Job ID = 1304970 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:01:34 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 ) 2019-06-03T12:01:34 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 : 18,188,898 reads read : 18,188,898 reads written : 18,188,898 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: 00:04:28 18188898 reads; of these: 18188898 (100.00%) were unpaired; of these: 437045 (2.40%) aligned 0 times 15961461 (87.75%) aligned exactly 1 time 1790392 (9.84%) aligned >1 times 97.60% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 8833728 / 17751853 = 0.4976 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 21:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.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 21:16:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.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 21:16:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.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 21:16:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:49: 1000000 INFO @ Mon, 03 Jun 2019 21:16:50: 1000000 INFO @ Mon, 03 Jun 2019 21:16:50: 1000000 INFO @ Mon, 03 Jun 2019 21:16:56: 2000000 INFO @ Mon, 03 Jun 2019 21:16:57: 2000000 INFO @ Mon, 03 Jun 2019 21:16:57: 2000000 INFO @ Mon, 03 Jun 2019 21:17:02: 3000000 INFO @ Mon, 03 Jun 2019 21:17:04: 3000000 INFO @ Mon, 03 Jun 2019 21:17:04: 3000000 INFO @ Mon, 03 Jun 2019 21:17:08: 4000000 INFO @ Mon, 03 Jun 2019 21:17:11: 4000000 INFO @ Mon, 03 Jun 2019 21:17:11: 4000000 INFO @ Mon, 03 Jun 2019 21:17:15: 5000000 INFO @ Mon, 03 Jun 2019 21:17:18: 5000000 INFO @ Mon, 03 Jun 2019 21:17:18: 5000000 INFO @ Mon, 03 Jun 2019 21:17:21: 6000000 INFO @ Mon, 03 Jun 2019 21:17:25: 6000000 INFO @ Mon, 03 Jun 2019 21:17:25: 6000000 INFO @ Mon, 03 Jun 2019 21:17:27: 7000000 INFO @ Mon, 03 Jun 2019 21:17:32: 7000000 INFO @ Mon, 03 Jun 2019 21:17:32: 7000000 INFO @ Mon, 03 Jun 2019 21:17:34: 8000000 INFO @ Mon, 03 Jun 2019 21:17:39: 8000000 INFO @ Mon, 03 Jun 2019 21:17:39: 8000000 INFO @ Mon, 03 Jun 2019 21:17:39: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:17:39: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:17:39: #1 total tags in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:17:39: #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 21:17:40: #1 tags after filtering in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:17:40: #1 finished! INFO @ Mon, 03 Jun 2019 21:17:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:17:41: #2 number of paired peaks: 6025 INFO @ Mon, 03 Jun 2019 21:17:41: start model_add_line... INFO @ Mon, 03 Jun 2019 21:17:41: start X-correlation... INFO @ Mon, 03 Jun 2019 21:17:41: end of X-cor INFO @ Mon, 03 Jun 2019 21:17:41: #2 finished! INFO @ Mon, 03 Jun 2019 21:17:41: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 21:17:41: #2 alternative fragment length(s) may be 3 bps INFO @ Mon, 03 Jun 2019 21:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10_model.r WARNING @ Mon, 03 Jun 2019 21:17:41: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:17:41: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Mon, 03 Jun 2019 21:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:17:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:17:45: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:17:45: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:17:45: #1 total tags in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:17:45: #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 21:17:45: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:17:45: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:17:45: #1 total tags in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:17:45: #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 21:17:45: #1 tags after filtering in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:17:45: #1 finished! INFO @ Mon, 03 Jun 2019 21:17:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:17:45: #1 tags after filtering in treatment: 8918125 INFO @ Mon, 03 Jun 2019 21:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:17:45: #1 finished! INFO @ Mon, 03 Jun 2019 21:17:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:17:47: #2 number of paired peaks: 6025 INFO @ Mon, 03 Jun 2019 21:17:47: start model_add_line... INFO @ Mon, 03 Jun 2019 21:17:47: #2 number of paired peaks: 6025 INFO @ Mon, 03 Jun 2019 21:17:47: start model_add_line... INFO @ Mon, 03 Jun 2019 21:17:47: start X-correlation... INFO @ Mon, 03 Jun 2019 21:17:47: end of X-cor INFO @ Mon, 03 Jun 2019 21:17:47: #2 finished! INFO @ Mon, 03 Jun 2019 21:17:47: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 21:17:47: #2 alternative fragment length(s) may be 3 bps INFO @ Mon, 03 Jun 2019 21:17:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20_model.r WARNING @ Mon, 03 Jun 2019 21:17:47: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:17:47: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Mon, 03 Jun 2019 21:17:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:17:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:17:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:17:47: start X-correlation... INFO @ Mon, 03 Jun 2019 21:17:47: end of X-cor INFO @ Mon, 03 Jun 2019 21:17:47: #2 finished! INFO @ Mon, 03 Jun 2019 21:17:47: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 21:17:47: #2 alternative fragment length(s) may be 3 bps INFO @ Mon, 03 Jun 2019 21:17:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05_model.r WARNING @ Mon, 03 Jun 2019 21:17:47: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:17:47: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Mon, 03 Jun 2019 21:17:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:17:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:17:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:18:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:18:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:18:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.10_summits.bed INFO @ Mon, 03 Jun 2019 21:18:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.20_summits.bed INFO @ Mon, 03 Jun 2019 21:18:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495257/SRX495257.05_summits.bed INFO @ Mon, 03 Jun 2019 21:18:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。