Job ID = 2640725 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:36:19 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 ) 2019-08-24T09:36:19 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 ) 2019-08-24T09:36:19 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 : 23,657,298 reads read : 23,657,298 reads written : 23,657,298 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: 00:06:00 23657298 reads; of these: 23657298 (100.00%) were unpaired; of these: 6705593 (28.34%) aligned 0 times 13807022 (58.36%) aligned exactly 1 time 3144683 (13.29%) aligned >1 times 71.66% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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 8 files... [bam_rmdupse_core] 545412 / 16951705 = 0.0322 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.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 18:53:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:53:32: 1000000 INFO @ Sat, 24 Aug 2019 18:53:41: 2000000 INFO @ Sat, 24 Aug 2019 18:53:50: 3000000 INFO @ Sat, 24 Aug 2019 18:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.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 18:53:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:00: 4000000 INFO @ Sat, 24 Aug 2019 18:54:01: 1000000 INFO @ Sat, 24 Aug 2019 18:54:10: 2000000 INFO @ Sat, 24 Aug 2019 18:54:11: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:54:20: 3000000 INFO @ Sat, 24 Aug 2019 18:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.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 18:54:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:21: 6000000 INFO @ Sat, 24 Aug 2019 18:54:29: 4000000 INFO @ Sat, 24 Aug 2019 18:54:30: 1000000 INFO @ Sat, 24 Aug 2019 18:54:32: 7000000 INFO @ Sat, 24 Aug 2019 18:54:37: 5000000 INFO @ Sat, 24 Aug 2019 18:54:39: 2000000 INFO @ Sat, 24 Aug 2019 18:54:42: 8000000 INFO @ Sat, 24 Aug 2019 18:54:46: 6000000 INFO @ Sat, 24 Aug 2019 18:54:49: 3000000 INFO @ Sat, 24 Aug 2019 18:54:53: 9000000 INFO @ Sat, 24 Aug 2019 18:54:55: 7000000 INFO @ Sat, 24 Aug 2019 18:54:59: 4000000 INFO @ Sat, 24 Aug 2019 18:55:04: 10000000 INFO @ Sat, 24 Aug 2019 18:55:04: 8000000 INFO @ Sat, 24 Aug 2019 18:55:08: 5000000 INFO @ Sat, 24 Aug 2019 18:55:13: 9000000 INFO @ Sat, 24 Aug 2019 18:55:14: 11000000 INFO @ Sat, 24 Aug 2019 18:55:17: 6000000 INFO @ Sat, 24 Aug 2019 18:55:22: 10000000 INFO @ Sat, 24 Aug 2019 18:55:25: 12000000 INFO @ Sat, 24 Aug 2019 18:55:26: 7000000 INFO @ Sat, 24 Aug 2019 18:55:31: 11000000 INFO @ Sat, 24 Aug 2019 18:55:35: 13000000 INFO @ Sat, 24 Aug 2019 18:55:36: 8000000 INFO @ Sat, 24 Aug 2019 18:55:40: 12000000 INFO @ Sat, 24 Aug 2019 18:55:45: 9000000 INFO @ Sat, 24 Aug 2019 18:55:46: 14000000 INFO @ Sat, 24 Aug 2019 18:55:48: 13000000 INFO @ Sat, 24 Aug 2019 18:55:54: 10000000 INFO @ Sat, 24 Aug 2019 18:55:57: 15000000 INFO @ Sat, 24 Aug 2019 18:55:57: 14000000 INFO @ Sat, 24 Aug 2019 18:56:03: 11000000 INFO @ Sat, 24 Aug 2019 18:56:06: 15000000 INFO @ Sat, 24 Aug 2019 18:56:07: 16000000 INFO @ Sat, 24 Aug 2019 18:56:12: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:56:12: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:56:12: #1 total tags in treatment: 16406293 INFO @ Sat, 24 Aug 2019 18:56:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:12: #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 18:56:12: 12000000 INFO @ Sat, 24 Aug 2019 18:56:12: #1 tags after filtering in treatment: 16406044 INFO @ Sat, 24 Aug 2019 18:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:12: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:15: 16000000 INFO @ Sat, 24 Aug 2019 18:56:18: #2 number of paired peaks: 125918 INFO @ Sat, 24 Aug 2019 18:56:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:19: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:56:19: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:56:19: #1 total tags in treatment: 16406293 INFO @ Sat, 24 Aug 2019 18:56:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:19: #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 18:56:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:19: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:56:19: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05_model.r INFO @ Sat, 24 Aug 2019 18:56:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:19: #1 tags after filtering in treatment: 16406044 INFO @ Sat, 24 Aug 2019 18:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:19: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:21: 13000000 INFO @ Sat, 24 Aug 2019 18:56:25: #2 number of paired peaks: 125918 INFO @ Sat, 24 Aug 2019 18:56:25: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:26: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:26: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:26: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:26: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:56:26: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10_model.r INFO @ Sat, 24 Aug 2019 18:56:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:29: 14000000 INFO @ Sat, 24 Aug 2019 18:56:38: 15000000 INFO @ Sat, 24 Aug 2019 18:56:48: 16000000 INFO @ Sat, 24 Aug 2019 18:56:51: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:56:51: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:56:51: #1 total tags in treatment: 16406293 INFO @ Sat, 24 Aug 2019 18:56:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:51: #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 18:56:52: #1 tags after filtering in treatment: 16406044 INFO @ Sat, 24 Aug 2019 18:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:58: #2 number of paired peaks: 125918 INFO @ Sat, 24 Aug 2019 18:56:58: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:58: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:58: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:56:58: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20_model.r INFO @ Sat, 24 Aug 2019 18:56:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:57:12: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.05_summits.bed INFO @ Sat, 24 Aug 2019 18:57:41: Done! pass1 - making usageList (95 chroms): 13 millis pass2 - checking and writing primary data (39103 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.10_summits.bed INFO @ Sat, 24 Aug 2019 18:57:45: Done! pass1 - making usageList (40 chroms): 3 millis pass2 - checking and writing primary data (10840 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:57:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555169/SRX555169.20_summits.bed INFO @ Sat, 24 Aug 2019 18:58:19: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。