Job ID = 10609068 sra ファイルのダウンロード中... Completed: 308366K bytes transferred in 10 seconds (244497K 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... 2018-05-03T22:03:17 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 24778030 spots for /home/okishinya/chipatlas/results/ce10/SRX2599461/SRR5297105.sra Written 24778030 spots for /home/okishinya/chipatlas/results/ce10/SRX2599461/SRR5297105.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: 00:00:01 Multiseed full-index search: 00:05:25 24778030 reads; of these: 24778030 (100.00%) were unpaired; of these: 1034008 (4.17%) aligned 0 times 16646216 (67.18%) aligned exactly 1 time 7097806 (28.65%) aligned >1 times 95.83% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 5796072 / 23744022 = 0.2441 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 07:15:32: # Command line: callpeak -t SRX2599461.bam -f BAM -g ce -n SRX2599461.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2599461.05 # format = BAM # ChIP-seq file = ['SRX2599461.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 07:15:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:32: # Command line: callpeak -t SRX2599461.bam -f BAM -g ce -n SRX2599461.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2599461.20 # format = BAM # ChIP-seq file = ['SRX2599461.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 07:15:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:32: # Command line: callpeak -t SRX2599461.bam -f BAM -g ce -n SRX2599461.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2599461.10 # format = BAM # ChIP-seq file = ['SRX2599461.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 07:15:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:39: 1000000 INFO @ Fri, 04 May 2018 07:15:39: 1000000 INFO @ Fri, 04 May 2018 07:15:39: 1000000 INFO @ Fri, 04 May 2018 07:15:46: 2000000 INFO @ Fri, 04 May 2018 07:15:46: 2000000 INFO @ Fri, 04 May 2018 07:15:46: 2000000 INFO @ Fri, 04 May 2018 07:15:53: 3000000 INFO @ Fri, 04 May 2018 07:15:53: 3000000 INFO @ Fri, 04 May 2018 07:15:53: 3000000 INFO @ Fri, 04 May 2018 07:16:00: 4000000 INFO @ Fri, 04 May 2018 07:16:00: 4000000 INFO @ Fri, 04 May 2018 07:16:00: 4000000 INFO @ Fri, 04 May 2018 07:16:07: 5000000 INFO @ Fri, 04 May 2018 07:16:07: 5000000 INFO @ Fri, 04 May 2018 07:16:07: 5000000 INFO @ Fri, 04 May 2018 07:16:14: 6000000 INFO @ Fri, 04 May 2018 07:16:14: 6000000 INFO @ Fri, 04 May 2018 07:16:14: 6000000 INFO @ Fri, 04 May 2018 07:16:21: 7000000 INFO @ Fri, 04 May 2018 07:16:22: 7000000 INFO @ Fri, 04 May 2018 07:16:22: 7000000 INFO @ Fri, 04 May 2018 07:16:28: 8000000 INFO @ Fri, 04 May 2018 07:16:29: 8000000 INFO @ Fri, 04 May 2018 07:16:29: 8000000 INFO @ Fri, 04 May 2018 07:16:35: 9000000 INFO @ Fri, 04 May 2018 07:16:36: 9000000 INFO @ Fri, 04 May 2018 07:16:36: 9000000 INFO @ Fri, 04 May 2018 07:16:42: 10000000 INFO @ Fri, 04 May 2018 07:16:43: 10000000 INFO @ Fri, 04 May 2018 07:16:43: 10000000 INFO @ Fri, 04 May 2018 07:16:49: 11000000 INFO @ Fri, 04 May 2018 07:16:50: 11000000 INFO @ Fri, 04 May 2018 07:16:50: 11000000 INFO @ Fri, 04 May 2018 07:16:56: 12000000 INFO @ Fri, 04 May 2018 07:16:57: 12000000 INFO @ Fri, 04 May 2018 07:16:57: 12000000 INFO @ Fri, 04 May 2018 07:17:03: 13000000 INFO @ Fri, 04 May 2018 07:17:04: 13000000 INFO @ Fri, 04 May 2018 07:17:04: 13000000 INFO @ Fri, 04 May 2018 07:17:11: 14000000 INFO @ Fri, 04 May 2018 07:17:11: 14000000 INFO @ Fri, 04 May 2018 07:17:12: 14000000 INFO @ Fri, 04 May 2018 07:17:18: 15000000 INFO @ Fri, 04 May 2018 07:17:18: 15000000 INFO @ Fri, 04 May 2018 07:17:19: 15000000 INFO @ Fri, 04 May 2018 07:17:25: 16000000 INFO @ Fri, 04 May 2018 07:17:25: 16000000 INFO @ Fri, 04 May 2018 07:17:27: 16000000 INFO @ Fri, 04 May 2018 07:17:32: 17000000 INFO @ Fri, 04 May 2018 07:17:32: 17000000 INFO @ Fri, 04 May 2018 07:17:35: 17000000 INFO @ Fri, 04 May 2018 07:17:39: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:17:39: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:17:39: #1 total tags in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:39: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:39: #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 07:17:39: #1 tags after filtering in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:39: #1 finished! INFO @ Fri, 04 May 2018 07:17:39: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:39: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:17:39: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:17:39: #1 total tags in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:39: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:39: #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 07:17:39: #1 tags after filtering in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:39: #1 finished! INFO @ Fri, 04 May 2018 07:17:39: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:40: #2 number of paired peaks: 2491 INFO @ Fri, 04 May 2018 07:17:40: start model_add_line... INFO @ Fri, 04 May 2018 07:17:41: start X-correlation... INFO @ Fri, 04 May 2018 07:17:41: end of X-cor INFO @ Fri, 04 May 2018 07:17:41: #2 finished! INFO @ Fri, 04 May 2018 07:17:41: #2 predicted fragment length is 148 bps INFO @ Fri, 04 May 2018 07:17:41: #2 alternative fragment length(s) may be 2,148 bps INFO @ Fri, 04 May 2018 07:17:41: #2.2 Generate R script for model : SRX2599461.20_model.r INFO @ Fri, 04 May 2018 07:17:41: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:41: #2 number of paired peaks: 2491 INFO @ Fri, 04 May 2018 07:17:41: start model_add_line... INFO @ Fri, 04 May 2018 07:17:41: start X-correlation... INFO @ Fri, 04 May 2018 07:17:41: end of X-cor INFO @ Fri, 04 May 2018 07:17:41: #2 finished! INFO @ Fri, 04 May 2018 07:17:41: #2 predicted fragment length is 148 bps INFO @ Fri, 04 May 2018 07:17:41: #2 alternative fragment length(s) may be 2,148 bps INFO @ Fri, 04 May 2018 07:17:41: #2.2 Generate R script for model : SRX2599461.05_model.r INFO @ Fri, 04 May 2018 07:17:41: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:43: #1 tag size is determined as 49 bps INFO @ Fri, 04 May 2018 07:17:43: #1 tag size = 49 INFO @ Fri, 04 May 2018 07:17:43: #1 total tags in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:43: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:43: #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 07:17:43: #1 tags after filtering in treatment: 17947950 INFO @ Fri, 04 May 2018 07:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:43: #1 finished! INFO @ Fri, 04 May 2018 07:17:43: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:45: #2 number of paired peaks: 2491 INFO @ Fri, 04 May 2018 07:17:45: start model_add_line... INFO @ Fri, 04 May 2018 07:17:45: start X-correlation... INFO @ Fri, 04 May 2018 07:17:45: end of X-cor INFO @ Fri, 04 May 2018 07:17:45: #2 finished! INFO @ Fri, 04 May 2018 07:17:45: #2 predicted fragment length is 148 bps INFO @ Fri, 04 May 2018 07:17:45: #2 alternative fragment length(s) may be 2,148 bps INFO @ Fri, 04 May 2018 07:17:45: #2.2 Generate R script for model : SRX2599461.10_model.r INFO @ Fri, 04 May 2018 07:17:45: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:18:32: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:32: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:34: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:49: #4 Write output xls file... SRX2599461.05_peaks.xls INFO @ Fri, 04 May 2018 07:18:50: #4 Write peak in narrowPeak format file... SRX2599461.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:50: #4 Write summits bed file... SRX2599461.05_summits.bed INFO @ Fri, 04 May 2018 07:18:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4558 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:50: #4 Write output xls file... SRX2599461.20_peaks.xls INFO @ Fri, 04 May 2018 07:18:50: #4 Write peak in narrowPeak format file... SRX2599461.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:50: #4 Write summits bed file... SRX2599461.20_summits.bed INFO @ Fri, 04 May 2018 07:18:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (706 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:53: #4 Write output xls file... SRX2599461.10_peaks.xls INFO @ Fri, 04 May 2018 07:18:53: #4 Write peak in narrowPeak format file... SRX2599461.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:53: #4 Write summits bed file... SRX2599461.10_summits.bed INFO @ Fri, 04 May 2018 07:18:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2200 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。