Job ID = 2640709 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:21:45 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 : 24,754,800 reads read : 49,509,600 reads written : 24,754,800 reads 0-length : 24,754,800 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:41 24754800 reads; of these: 24754800 (100.00%) were unpaired; of these: 578978 (2.34%) aligned 0 times 18675272 (75.44%) aligned exactly 1 time 5500550 (22.22%) aligned >1 times 97.66% overall alignment rate Time searching: 00:17:44 Overall time: 00:17:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3270872 / 24175822 = 0.1353 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:52:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:52:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:52:28: 1000000 INFO @ Sat, 24 Aug 2019 18:52:36: 2000000 INFO @ Sat, 24 Aug 2019 18:52:44: 3000000 INFO @ Sat, 24 Aug 2019 18:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:52:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:52:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:52:51: 4000000 INFO @ Sat, 24 Aug 2019 18:52:59: 1000000 INFO @ Sat, 24 Aug 2019 18:52:59: 5000000 INFO @ Sat, 24 Aug 2019 18:53:06: 2000000 INFO @ Sat, 24 Aug 2019 18:53:06: 6000000 INFO @ Sat, 24 Aug 2019 18:53:13: 7000000 INFO @ Sat, 24 Aug 2019 18:53:14: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:53:20: 8000000 INFO @ Sat, 24 Aug 2019 18:53:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:53:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:53:22: 4000000 INFO @ Sat, 24 Aug 2019 18:53:27: 9000000 INFO @ Sat, 24 Aug 2019 18:53:28: 1000000 INFO @ Sat, 24 Aug 2019 18:53:30: 5000000 INFO @ Sat, 24 Aug 2019 18:53:34: 10000000 INFO @ Sat, 24 Aug 2019 18:53:35: 2000000 INFO @ Sat, 24 Aug 2019 18:53:38: 6000000 INFO @ Sat, 24 Aug 2019 18:53:41: 11000000 INFO @ Sat, 24 Aug 2019 18:53:42: 3000000 INFO @ Sat, 24 Aug 2019 18:53:46: 7000000 INFO @ Sat, 24 Aug 2019 18:53:48: 12000000 INFO @ Sat, 24 Aug 2019 18:53:49: 4000000 INFO @ Sat, 24 Aug 2019 18:53:54: 8000000 INFO @ Sat, 24 Aug 2019 18:53:55: 13000000 INFO @ Sat, 24 Aug 2019 18:53:56: 5000000 INFO @ Sat, 24 Aug 2019 18:54:02: 14000000 INFO @ Sat, 24 Aug 2019 18:54:02: 9000000 INFO @ Sat, 24 Aug 2019 18:54:04: 6000000 INFO @ Sat, 24 Aug 2019 18:54:09: 15000000 INFO @ Sat, 24 Aug 2019 18:54:11: 10000000 INFO @ Sat, 24 Aug 2019 18:54:11: 7000000 INFO @ Sat, 24 Aug 2019 18:54:16: 16000000 INFO @ Sat, 24 Aug 2019 18:54:18: 8000000 INFO @ Sat, 24 Aug 2019 18:54:18: 11000000 INFO @ Sat, 24 Aug 2019 18:54:23: 17000000 INFO @ Sat, 24 Aug 2019 18:54:25: 9000000 INFO @ Sat, 24 Aug 2019 18:54:26: 12000000 INFO @ Sat, 24 Aug 2019 18:54:30: 18000000 INFO @ Sat, 24 Aug 2019 18:54:32: 10000000 INFO @ Sat, 24 Aug 2019 18:54:34: 13000000 INFO @ Sat, 24 Aug 2019 18:54:36: 19000000 INFO @ Sat, 24 Aug 2019 18:54:39: 11000000 INFO @ Sat, 24 Aug 2019 18:54:42: 14000000 INFO @ Sat, 24 Aug 2019 18:54:43: 20000000 INFO @ Sat, 24 Aug 2019 18:54:46: 12000000 INFO @ Sat, 24 Aug 2019 18:54:50: 15000000 INFO @ Sat, 24 Aug 2019 18:54:50: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:54:50: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:54:50: #1 total tags in treatment: 20904950 INFO @ Sat, 24 Aug 2019 18:54:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:54:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:54:51: #1 tags after filtering in treatment: 20904787 INFO @ Sat, 24 Aug 2019 18:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:54:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:54:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:54:53: 13000000 INFO @ Sat, 24 Aug 2019 18:54:55: #2 number of paired peaks: 42524 INFO @ Sat, 24 Aug 2019 18:54:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:54:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:54:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:54:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:54:55: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:54:55: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05_model.r INFO @ Sat, 24 Aug 2019 18:54:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:58: 16000000 INFO @ Sat, 24 Aug 2019 18:55:00: 14000000 INFO @ Sat, 24 Aug 2019 18:55:05: 17000000 INFO @ Sat, 24 Aug 2019 18:55:08: 15000000 INFO @ Sat, 24 Aug 2019 18:55:13: 18000000 INFO @ Sat, 24 Aug 2019 18:55:15: 16000000 INFO @ Sat, 24 Aug 2019 18:55:21: 19000000 INFO @ Sat, 24 Aug 2019 18:55:23: 17000000 INFO @ Sat, 24 Aug 2019 18:55:29: 20000000 INFO @ Sat, 24 Aug 2019 18:55:30: 18000000 INFO @ Sat, 24 Aug 2019 18:55:37: 19000000 INFO @ Sat, 24 Aug 2019 18:55:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:55:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:55:37: #1 total tags in treatment: 20904950 INFO @ Sat, 24 Aug 2019 18:55:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:55:37: #1 tags after filtering in treatment: 20904787 INFO @ Sat, 24 Aug 2019 18:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:55:37: #1 finished! INFO @ Sat, 24 Aug 2019 18:55:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:55:41: #2 number of paired peaks: 42524 INFO @ Sat, 24 Aug 2019 18:55:41: start model_add_line... INFO @ Sat, 24 Aug 2019 18:55:42: start X-correlation... INFO @ Sat, 24 Aug 2019 18:55:42: end of X-cor INFO @ Sat, 24 Aug 2019 18:55:42: #2 finished! INFO @ Sat, 24 Aug 2019 18:55:42: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:55:42: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10_model.r INFO @ Sat, 24 Aug 2019 18:55:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:55:44: 20000000 INFO @ Sat, 24 Aug 2019 18:55:50: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:55:50: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:55:50: #1 total tags in treatment: 20904950 INFO @ Sat, 24 Aug 2019 18:55:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:55:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:55:51: #1 tags after filtering in treatment: 20904787 INFO @ Sat, 24 Aug 2019 18:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:55:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:55:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:55:55: #2 number of paired peaks: 42524 INFO @ Sat, 24 Aug 2019 18:55:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:55:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:55:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:55:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:55:55: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:55:55: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20_model.r INFO @ Sat, 24 Aug 2019 18:55:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:56:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:56:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:56:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.05_summits.bed INFO @ Sat, 24 Aug 2019 18:56:39: Done! pass1 - making usageList (85 chroms): 4 millis pass2 - checking and writing primary data (13774 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:56:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.10_summits.bed INFO @ Sat, 24 Aug 2019 18:57:29: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (9317 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375065/SRX5375065.20_summits.bed INFO @ Sat, 24 Aug 2019 18:57:38: Done! pass1 - making usageList (42 chroms): 4 millis pass2 - checking and writing primary data (4815 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。