Job ID = 10609050 sra ファイルのダウンロード中... Completed: 188713K bytes transferred in 24 seconds (64137K 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... 2018-05-03T22:03:22 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 16937099 spots for /home/okishinya/chipatlas/results/ce10/SRX2202775/SRR4319281.sra Written 16937099 spots for /home/okishinya/chipatlas/results/ce10/SRX2202775/SRR4319281.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: 00:04:30 16937099 reads; of these: 16937099 (100.00%) were unpaired; of these: 2404225 (14.20%) aligned 0 times 8460626 (49.95%) aligned exactly 1 time 6072248 (35.85%) aligned >1 times 85.80% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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 8 files... [bam_rmdupse_core] 4419579 / 14532874 = 0.3041 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 07:11:32: # Command line: callpeak -t SRX2202775.bam -f BAM -g ce -n SRX2202775.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202775.20 # format = BAM # ChIP-seq file = ['SRX2202775.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 07:11:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:32: # Command line: callpeak -t SRX2202775.bam -f BAM -g ce -n SRX2202775.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202775.10 # format = BAM # ChIP-seq file = ['SRX2202775.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 07:11:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:32: # Command line: callpeak -t SRX2202775.bam -f BAM -g ce -n SRX2202775.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202775.05 # format = BAM # ChIP-seq file = ['SRX2202775.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 07:11:32: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:32: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:37: 1000000 INFO @ Fri, 04 May 2018 07:11:38: 1000000 INFO @ Fri, 04 May 2018 07:11:38: 1000000 INFO @ Fri, 04 May 2018 07:11:43: 2000000 INFO @ Fri, 04 May 2018 07:11:43: 2000000 INFO @ Fri, 04 May 2018 07:11:43: 2000000 INFO @ Fri, 04 May 2018 07:11:49: 3000000 INFO @ Fri, 04 May 2018 07:11:49: 3000000 INFO @ Fri, 04 May 2018 07:11:50: 3000000 INFO @ Fri, 04 May 2018 07:11:54: 4000000 INFO @ Fri, 04 May 2018 07:11:55: 4000000 INFO @ Fri, 04 May 2018 07:11:56: 4000000 INFO @ Fri, 04 May 2018 07:12:00: 5000000 INFO @ Fri, 04 May 2018 07:12:01: 5000000 INFO @ Fri, 04 May 2018 07:12:02: 5000000 INFO @ Fri, 04 May 2018 07:12:06: 6000000 INFO @ Fri, 04 May 2018 07:12:07: 6000000 INFO @ Fri, 04 May 2018 07:12:08: 6000000 INFO @ Fri, 04 May 2018 07:12:12: 7000000 INFO @ Fri, 04 May 2018 07:12:13: 7000000 INFO @ Fri, 04 May 2018 07:12:14: 7000000 INFO @ Fri, 04 May 2018 07:12:18: 8000000 INFO @ Fri, 04 May 2018 07:12:19: 8000000 INFO @ Fri, 04 May 2018 07:12:20: 8000000 INFO @ Fri, 04 May 2018 07:12:24: 9000000 INFO @ Fri, 04 May 2018 07:12:24: 9000000 INFO @ Fri, 04 May 2018 07:12:26: 9000000 INFO @ Fri, 04 May 2018 07:12:29: 10000000 INFO @ Fri, 04 May 2018 07:12:30: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:12:30: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:12:30: #1 total tags in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:30: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:30: #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 07:12:30: 10000000 INFO @ Fri, 04 May 2018 07:12:30: #1 tags after filtering in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:30: #1 finished! INFO @ Fri, 04 May 2018 07:12:30: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:31: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:12:31: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:12:31: #1 total tags in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:31: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:31: #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 07:12:31: #1 tags after filtering in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:31: #1 finished! INFO @ Fri, 04 May 2018 07:12:31: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:31: #2 number of paired peaks: 2708 INFO @ Fri, 04 May 2018 07:12:31: start model_add_line... INFO @ Fri, 04 May 2018 07:12:32: start X-correlation... INFO @ Fri, 04 May 2018 07:12:32: end of X-cor INFO @ Fri, 04 May 2018 07:12:32: #2 finished! INFO @ Fri, 04 May 2018 07:12:32: #2 predicted fragment length is 120 bps INFO @ Fri, 04 May 2018 07:12:32: #2 alternative fragment length(s) may be 3,120 bps INFO @ Fri, 04 May 2018 07:12:32: #2.2 Generate R script for model : SRX2202775.10_model.r INFO @ Fri, 04 May 2018 07:12:32: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:32: 10000000 INFO @ Fri, 04 May 2018 07:12:32: #2 number of paired peaks: 2708 INFO @ Fri, 04 May 2018 07:12:32: start model_add_line... INFO @ Fri, 04 May 2018 07:12:33: start X-correlation... INFO @ Fri, 04 May 2018 07:12:33: end of X-cor INFO @ Fri, 04 May 2018 07:12:33: #2 finished! INFO @ Fri, 04 May 2018 07:12:33: #2 predicted fragment length is 120 bps INFO @ Fri, 04 May 2018 07:12:33: #2 alternative fragment length(s) may be 3,120 bps INFO @ Fri, 04 May 2018 07:12:33: #2.2 Generate R script for model : SRX2202775.05_model.r INFO @ Fri, 04 May 2018 07:12:33: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:33: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:12:33: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:12:33: #1 total tags in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:33: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:33: #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 07:12:33: #1 tags after filtering in treatment: 10113295 INFO @ Fri, 04 May 2018 07:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:33: #1 finished! INFO @ Fri, 04 May 2018 07:12:33: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:34: #2 number of paired peaks: 2708 INFO @ Fri, 04 May 2018 07:12:34: start model_add_line... INFO @ Fri, 04 May 2018 07:12:34: start X-correlation... INFO @ Fri, 04 May 2018 07:12:34: end of X-cor INFO @ Fri, 04 May 2018 07:12:34: #2 finished! INFO @ Fri, 04 May 2018 07:12:34: #2 predicted fragment length is 120 bps INFO @ Fri, 04 May 2018 07:12:34: #2 alternative fragment length(s) may be 3,120 bps INFO @ Fri, 04 May 2018 07:12:34: #2.2 Generate R script for model : SRX2202775.20_model.r INFO @ Fri, 04 May 2018 07:12:34: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:00: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:01: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:12: #4 Write output xls file... SRX2202775.10_peaks.xls INFO @ Fri, 04 May 2018 07:13:12: #4 Write peak in narrowPeak format file... SRX2202775.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:12: #4 Write summits bed file... SRX2202775.10_summits.bed INFO @ Fri, 04 May 2018 07:13:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2364 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:13:13: #4 Write output xls file... SRX2202775.05_peaks.xls INFO @ Fri, 04 May 2018 07:13:13: #4 Write peak in narrowPeak format file... SRX2202775.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:13: #4 Write summits bed file... SRX2202775.05_summits.bed INFO @ Fri, 04 May 2018 07:13:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4601 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:13:15: #4 Write output xls file... SRX2202775.20_peaks.xls INFO @ Fri, 04 May 2018 07:13:15: #4 Write peak in narrowPeak format file... SRX2202775.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:15: #4 Write summits bed file... SRX2202775.20_summits.bed INFO @ Fri, 04 May 2018 07:13:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (916 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。