Job ID = 1295709 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:13:33 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 : 75,434,220 reads read : 150,868,440 reads written : 75,434,220 reads 0-length : 75,434,220 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: 00:25:02 75434220 reads; of these: 75434220 (100.00%) were unpaired; of these: 2001720 (2.65%) aligned 0 times 55761422 (73.92%) aligned exactly 1 time 17671078 (23.43%) aligned >1 times 97.35% overall alignment rate Time searching: 00:25:02 Overall time: 00:25:02 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 32 files... [bam_rmdupse_core] 37504496 / 73432500 = 0.5107 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 16:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.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 16:04:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:04:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.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 16:04:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:04:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.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 16:04:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:04:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:04:20: 1000000 INFO @ Mon, 03 Jun 2019 16:04:20: 1000000 INFO @ Mon, 03 Jun 2019 16:04:21: 1000000 INFO @ Mon, 03 Jun 2019 16:04:26: 2000000 INFO @ Mon, 03 Jun 2019 16:04:27: 2000000 INFO @ Mon, 03 Jun 2019 16:04:29: 2000000 INFO @ Mon, 03 Jun 2019 16:04:33: 3000000 INFO @ Mon, 03 Jun 2019 16:04:34: 3000000 INFO @ Mon, 03 Jun 2019 16:04:37: 3000000 INFO @ Mon, 03 Jun 2019 16:04:40: 4000000 INFO @ Mon, 03 Jun 2019 16:04:41: 4000000 INFO @ Mon, 03 Jun 2019 16:04:45: 4000000 INFO @ Mon, 03 Jun 2019 16:04:46: 5000000 INFO @ Mon, 03 Jun 2019 16:04:47: 5000000 INFO @ Mon, 03 Jun 2019 16:04:52: 5000000 INFO @ Mon, 03 Jun 2019 16:04:53: 6000000 INFO @ Mon, 03 Jun 2019 16:04:54: 6000000 INFO @ Mon, 03 Jun 2019 16:05:00: 7000000 INFO @ Mon, 03 Jun 2019 16:05:00: 6000000 INFO @ Mon, 03 Jun 2019 16:05:01: 7000000 INFO @ Mon, 03 Jun 2019 16:05:06: 8000000 INFO @ Mon, 03 Jun 2019 16:05:07: 8000000 INFO @ Mon, 03 Jun 2019 16:05:08: 7000000 INFO @ Mon, 03 Jun 2019 16:05:12: 9000000 INFO @ Mon, 03 Jun 2019 16:05:14: 9000000 INFO @ Mon, 03 Jun 2019 16:05:15: 8000000 INFO @ Mon, 03 Jun 2019 16:05:19: 10000000 INFO @ Mon, 03 Jun 2019 16:05:20: 10000000 INFO @ Mon, 03 Jun 2019 16:05:23: 9000000 INFO @ Mon, 03 Jun 2019 16:05:26: 11000000 INFO @ Mon, 03 Jun 2019 16:05:27: 11000000 INFO @ Mon, 03 Jun 2019 16:05:30: 10000000 INFO @ Mon, 03 Jun 2019 16:05:32: 12000000 INFO @ Mon, 03 Jun 2019 16:05:34: 12000000 INFO @ Mon, 03 Jun 2019 16:05:38: 11000000 INFO @ Mon, 03 Jun 2019 16:05:39: 13000000 INFO @ Mon, 03 Jun 2019 16:05:41: 13000000 INFO @ Mon, 03 Jun 2019 16:05:45: 14000000 INFO @ Mon, 03 Jun 2019 16:05:46: 12000000 INFO @ Mon, 03 Jun 2019 16:05:49: 14000000 INFO @ Mon, 03 Jun 2019 16:05:52: 15000000 INFO @ Mon, 03 Jun 2019 16:05:53: 13000000 INFO @ Mon, 03 Jun 2019 16:05:56: 15000000 INFO @ Mon, 03 Jun 2019 16:05:58: 16000000 INFO @ Mon, 03 Jun 2019 16:06:01: 14000000 INFO @ Mon, 03 Jun 2019 16:06:04: 16000000 INFO @ Mon, 03 Jun 2019 16:06:05: 17000000 INFO @ Mon, 03 Jun 2019 16:06:08: 15000000 INFO @ Mon, 03 Jun 2019 16:06:11: 17000000 INFO @ Mon, 03 Jun 2019 16:06:11: 18000000 INFO @ Mon, 03 Jun 2019 16:06:16: 16000000 INFO @ Mon, 03 Jun 2019 16:06:18: 19000000 INFO @ Mon, 03 Jun 2019 16:06:19: 18000000 INFO @ Mon, 03 Jun 2019 16:06:24: 17000000 INFO @ Mon, 03 Jun 2019 16:06:24: 20000000 INFO @ Mon, 03 Jun 2019 16:06:26: 19000000 INFO @ Mon, 03 Jun 2019 16:06:31: 21000000 INFO @ Mon, 03 Jun 2019 16:06:31: 18000000 INFO @ Mon, 03 Jun 2019 16:06:33: 20000000 INFO @ Mon, 03 Jun 2019 16:06:37: 22000000 INFO @ Mon, 03 Jun 2019 16:06:39: 19000000 INFO @ Mon, 03 Jun 2019 16:06:41: 21000000 INFO @ Mon, 03 Jun 2019 16:06:44: 23000000 INFO @ Mon, 03 Jun 2019 16:06:46: 20000000 INFO @ Mon, 03 Jun 2019 16:06:48: 22000000 INFO @ Mon, 03 Jun 2019 16:06:50: 24000000 INFO @ Mon, 03 Jun 2019 16:06:54: 21000000 INFO @ Mon, 03 Jun 2019 16:06:56: 23000000 INFO @ Mon, 03 Jun 2019 16:06:57: 25000000 INFO @ Mon, 03 Jun 2019 16:07:01: 22000000 INFO @ Mon, 03 Jun 2019 16:07:03: 24000000 INFO @ Mon, 03 Jun 2019 16:07:03: 26000000 INFO @ Mon, 03 Jun 2019 16:07:09: 23000000 INFO @ Mon, 03 Jun 2019 16:07:10: 27000000 INFO @ Mon, 03 Jun 2019 16:07:11: 25000000 INFO @ Mon, 03 Jun 2019 16:07:16: 24000000 INFO @ Mon, 03 Jun 2019 16:07:17: 28000000 INFO @ Mon, 03 Jun 2019 16:07:19: 26000000 INFO @ Mon, 03 Jun 2019 16:07:23: 29000000 INFO @ Mon, 03 Jun 2019 16:07:24: 25000000 INFO @ Mon, 03 Jun 2019 16:07:27: 27000000 INFO @ Mon, 03 Jun 2019 16:07:30: 30000000 INFO @ Mon, 03 Jun 2019 16:07:31: 26000000 INFO @ Mon, 03 Jun 2019 16:07:34: 28000000 INFO @ Mon, 03 Jun 2019 16:07:36: 31000000 INFO @ Mon, 03 Jun 2019 16:07:39: 27000000 INFO @ Mon, 03 Jun 2019 16:07:42: 29000000 INFO @ Mon, 03 Jun 2019 16:07:43: 32000000 INFO @ Mon, 03 Jun 2019 16:07:47: 28000000 INFO @ Mon, 03 Jun 2019 16:07:49: 33000000 INFO @ Mon, 03 Jun 2019 16:07:49: 30000000 INFO @ Mon, 03 Jun 2019 16:07:54: 29000000 INFO @ Mon, 03 Jun 2019 16:07:56: 34000000 INFO @ Mon, 03 Jun 2019 16:07:57: 31000000 INFO @ Mon, 03 Jun 2019 16:08:02: 30000000 INFO @ Mon, 03 Jun 2019 16:08:03: 35000000 INFO @ Mon, 03 Jun 2019 16:08:05: 32000000 INFO @ Mon, 03 Jun 2019 16:08:09: 31000000 INFO @ Mon, 03 Jun 2019 16:08:09: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 16:08:09: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 16:08:09: #1 total tags in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:08:09: #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 16:08:10: #1 tags after filtering in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:08:10: #1 finished! INFO @ Mon, 03 Jun 2019 16:08:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:08:13: 33000000 INFO @ Mon, 03 Jun 2019 16:08:14: #2 number of paired peaks: 2774 INFO @ Mon, 03 Jun 2019 16:08:14: start model_add_line... INFO @ Mon, 03 Jun 2019 16:08:14: start X-correlation... INFO @ Mon, 03 Jun 2019 16:08:14: end of X-cor INFO @ Mon, 03 Jun 2019 16:08:14: #2 finished! INFO @ Mon, 03 Jun 2019 16:08:14: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 16:08:14: #2 alternative fragment length(s) may be 1,11,36 bps INFO @ Mon, 03 Jun 2019 16:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10_model.r WARNING @ Mon, 03 Jun 2019 16:08:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 16:08:14: #2 You may need to consider one of the other alternative d(s): 1,11,36 WARNING @ Mon, 03 Jun 2019 16:08:14: #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 16:08:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:08:17: 32000000 INFO @ Mon, 03 Jun 2019 16:08:22: 34000000 INFO @ Mon, 03 Jun 2019 16:08:25: 33000000 INFO @ Mon, 03 Jun 2019 16:08:30: 35000000 INFO @ Mon, 03 Jun 2019 16:08:32: 34000000 INFO @ Mon, 03 Jun 2019 16:08:37: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 16:08:37: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 16:08:37: #1 total tags in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:08:37: #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 16:08:38: #1 tags after filtering in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:08:38: #1 finished! INFO @ Mon, 03 Jun 2019 16:08:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:08:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:08:40: 35000000 INFO @ Mon, 03 Jun 2019 16:08:41: #2 number of paired peaks: 2774 INFO @ Mon, 03 Jun 2019 16:08:41: start model_add_line... INFO @ Mon, 03 Jun 2019 16:08:42: start X-correlation... INFO @ Mon, 03 Jun 2019 16:08:42: end of X-cor INFO @ Mon, 03 Jun 2019 16:08:42: #2 finished! INFO @ Mon, 03 Jun 2019 16:08:42: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 16:08:42: #2 alternative fragment length(s) may be 1,11,36 bps INFO @ Mon, 03 Jun 2019 16:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05_model.r WARNING @ Mon, 03 Jun 2019 16:08:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 16:08:42: #2 You may need to consider one of the other alternative d(s): 1,11,36 WARNING @ Mon, 03 Jun 2019 16:08:42: #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 16:08:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:08:47: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 16:08:47: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 16:08:47: #1 total tags in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:08:47: #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 16:08:48: #1 tags after filtering in treatment: 35928004 INFO @ Mon, 03 Jun 2019 16:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:08:48: #1 finished! INFO @ Mon, 03 Jun 2019 16:08:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:08:51: #2 number of paired peaks: 2774 INFO @ Mon, 03 Jun 2019 16:08:51: start model_add_line... INFO @ Mon, 03 Jun 2019 16:08:52: start X-correlation... INFO @ Mon, 03 Jun 2019 16:08:52: end of X-cor INFO @ Mon, 03 Jun 2019 16:08:52: #2 finished! INFO @ Mon, 03 Jun 2019 16:08:52: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 16:08:52: #2 alternative fragment length(s) may be 1,11,36 bps INFO @ Mon, 03 Jun 2019 16:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20_model.r WARNING @ Mon, 03 Jun 2019 16:08:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 16:08:52: #2 You may need to consider one of the other alternative d(s): 1,11,36 WARNING @ Mon, 03 Jun 2019 16:08:52: #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 16:08:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:08:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:09:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.10_summits.bed INFO @ Mon, 03 Jun 2019 16:09:40: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:09:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:09:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.05_summits.bed INFO @ Mon, 03 Jun 2019 16:10:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370070/SRX4370070.20_summits.bed INFO @ Mon, 03 Jun 2019 16:10:16: Done! pass1 - making usageList (0 chroms): 2 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。