Job ID = 1294179 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:19:51 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 : 37,678,041 reads read : 37,678,041 reads written : 37,678,041 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:58 37678041 reads; of these: 37678041 (100.00%) were unpaired; of these: 6726116 (17.85%) aligned 0 times 21690324 (57.57%) aligned exactly 1 time 9261601 (24.58%) aligned >1 times 82.15% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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] 12443325 / 30951925 = 0.4020 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 05:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.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 05:42:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.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 05:42:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.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 05:42:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:10: 1000000 INFO @ Mon, 03 Jun 2019 05:42:11: 1000000 INFO @ Mon, 03 Jun 2019 05:42:11: 1000000 INFO @ Mon, 03 Jun 2019 05:42:18: 2000000 INFO @ Mon, 03 Jun 2019 05:42:21: 2000000 INFO @ Mon, 03 Jun 2019 05:42:21: 2000000 INFO @ Mon, 03 Jun 2019 05:42:26: 3000000 INFO @ Mon, 03 Jun 2019 05:42:31: 3000000 INFO @ Mon, 03 Jun 2019 05:42:32: 3000000 INFO @ Mon, 03 Jun 2019 05:42:35: 4000000 INFO @ Mon, 03 Jun 2019 05:42:41: 4000000 INFO @ Mon, 03 Jun 2019 05:42:42: 4000000 INFO @ Mon, 03 Jun 2019 05:42:43: 5000000 INFO @ Mon, 03 Jun 2019 05:42:51: 6000000 INFO @ Mon, 03 Jun 2019 05:42:52: 5000000 INFO @ Mon, 03 Jun 2019 05:42:52: 5000000 INFO @ Mon, 03 Jun 2019 05:42:59: 7000000 INFO @ Mon, 03 Jun 2019 05:43:03: 6000000 INFO @ Mon, 03 Jun 2019 05:43:04: 6000000 INFO @ Mon, 03 Jun 2019 05:43:06: 8000000 INFO @ Mon, 03 Jun 2019 05:43:15: 7000000 INFO @ Mon, 03 Jun 2019 05:43:15: 7000000 INFO @ Mon, 03 Jun 2019 05:43:15: 9000000 INFO @ Mon, 03 Jun 2019 05:43:24: 10000000 INFO @ Mon, 03 Jun 2019 05:43:26: 8000000 INFO @ Mon, 03 Jun 2019 05:43:26: 8000000 INFO @ Mon, 03 Jun 2019 05:43:33: 11000000 INFO @ Mon, 03 Jun 2019 05:43:36: 9000000 INFO @ Mon, 03 Jun 2019 05:43:37: 9000000 INFO @ Mon, 03 Jun 2019 05:43:41: 12000000 INFO @ Mon, 03 Jun 2019 05:43:46: 10000000 INFO @ Mon, 03 Jun 2019 05:43:47: 10000000 INFO @ Mon, 03 Jun 2019 05:43:49: 13000000 INFO @ Mon, 03 Jun 2019 05:43:55: 11000000 INFO @ Mon, 03 Jun 2019 05:43:57: 14000000 INFO @ Mon, 03 Jun 2019 05:43:58: 11000000 INFO @ Mon, 03 Jun 2019 05:44:05: 12000000 INFO @ Mon, 03 Jun 2019 05:44:05: 15000000 INFO @ Mon, 03 Jun 2019 05:44:10: 12000000 INFO @ Mon, 03 Jun 2019 05:44:13: 16000000 INFO @ Mon, 03 Jun 2019 05:44:15: 13000000 INFO @ Mon, 03 Jun 2019 05:44:20: 13000000 INFO @ Mon, 03 Jun 2019 05:44:21: 17000000 INFO @ Mon, 03 Jun 2019 05:44:24: 14000000 INFO @ Mon, 03 Jun 2019 05:44:29: 18000000 INFO @ Mon, 03 Jun 2019 05:44:31: 14000000 INFO @ Mon, 03 Jun 2019 05:44:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:44:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:44:34: #1 total tags in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:44:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:44:34: #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 05:44:34: #1 tags after filtering in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:44:34: #1 finished! INFO @ Mon, 03 Jun 2019 05:44:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:44:34: 15000000 INFO @ Mon, 03 Jun 2019 05:44:36: #2 number of paired peaks: 2419 INFO @ Mon, 03 Jun 2019 05:44:36: start model_add_line... INFO @ Mon, 03 Jun 2019 05:44:36: start X-correlation... INFO @ Mon, 03 Jun 2019 05:44:36: end of X-cor INFO @ Mon, 03 Jun 2019 05:44:36: #2 finished! INFO @ Mon, 03 Jun 2019 05:44:36: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 05:44:36: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 05:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05_model.r INFO @ Mon, 03 Jun 2019 05:44:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:44:42: 15000000 INFO @ Mon, 03 Jun 2019 05:44:45: 16000000 INFO @ Mon, 03 Jun 2019 05:44:53: 16000000 INFO @ Mon, 03 Jun 2019 05:44:55: 17000000 INFO @ Mon, 03 Jun 2019 05:45:04: 17000000 INFO @ Mon, 03 Jun 2019 05:45:04: 18000000 INFO @ Mon, 03 Jun 2019 05:45:09: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:45:09: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:45:09: #1 total tags in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:45:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:45:09: #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 05:45:09: #1 tags after filtering in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:45:09: #1 finished! INFO @ Mon, 03 Jun 2019 05:45:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:45:11: #2 number of paired peaks: 2419 INFO @ Mon, 03 Jun 2019 05:45:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:45:12: start X-correlation... INFO @ Mon, 03 Jun 2019 05:45:12: end of X-cor INFO @ Mon, 03 Jun 2019 05:45:12: #2 finished! INFO @ Mon, 03 Jun 2019 05:45:12: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 05:45:12: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 05:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10_model.r INFO @ Mon, 03 Jun 2019 05:45:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:45:14: 18000000 INFO @ Mon, 03 Jun 2019 05:45:19: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:45:19: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:45:19: #1 total tags in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:45:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:45:19: #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 05:45:20: #1 tags after filtering in treatment: 18508600 INFO @ Mon, 03 Jun 2019 05:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:45:20: #1 finished! INFO @ Mon, 03 Jun 2019 05:45:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:45:22: #2 number of paired peaks: 2419 INFO @ Mon, 03 Jun 2019 05:45:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:45:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:45:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:45:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:45:22: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 05:45:22: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 05:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20_model.r INFO @ Mon, 03 Jun 2019 05:45:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:45:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.05_summits.bed INFO @ Mon, 03 Jun 2019 05:45:59: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8712 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:46:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:46:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.10_summits.bed INFO @ Mon, 03 Jun 2019 05:46:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6890 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197567/SRX197567.20_summits.bed INFO @ Mon, 03 Jun 2019 05:46:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5006 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。