Job ID = 1293599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T15:59:40 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 : 39,221,792 reads read : 39,221,792 reads written : 39,221,792 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: 00:10:58 39221792 reads; of these: 39221792 (100.00%) were unpaired; of these: 2784049 (7.10%) aligned 0 times 29633627 (75.55%) aligned exactly 1 time 6804116 (17.35%) aligned >1 times 92.90% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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 16 files... [bam_rmdupse_core] 19962632 / 36437743 = 0.5479 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 01:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.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 01:22:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.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 01:22:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.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 01:22:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:37: 1000000 INFO @ Mon, 03 Jun 2019 01:22:37: 1000000 INFO @ Mon, 03 Jun 2019 01:22:38: 1000000 INFO @ Mon, 03 Jun 2019 01:22:43: 2000000 INFO @ Mon, 03 Jun 2019 01:22:44: 2000000 INFO @ Mon, 03 Jun 2019 01:22:46: 2000000 INFO @ Mon, 03 Jun 2019 01:22:50: 3000000 INFO @ Mon, 03 Jun 2019 01:22:52: 3000000 INFO @ Mon, 03 Jun 2019 01:22:55: 3000000 INFO @ Mon, 03 Jun 2019 01:22:56: 4000000 INFO @ Mon, 03 Jun 2019 01:22:59: 4000000 INFO @ Mon, 03 Jun 2019 01:23:03: 5000000 INFO @ Mon, 03 Jun 2019 01:23:03: 4000000 INFO @ Mon, 03 Jun 2019 01:23:06: 5000000 INFO @ Mon, 03 Jun 2019 01:23:09: 6000000 INFO @ Mon, 03 Jun 2019 01:23:11: 5000000 INFO @ Mon, 03 Jun 2019 01:23:13: 6000000 INFO @ Mon, 03 Jun 2019 01:23:15: 7000000 INFO @ Mon, 03 Jun 2019 01:23:19: 6000000 INFO @ Mon, 03 Jun 2019 01:23:20: 7000000 INFO @ Mon, 03 Jun 2019 01:23:22: 8000000 INFO @ Mon, 03 Jun 2019 01:23:27: 8000000 INFO @ Mon, 03 Jun 2019 01:23:27: 7000000 INFO @ Mon, 03 Jun 2019 01:23:28: 9000000 INFO @ Mon, 03 Jun 2019 01:23:34: 9000000 INFO @ Mon, 03 Jun 2019 01:23:34: 10000000 INFO @ Mon, 03 Jun 2019 01:23:35: 8000000 INFO @ Mon, 03 Jun 2019 01:23:41: 11000000 INFO @ Mon, 03 Jun 2019 01:23:41: 10000000 INFO @ Mon, 03 Jun 2019 01:23:43: 9000000 INFO @ Mon, 03 Jun 2019 01:23:47: 12000000 INFO @ Mon, 03 Jun 2019 01:23:48: 11000000 INFO @ Mon, 03 Jun 2019 01:23:51: 10000000 INFO @ Mon, 03 Jun 2019 01:23:54: 13000000 INFO @ Mon, 03 Jun 2019 01:23:55: 12000000 INFO @ Mon, 03 Jun 2019 01:23:59: 11000000 INFO @ Mon, 03 Jun 2019 01:24:00: 14000000 INFO @ Mon, 03 Jun 2019 01:24:02: 13000000 INFO @ Mon, 03 Jun 2019 01:24:07: 15000000 INFO @ Mon, 03 Jun 2019 01:24:08: 12000000 INFO @ Mon, 03 Jun 2019 01:24:09: 14000000 INFO @ Mon, 03 Jun 2019 01:24:13: 16000000 INFO @ Mon, 03 Jun 2019 01:24:16: 13000000 INFO @ Mon, 03 Jun 2019 01:24:16: 15000000 INFO @ Mon, 03 Jun 2019 01:24:16: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:24:16: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:24:16: #1 total tags in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:16: #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 01:24:17: #1 tags after filtering in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:17: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:18: #2 number of paired peaks: 1891 INFO @ Mon, 03 Jun 2019 01:24:18: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:19: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:19: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:19: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:19: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 01:24:19: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 01:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05_model.r INFO @ Mon, 03 Jun 2019 01:24:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:24:23: 16000000 INFO @ Mon, 03 Jun 2019 01:24:24: 14000000 INFO @ Mon, 03 Jun 2019 01:24:27: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:24:27: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:24:27: #1 total tags in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:27: #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 01:24:27: #1 tags after filtering in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:27: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:29: #2 number of paired peaks: 1891 INFO @ Mon, 03 Jun 2019 01:24:29: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:29: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:29: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:29: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:29: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 01:24:29: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 01:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20_model.r INFO @ Mon, 03 Jun 2019 01:24:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:24:32: 15000000 INFO @ Mon, 03 Jun 2019 01:24:39: 16000000 INFO @ Mon, 03 Jun 2019 01:24:43: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:24:43: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:24:43: #1 total tags in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:43: #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 01:24:44: #1 tags after filtering in treatment: 16475111 INFO @ Mon, 03 Jun 2019 01:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:44: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:45: #2 number of paired peaks: 1891 INFO @ Mon, 03 Jun 2019 01:24:45: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:46: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:46: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:46: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:46: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 01:24:46: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 01:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10_model.r INFO @ Mon, 03 Jun 2019 01:24:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:25:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.05_summits.bed INFO @ Mon, 03 Jun 2019 01:25:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11574 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:25:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.20_summits.bed INFO @ Mon, 03 Jun 2019 01:25:40: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4630 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032387/SRX1032387.10_summits.bed INFO @ Mon, 03 Jun 2019 01:25:56: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8050 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。