Job ID = 10609069 sra ファイルのダウンロード中... Completed: 292434K bytes transferred in 28 seconds (83221K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... 2018-05-03T22:03:15 fastq-dump.2.9.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) Read 23182877 spots for /home/okishinya/chipatlas/results/ce10/SRX2599462/SRR5297106.sra Written 23182877 spots for /home/okishinya/chipatlas/results/ce10/SRX2599462/SRR5297106.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:05:02 23182877 reads; of these: 23182877 (100.00%) were unpaired; of these: 948854 (4.09%) aligned 0 times 16381557 (70.66%) aligned exactly 1 time 5852466 (25.24%) aligned >1 times 95.91% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4447583 / 22234023 = 0.2000 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 @ Fri, 04 May 2018 07:14:51: # Command line: callpeak -t SRX2599462.bam -f BAM -g ce -n SRX2599462.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2599462.05 # format = BAM # ChIP-seq file = ['SRX2599462.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 04 May 2018 07:14:51: # Command line: callpeak -t SRX2599462.bam -f BAM -g ce -n SRX2599462.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2599462.20 # format = BAM # ChIP-seq file = ['SRX2599462.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 04 May 2018 07:14:51: # Command line: callpeak -t SRX2599462.bam -f BAM -g ce -n SRX2599462.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2599462.10 # format = BAM # ChIP-seq file = ['SRX2599462.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 04 May 2018 07:14:51: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:51: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:51: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:51: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:51: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:51: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:57: 1000000 INFO @ Fri, 04 May 2018 07:14:57: 1000000 INFO @ Fri, 04 May 2018 07:14:57: 1000000 INFO @ Fri, 04 May 2018 07:15:03: 2000000 INFO @ Fri, 04 May 2018 07:15:03: 2000000 INFO @ Fri, 04 May 2018 07:15:04: 2000000 INFO @ Fri, 04 May 2018 07:15:09: 3000000 INFO @ Fri, 04 May 2018 07:15:10: 3000000 INFO @ Fri, 04 May 2018 07:15:10: 3000000 INFO @ Fri, 04 May 2018 07:15:16: 4000000 INFO @ Fri, 04 May 2018 07:15:16: 4000000 INFO @ Fri, 04 May 2018 07:15:16: 4000000 INFO @ Fri, 04 May 2018 07:15:22: 5000000 INFO @ Fri, 04 May 2018 07:15:22: 5000000 INFO @ Fri, 04 May 2018 07:15:23: 5000000 INFO @ Fri, 04 May 2018 07:15:28: 6000000 INFO @ Fri, 04 May 2018 07:15:29: 6000000 INFO @ Fri, 04 May 2018 07:15:29: 6000000 INFO @ Fri, 04 May 2018 07:15:35: 7000000 INFO @ Fri, 04 May 2018 07:15:35: 7000000 INFO @ Fri, 04 May 2018 07:15:35: 7000000 INFO @ Fri, 04 May 2018 07:15:41: 8000000 INFO @ Fri, 04 May 2018 07:15:42: 8000000 INFO @ Fri, 04 May 2018 07:15:42: 8000000 INFO @ Fri, 04 May 2018 07:15:47: 9000000 INFO @ Fri, 04 May 2018 07:15:48: 9000000 INFO @ Fri, 04 May 2018 07:15:49: 9000000 INFO @ Fri, 04 May 2018 07:15:53: 10000000 INFO @ Fri, 04 May 2018 07:15:55: 10000000 INFO @ Fri, 04 May 2018 07:15:55: 10000000 INFO @ Fri, 04 May 2018 07:15:59: 11000000 INFO @ Fri, 04 May 2018 07:16:02: 11000000 INFO @ Fri, 04 May 2018 07:16:02: 11000000 INFO @ Fri, 04 May 2018 07:16:05: 12000000 INFO @ Fri, 04 May 2018 07:16:08: 12000000 INFO @ Fri, 04 May 2018 07:16:09: 12000000 INFO @ Fri, 04 May 2018 07:16:11: 13000000 INFO @ Fri, 04 May 2018 07:16:15: 13000000 INFO @ Fri, 04 May 2018 07:16:15: 13000000 INFO @ Fri, 04 May 2018 07:16:18: 14000000 INFO @ Fri, 04 May 2018 07:16:21: 14000000 INFO @ Fri, 04 May 2018 07:16:21: 14000000 INFO @ Fri, 04 May 2018 07:16:24: 15000000 INFO @ Fri, 04 May 2018 07:16:27: 15000000 INFO @ Fri, 04 May 2018 07:16:28: 15000000 INFO @ Fri, 04 May 2018 07:16:30: 16000000 INFO @ Fri, 04 May 2018 07:16:34: 16000000 INFO @ Fri, 04 May 2018 07:16:34: 16000000 INFO @ Fri, 04 May 2018 07:16:36: 17000000 INFO @ Fri, 04 May 2018 07:16:40: 17000000 INFO @ Fri, 04 May 2018 07:16:40: 17000000 INFO @ Fri, 04 May 2018 07:16:41: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:16:41: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:16:41: #1 total tags in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:41: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:16:41: #1 tags after filtering in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:41: #1 finished! INFO @ Fri, 04 May 2018 07:16:41: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:43: #2 number of paired peaks: 1414 INFO @ Fri, 04 May 2018 07:16:43: start model_add_line... INFO @ Fri, 04 May 2018 07:16:43: start X-correlation... INFO @ Fri, 04 May 2018 07:16:43: end of X-cor INFO @ Fri, 04 May 2018 07:16:43: #2 finished! INFO @ Fri, 04 May 2018 07:16:43: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:16:43: #2 alternative fragment length(s) may be 2,146,163 bps INFO @ Fri, 04 May 2018 07:16:43: #2.2 Generate R script for model : SRX2599462.05_model.r INFO @ Fri, 04 May 2018 07:16:43: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:45: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:16:45: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:16:45: #1 total tags in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:45: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:16:46: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:16:46: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:16:46: #1 total tags in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:46: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:16:46: #1 tags after filtering in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:46: #1 finished! INFO @ Fri, 04 May 2018 07:16:46: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:46: #1 tags after filtering in treatment: 17786440 INFO @ Fri, 04 May 2018 07:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:46: #1 finished! INFO @ Fri, 04 May 2018 07:16:46: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:47: #2 number of paired peaks: 1414 INFO @ Fri, 04 May 2018 07:16:47: start model_add_line... INFO @ Fri, 04 May 2018 07:16:47: #2 number of paired peaks: 1414 INFO @ Fri, 04 May 2018 07:16:47: start model_add_line... INFO @ Fri, 04 May 2018 07:16:47: start X-correlation... INFO @ Fri, 04 May 2018 07:16:47: end of X-cor INFO @ Fri, 04 May 2018 07:16:47: #2 finished! INFO @ Fri, 04 May 2018 07:16:47: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:16:47: #2 alternative fragment length(s) may be 2,146,163 bps INFO @ Fri, 04 May 2018 07:16:47: #2.2 Generate R script for model : SRX2599462.20_model.r INFO @ Fri, 04 May 2018 07:16:47: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:48: start X-correlation... INFO @ Fri, 04 May 2018 07:16:48: end of X-cor INFO @ Fri, 04 May 2018 07:16:48: #2 finished! INFO @ Fri, 04 May 2018 07:16:48: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:16:48: #2 alternative fragment length(s) may be 2,146,163 bps INFO @ Fri, 04 May 2018 07:16:48: #2.2 Generate R script for model : SRX2599462.10_model.r INFO @ Fri, 04 May 2018 07:16:48: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:32: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:34: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:35: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:50: #4 Write output xls file... SRX2599462.05_peaks.xls INFO @ Fri, 04 May 2018 07:17:50: #4 Write peak in narrowPeak format file... SRX2599462.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:50: #4 Write summits bed file... SRX2599462.05_summits.bed INFO @ Fri, 04 May 2018 07:17:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3206 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:54: #4 Write output xls file... SRX2599462.20_peaks.xls INFO @ Fri, 04 May 2018 07:17:54: #4 Write peak in narrowPeak format file... SRX2599462.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:54: #4 Write summits bed file... SRX2599462.20_summits.bed INFO @ Fri, 04 May 2018 07:17:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:55: #4 Write output xls file... SRX2599462.10_peaks.xls INFO @ Fri, 04 May 2018 07:17:55: #4 Write peak in narrowPeak format file... SRX2599462.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:55: #4 Write summits bed file... SRX2599462.10_summits.bed INFO @ Fri, 04 May 2018 07:17:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1362 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。