11:48:07: 5000000 INFO @ Mon, 03 Jun 2019 11:48:09: 6000000 INFO @ Mon, 03 Jun 2019 11:48:10: 6000000 INFO @ Mon, 03 Jun 2019 11:48:18: 6000000 INFO @ Mon, 03 Jun 2019 11:48:19: 7000000 INFO @ Mon, 03 Jun 2019 11:48:19: 7000000 INFO @ Mon, 03 Jun 2019 11:48:28: 8000000 INFO @ Mon, 03 Jun 2019 11:48:29: 8000000 INFO @ Mon, 03 Jun 2019 11:48:30: 7000000 INFO @ Mon, 03 Jun 2019 11:48:38: 9000000 INFO @ Mon, 03 Jun 2019 11:48:38: 9000000 INFO @ Mon, 03 Jun 2019 11:48:41: 8000000 INFO @ Mon, 03 Jun 2019 11:48:47: 10000000 INFO @ Mon, 03 Jun 2019 11:48:47: 10000000 INFO @ Mon, 03 Jun 2019 11:48:53: 9000000 INFO @ Mon, 03 Jun 2019 11:48:56: 11000000 INFO @ Mon, 03 Jun 2019 11:48:57: 11000000 INFO @ Mon, 03 Jun 2019 11:49:04: 10000000 INFO @ Mon, 03 Jun 2019 11:49:06: 12000000 INFO @ Mon, 03 Jun 2019 11:49:07: 12000000 INFO @ Mon, 03 Jun 2019 11:49:15: 13000000 INFO @ Mon, 03 Jun 2019 11:49:15: 11000000 INFO @ Mon, 03 Jun 2019 11:49:16: 13000000 INFO @ Mon, 03 Jun 2019 11:49:24: 14000000 INFO @ Mon, 03 Jun 2019 11:49:25: 14000000 INFO @ Mon, 03 Jun 2019 11:49:26: 12000000 INFO @ Mon, 03 Jun 2019 11:49:34: 15000000 INFO @ Mon, 03 Jun 2019 11:49:35: 15000000 INFO @ Mon, 03 Jun 2019 11:49:37: 13000000 INFO @ Mon, 03 Jun 2019 11:49:43: 16000000 INFO @ Mon, 03 Jun 2019 11:49:45: 16000000 INFO @ Mon, 03 Jun 2019 11:49:49: 14000000 INFO @ Mon, 03 Jun 2019 11:49:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:49:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:49:50: #1 total tags in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:49:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:49:50: #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 11:49:50: #1 tags after filtering in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:49:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:49:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:49:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:49:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:49:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:49:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:49:52: #1 total tags in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:49:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:49:52: #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 11:49:52: #2 number of paired peaks: 2611 INFO @ Mon, 03 Jun 2019 11:49:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:49:52: #1 tags after filtering in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:49:52: #1 finished! INFO @ Mon, 03 Jun 2019 11:49:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:49:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:49:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:49:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:49:52: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:49:52: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10_model.r INFO @ Mon, 03 Jun 2019 11:49:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:49:54: #2 number of paired peaks: 2611 INFO @ Mon, 03 Jun 2019 11:49:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:49:55: start X-correlation... INFO @ Mon, 03 Jun 2019 11:49:55: end of X-cor INFO @ Mon, 03 Jun 2019 11:49:55: #2 finished! INFO @ Mon, 03 Jun 2019 11:49:55: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:49:55: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05_model.r INFO @ Mon, 03 Jun 2019 11:49:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:50:00: 15000000 INFO @ Mon, 03 Jun 2019 11:50:10: 16000000 INFO @ Mon, 03 Jun 2019 11:50:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:50:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:50:17: #1 total tags in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:50:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:50:17: #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 11:50:18: #1 tags after filtering in treatment: 16701619 INFO @ Mon, 03 Jun 2019 11:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:50:18: #1 finished! INFO @ Mon, 03 Jun 2019 11:50:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:50:19: #2 number of paired peaks: 2611 INFO @ Mon, 03 Jun 2019 11:50:19: start model_add_line... INFO @ Mon, 03 Jun 2019 11:50:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:50:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:50:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:50:20: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:50:20: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20_model.r INFO @ Mon, 03 Jun 2019 11:50:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:50:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:50:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.10_summits.bed INFO @ Mon, 03 Jun 2019 11:51:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8017 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:51:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.05_summits.bed INFO @ Mon, 03 Jun 2019 11:51:15: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (10154 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306199/SRX306199.20_summits.bed INFO @ Mon, 03 Jun 2019 11:51:37: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5869 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。