Job ID = 1301163 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:38:26 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 ) 2019-06-03T10:42:07 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 ) 2019-06-03T10:42:07 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 : 27,307,334 reads read : 27,307,334 reads written : 27,307,334 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: 00:08:59 27307334 reads; of these: 27307334 (100.00%) were unpaired; of these: 4376231 (16.03%) aligned 0 times 15378533 (56.32%) aligned exactly 1 time 7552570 (27.66%) aligned >1 times 83.97% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 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 12 files... [bam_rmdupse_core] 8744081 / 22931103 = 0.3813 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 20:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.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 20:05:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.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 20:05:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.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 20:05:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:53: 1000000 INFO @ Mon, 03 Jun 2019 20:05:54: 1000000 INFO @ Mon, 03 Jun 2019 20:05:55: 1000000 INFO @ Mon, 03 Jun 2019 20:06:00: 2000000 INFO @ Mon, 03 Jun 2019 20:06:02: 2000000 INFO @ Mon, 03 Jun 2019 20:06:04: 2000000 INFO @ Mon, 03 Jun 2019 20:06:08: 3000000 INFO @ Mon, 03 Jun 2019 20:06:10: 3000000 INFO @ Mon, 03 Jun 2019 20:06:13: 3000000 INFO @ Mon, 03 Jun 2019 20:06:15: 4000000 INFO @ Mon, 03 Jun 2019 20:06:18: 4000000 INFO @ Mon, 03 Jun 2019 20:06:21: 4000000 INFO @ Mon, 03 Jun 2019 20:06:22: 5000000 INFO @ Mon, 03 Jun 2019 20:06:26: 5000000 INFO @ Mon, 03 Jun 2019 20:06:29: 5000000 INFO @ Mon, 03 Jun 2019 20:06:29: 6000000 INFO @ Mon, 03 Jun 2019 20:06:34: 6000000 INFO @ Mon, 03 Jun 2019 20:06:37: 7000000 INFO @ Mon, 03 Jun 2019 20:06:37: 6000000 INFO @ Mon, 03 Jun 2019 20:06:42: 7000000 INFO @ Mon, 03 Jun 2019 20:06:44: 8000000 INFO @ Mon, 03 Jun 2019 20:06:46: 7000000 INFO @ Mon, 03 Jun 2019 20:06:50: 8000000 INFO @ Mon, 03 Jun 2019 20:06:51: 9000000 INFO @ Mon, 03 Jun 2019 20:06:54: 8000000 INFO @ Mon, 03 Jun 2019 20:06:57: 9000000 INFO @ Mon, 03 Jun 2019 20:06:58: 10000000 INFO @ Mon, 03 Jun 2019 20:07:02: 9000000 INFO @ Mon, 03 Jun 2019 20:07:05: 10000000 INFO @ Mon, 03 Jun 2019 20:07:06: 11000000 INFO @ Mon, 03 Jun 2019 20:07:11: 10000000 INFO @ Mon, 03 Jun 2019 20:07:13: 12000000 INFO @ Mon, 03 Jun 2019 20:07:13: 11000000 INFO @ Mon, 03 Jun 2019 20:07:19: 11000000 INFO @ Mon, 03 Jun 2019 20:07:20: 13000000 INFO @ Mon, 03 Jun 2019 20:07:21: 12000000 INFO @ Mon, 03 Jun 2019 20:07:28: 12000000 INFO @ Mon, 03 Jun 2019 20:07:28: 14000000 INFO @ Mon, 03 Jun 2019 20:07:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:29: #1 total tags in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:29: #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 20:07:30: #1 tags after filtering in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:30: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:30: 13000000 INFO @ Mon, 03 Jun 2019 20:07:31: #2 number of paired peaks: 1160 INFO @ Mon, 03 Jun 2019 20:07:31: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:31: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:31: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:31: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:31: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 20:07:31: #2 alternative fragment length(s) may be 3,101,119 bps INFO @ Mon, 03 Jun 2019 20:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10_model.r INFO @ Mon, 03 Jun 2019 20:07:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:07:36: 13000000 INFO @ Mon, 03 Jun 2019 20:07:38: 14000000 INFO @ Mon, 03 Jun 2019 20:07:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:39: #1 total tags in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:39: #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 20:07:40: #1 tags after filtering in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:41: #2 number of paired peaks: 1160 INFO @ Mon, 03 Jun 2019 20:07:41: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:41: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:41: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:41: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:41: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 20:07:41: #2 alternative fragment length(s) may be 3,101,119 bps INFO @ Mon, 03 Jun 2019 20:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05_model.r INFO @ Mon, 03 Jun 2019 20:07:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:07:45: 14000000 INFO @ Mon, 03 Jun 2019 20:07:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:47: #1 total tags in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:47: #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 20:07:47: #1 tags after filtering in treatment: 14187022 INFO @ Mon, 03 Jun 2019 20:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:47: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:48: #2 number of paired peaks: 1160 INFO @ Mon, 03 Jun 2019 20:07:48: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:48: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:48: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:48: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:48: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 20:07:48: #2 alternative fragment length(s) may be 3,101,119 bps INFO @ Mon, 03 Jun 2019 20:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20_model.r INFO @ Mon, 03 Jun 2019 20:07:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.10_summits.bed INFO @ Mon, 03 Jun 2019 20:08:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2656 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:08:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.05_summits.bed INFO @ Mon, 03 Jun 2019 20:08:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4765 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485203/SRX485203.20_summits.bed INFO @ Mon, 03 Jun 2019 20:08:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1279 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。