Job ID = 1294936 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:46:27 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 ) 2019-06-03T01:57:38 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 : 22,467,727 reads read : 22,467,727 reads written : 22,467,727 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: 00:05:49 22467727 reads; of these: 22467727 (100.00%) were unpaired; of these: 1800517 (8.01%) aligned 0 times 19312644 (85.96%) aligned exactly 1 time 1354566 (6.03%) aligned >1 times 91.99% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 3343760 / 20667210 = 0.1618 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 11:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.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 11:10:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.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 11:10:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.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 11:10:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:51: 1000000 INFO @ Mon, 03 Jun 2019 11:10:52: 1000000 INFO @ Mon, 03 Jun 2019 11:10:53: 1000000 INFO @ Mon, 03 Jun 2019 11:11:00: 2000000 INFO @ Mon, 03 Jun 2019 11:11:02: 2000000 INFO @ Mon, 03 Jun 2019 11:11:03: 2000000 INFO @ Mon, 03 Jun 2019 11:11:09: 3000000 INFO @ Mon, 03 Jun 2019 11:11:12: 3000000 INFO @ Mon, 03 Jun 2019 11:11:14: 3000000 INFO @ Mon, 03 Jun 2019 11:11:18: 4000000 INFO @ Mon, 03 Jun 2019 11:11:21: 4000000 INFO @ Mon, 03 Jun 2019 11:11:23: 4000000 INFO @ Mon, 03 Jun 2019 11:11:27: 5000000 INFO @ Mon, 03 Jun 2019 11:11:31: 5000000 INFO @ Mon, 03 Jun 2019 11:11:32: 5000000 INFO @ Mon, 03 Jun 2019 11:11:35: 6000000 INFO @ Mon, 03 Jun 2019 11:11:40: 6000000 INFO @ Mon, 03 Jun 2019 11:11:42: 6000000 INFO @ Mon, 03 Jun 2019 11:11:44: 7000000 INFO @ Mon, 03 Jun 2019 11:11:49: 7000000 INFO @ Mon, 03 Jun 2019 11:11:51: 7000000 INFO @ Mon, 03 Jun 2019 11:11:53: 8000000 INFO @ Mon, 03 Jun 2019 11:11:58: 8000000 INFO @ Mon, 03 Jun 2019 11:12:00: 8000000 INFO @ Mon, 03 Jun 2019 11:12:01: 9000000 INFO @ Mon, 03 Jun 2019 11:12:08: 9000000 INFO @ Mon, 03 Jun 2019 11:12:10: 9000000 INFO @ Mon, 03 Jun 2019 11:12:10: 10000000 INFO @ Mon, 03 Jun 2019 11:12:17: 10000000 INFO @ Mon, 03 Jun 2019 11:12:19: 11000000 INFO @ Mon, 03 Jun 2019 11:12:19: 10000000 INFO @ Mon, 03 Jun 2019 11:12:25: 11000000 INFO @ Mon, 03 Jun 2019 11:12:27: 12000000 INFO @ Mon, 03 Jun 2019 11:12:28: 11000000 INFO @ Mon, 03 Jun 2019 11:12:34: 12000000 INFO @ Mon, 03 Jun 2019 11:12:36: 13000000 INFO @ Mon, 03 Jun 2019 11:12:38: 12000000 INFO @ Mon, 03 Jun 2019 11:12:45: 13000000 INFO @ Mon, 03 Jun 2019 11:12:45: 14000000 INFO @ Mon, 03 Jun 2019 11:12:47: 13000000 INFO @ Mon, 03 Jun 2019 11:12:54: 15000000 INFO @ Mon, 03 Jun 2019 11:12:54: 14000000 INFO @ Mon, 03 Jun 2019 11:12:57: 14000000 INFO @ Mon, 03 Jun 2019 11:13:03: 16000000 INFO @ Mon, 03 Jun 2019 11:13:03: 15000000 INFO @ Mon, 03 Jun 2019 11:13:06: 15000000 INFO @ Mon, 03 Jun 2019 11:13:11: 17000000 INFO @ Mon, 03 Jun 2019 11:13:12: 16000000 INFO @ Mon, 03 Jun 2019 11:13:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:13:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:13:14: #1 total tags in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:13:14: #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 11:13:14: #1 tags after filtering in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:13:14: #1 finished! INFO @ Mon, 03 Jun 2019 11:13:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:13:16: 16000000 INFO @ Mon, 03 Jun 2019 11:13:17: #2 number of paired peaks: 4577 INFO @ Mon, 03 Jun 2019 11:13:17: start model_add_line... INFO @ Mon, 03 Jun 2019 11:13:17: start X-correlation... INFO @ Mon, 03 Jun 2019 11:13:17: end of X-cor INFO @ Mon, 03 Jun 2019 11:13:17: #2 finished! INFO @ Mon, 03 Jun 2019 11:13:17: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:13:17: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05_model.r INFO @ Mon, 03 Jun 2019 11:13:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:13:21: 17000000 INFO @ Mon, 03 Jun 2019 11:13:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:13:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:13:24: #1 total tags in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:13:25: #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 11:13:25: 17000000 INFO @ Mon, 03 Jun 2019 11:13:25: #1 tags after filtering in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:13:25: #1 finished! INFO @ Mon, 03 Jun 2019 11:13:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:13:27: #2 number of paired peaks: 4577 INFO @ Mon, 03 Jun 2019 11:13:27: start model_add_line... INFO @ Mon, 03 Jun 2019 11:13:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:13:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:13:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:13:27: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:13:27: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20_model.r INFO @ Mon, 03 Jun 2019 11:13:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:13:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:13:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:13:28: #1 total tags in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:13:28: #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 11:13:28: #1 tags after filtering in treatment: 17323450 INFO @ Mon, 03 Jun 2019 11:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:13:28: #1 finished! INFO @ Mon, 03 Jun 2019 11:13:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:13:30: #2 number of paired peaks: 4577 INFO @ Mon, 03 Jun 2019 11:13:30: start model_add_line... INFO @ Mon, 03 Jun 2019 11:13:31: start X-correlation... INFO @ Mon, 03 Jun 2019 11:13:31: end of X-cor INFO @ Mon, 03 Jun 2019 11:13:31: #2 finished! INFO @ Mon, 03 Jun 2019 11:13:31: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:13:31: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10_model.r INFO @ Mon, 03 Jun 2019 11:13:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:14:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:14:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.05_summits.bed INFO @ Mon, 03 Jun 2019 11:14:39: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (11614 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.20_summits.bed INFO @ Mon, 03 Jun 2019 11:14:52: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3699 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288001/SRX288001.10_summits.bed INFO @ Mon, 03 Jun 2019 11:14:54: Done! pass1 - making usageList (12 chroms): 4 millis pass2 - checking and writing primary data (7249 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。