Job ID = 2640710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:27:18 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 ) 2019-08-24T09:27:18 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 : 22,328,093 reads read : 44,656,186 reads written : 22,328,093 reads 0-length : 22,328,093 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: 00:17:14 22328093 reads; of these: 22328093 (100.00%) were unpaired; of these: 453572 (2.03%) aligned 0 times 18293812 (81.93%) aligned exactly 1 time 3580709 (16.04%) aligned >1 times 97.97% overall alignment rate Time searching: 00:17:18 Overall time: 00:17:18 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] 2403060 / 21874521 = 0.1099 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.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 18:53:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:53:37: 1000000 INFO @ Sat, 24 Aug 2019 18:53:47: 2000000 INFO @ Sat, 24 Aug 2019 18:53:56: 3000000 INFO @ Sat, 24 Aug 2019 18:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.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 18:53:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:05: 4000000 INFO @ Sat, 24 Aug 2019 18:54:08: 1000000 INFO @ Sat, 24 Aug 2019 18:54:15: 5000000 INFO @ Sat, 24 Aug 2019 18:54:18: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:54:25: 6000000 INFO @ Sat, 24 Aug 2019 18:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.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 18:54:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:29: 3000000 INFO @ Sat, 24 Aug 2019 18:54:34: 7000000 INFO @ Sat, 24 Aug 2019 18:54:39: 1000000 INFO @ Sat, 24 Aug 2019 18:54:40: 4000000 INFO @ Sat, 24 Aug 2019 18:54:44: 8000000 INFO @ Sat, 24 Aug 2019 18:54:51: 2000000 INFO @ Sat, 24 Aug 2019 18:54:53: 5000000 INFO @ Sat, 24 Aug 2019 18:54:54: 9000000 INFO @ Sat, 24 Aug 2019 18:55:02: 3000000 INFO @ Sat, 24 Aug 2019 18:55:03: 10000000 INFO @ Sat, 24 Aug 2019 18:55:05: 6000000 INFO @ Sat, 24 Aug 2019 18:55:13: 11000000 INFO @ Sat, 24 Aug 2019 18:55:14: 4000000 INFO @ Sat, 24 Aug 2019 18:55:17: 7000000 INFO @ Sat, 24 Aug 2019 18:55:22: 12000000 INFO @ Sat, 24 Aug 2019 18:55:27: 5000000 INFO @ Sat, 24 Aug 2019 18:55:29: 8000000 INFO @ Sat, 24 Aug 2019 18:55:32: 13000000 INFO @ Sat, 24 Aug 2019 18:55:39: 6000000 INFO @ Sat, 24 Aug 2019 18:55:41: 14000000 INFO @ Sat, 24 Aug 2019 18:55:41: 9000000 INFO @ Sat, 24 Aug 2019 18:55:51: 15000000 INFO @ Sat, 24 Aug 2019 18:55:51: 7000000 INFO @ Sat, 24 Aug 2019 18:55:53: 10000000 INFO @ Sat, 24 Aug 2019 18:56:00: 16000000 INFO @ Sat, 24 Aug 2019 18:56:03: 8000000 INFO @ Sat, 24 Aug 2019 18:56:05: 11000000 INFO @ Sat, 24 Aug 2019 18:56:10: 17000000 INFO @ Sat, 24 Aug 2019 18:56:15: 9000000 INFO @ Sat, 24 Aug 2019 18:56:17: 12000000 INFO @ Sat, 24 Aug 2019 18:56:19: 18000000 INFO @ Sat, 24 Aug 2019 18:56:27: 10000000 INFO @ Sat, 24 Aug 2019 18:56:29: 19000000 INFO @ Sat, 24 Aug 2019 18:56:29: 13000000 INFO @ Sat, 24 Aug 2019 18:56:34: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:56:34: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:56:34: #1 total tags in treatment: 19471461 INFO @ Sat, 24 Aug 2019 18:56:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:34: #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 18:56:34: #1 tags after filtering in treatment: 19471237 INFO @ Sat, 24 Aug 2019 18:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:34: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:39: 11000000 INFO @ Sat, 24 Aug 2019 18:56:40: #2 number of paired peaks: 89787 INFO @ Sat, 24 Aug 2019 18:56:40: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:40: 14000000 INFO @ Sat, 24 Aug 2019 18:56:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:41: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:56:41: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05_model.r INFO @ Sat, 24 Aug 2019 18:56:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:50: 12000000 INFO @ Sat, 24 Aug 2019 18:56:52: 15000000 INFO @ Sat, 24 Aug 2019 18:57:01: 13000000 INFO @ Sat, 24 Aug 2019 18:57:04: 16000000 INFO @ Sat, 24 Aug 2019 18:57:12: 14000000 INFO @ Sat, 24 Aug 2019 18:57:16: 17000000 INFO @ Sat, 24 Aug 2019 18:57:23: 15000000 INFO @ Sat, 24 Aug 2019 18:57:28: 18000000 INFO @ Sat, 24 Aug 2019 18:57:35: 16000000 INFO @ Sat, 24 Aug 2019 18:57:40: 19000000 INFO @ Sat, 24 Aug 2019 18:57:45: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:57:45: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:57:45: #1 total tags in treatment: 19471461 INFO @ Sat, 24 Aug 2019 18:57:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:57:45: #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 18:57:46: #1 tags after filtering in treatment: 19471237 INFO @ Sat, 24 Aug 2019 18:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:57:46: #1 finished! INFO @ Sat, 24 Aug 2019 18:57:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:57:47: 17000000 INFO @ Sat, 24 Aug 2019 18:57:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:52: #2 number of paired peaks: 89787 INFO @ Sat, 24 Aug 2019 18:57:52: start model_add_line... INFO @ Sat, 24 Aug 2019 18:57:52: start X-correlation... INFO @ Sat, 24 Aug 2019 18:57:52: end of X-cor INFO @ Sat, 24 Aug 2019 18:57:52: #2 finished! INFO @ Sat, 24 Aug 2019 18:57:52: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:57:52: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10_model.r INFO @ Sat, 24 Aug 2019 18:57:52: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:57:57: 18000000 INFO @ Sat, 24 Aug 2019 18:58:08: 19000000 INFO @ Sat, 24 Aug 2019 18:58:13: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:58:13: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:58:13: #1 total tags in treatment: 19471461 INFO @ Sat, 24 Aug 2019 18:58:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:58:13: #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 18:58:13: #1 tags after filtering in treatment: 19471237 INFO @ Sat, 24 Aug 2019 18:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:58:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:58:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:58:19: #2 number of paired peaks: 89787 INFO @ Sat, 24 Aug 2019 18:58:19: start model_add_line... INFO @ Sat, 24 Aug 2019 18:58:20: start X-correlation... INFO @ Sat, 24 Aug 2019 18:58:20: end of X-cor INFO @ Sat, 24 Aug 2019 18:58:20: #2 finished! INFO @ Sat, 24 Aug 2019 18:58:20: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:58:20: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20_model.r INFO @ Sat, 24 Aug 2019 18:58:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.05_summits.bed INFO @ Sat, 24 Aug 2019 18:58:30: Done! pass1 - making usageList (130 chroms): 14 millis pass2 - checking and writing primary data (45078 records, 4 fields): 68 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:59:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:59:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.10_summits.bed INFO @ Sat, 24 Aug 2019 18:59:39: Done! pass1 - making usageList (99 chroms): 7 millis pass2 - checking and writing primary data (29227 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375066/SRX5375066.20_summits.bed INFO @ Sat, 24 Aug 2019 19:00:03: Done! pass1 - making usageList (60 chroms): 7 millis pass2 - checking and writing primary data (13181 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。