Job ID = 2640590 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:54:26 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T09:04:06 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 ) 2019-08-24T09:04:06 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 : 44,782,975 reads read : 89,565,950 reads written : 44,782,975 reads 0-length : 44,782,975 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:30:25 44782975 reads; of these: 44782975 (100.00%) were unpaired; of these: 1080733 (2.41%) aligned 0 times 35679594 (79.67%) aligned exactly 1 time 8022648 (17.91%) aligned >1 times 97.59% overall alignment rate Time searching: 00:30:28 Overall time: 00:30:28 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 20 files... [bam_rmdupse_core] 11148572 / 43702242 = 0.2551 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.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 18:49:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:08: 1000000 INFO @ Sat, 24 Aug 2019 18:50:17: 2000000 INFO @ Sat, 24 Aug 2019 18:50:27: 3000000 INFO @ Sat, 24 Aug 2019 18:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.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 18:50:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:34: 1000000 INFO @ Sat, 24 Aug 2019 18:50:36: 4000000 INFO @ Sat, 24 Aug 2019 18:50:42: 2000000 INFO @ Sat, 24 Aug 2019 18:50:45: 5000000 INFO @ Sat, 24 Aug 2019 18:50:49: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:50:55: 6000000 INFO @ Sat, 24 Aug 2019 18:50:56: 4000000 INFO @ Sat, 24 Aug 2019 18:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.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 18:50:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:03: 5000000 INFO @ Sat, 24 Aug 2019 18:51:05: 7000000 INFO @ Sat, 24 Aug 2019 18:51:07: 1000000 INFO @ Sat, 24 Aug 2019 18:51:11: 6000000 INFO @ Sat, 24 Aug 2019 18:51:14: 8000000 INFO @ Sat, 24 Aug 2019 18:51:17: 2000000 INFO @ Sat, 24 Aug 2019 18:51:18: 7000000 INFO @ Sat, 24 Aug 2019 18:51:24: 9000000 INFO @ Sat, 24 Aug 2019 18:51:26: 8000000 INFO @ Sat, 24 Aug 2019 18:51:26: 3000000 INFO @ Sat, 24 Aug 2019 18:51:33: 9000000 INFO @ Sat, 24 Aug 2019 18:51:33: 10000000 INFO @ Sat, 24 Aug 2019 18:51:36: 4000000 INFO @ Sat, 24 Aug 2019 18:51:40: 10000000 INFO @ Sat, 24 Aug 2019 18:51:43: 11000000 INFO @ Sat, 24 Aug 2019 18:51:46: 5000000 INFO @ Sat, 24 Aug 2019 18:51:48: 11000000 INFO @ Sat, 24 Aug 2019 18:51:52: 12000000 INFO @ Sat, 24 Aug 2019 18:51:55: 6000000 INFO @ Sat, 24 Aug 2019 18:51:56: 12000000 INFO @ Sat, 24 Aug 2019 18:52:01: 13000000 INFO @ Sat, 24 Aug 2019 18:52:03: 13000000 INFO @ Sat, 24 Aug 2019 18:52:05: 7000000 INFO @ Sat, 24 Aug 2019 18:52:10: 14000000 INFO @ Sat, 24 Aug 2019 18:52:11: 14000000 INFO @ Sat, 24 Aug 2019 18:52:14: 8000000 INFO @ Sat, 24 Aug 2019 18:52:18: 15000000 INFO @ Sat, 24 Aug 2019 18:52:20: 15000000 INFO @ Sat, 24 Aug 2019 18:52:24: 9000000 INFO @ Sat, 24 Aug 2019 18:52:25: 16000000 INFO @ Sat, 24 Aug 2019 18:52:30: 16000000 INFO @ Sat, 24 Aug 2019 18:52:32: 17000000 INFO @ Sat, 24 Aug 2019 18:52:33: 10000000 INFO @ Sat, 24 Aug 2019 18:52:39: 17000000 INFO @ Sat, 24 Aug 2019 18:52:39: 18000000 INFO @ Sat, 24 Aug 2019 18:52:42: 11000000 INFO @ Sat, 24 Aug 2019 18:52:47: 19000000 INFO @ Sat, 24 Aug 2019 18:52:48: 18000000 INFO @ Sat, 24 Aug 2019 18:52:52: 12000000 INFO @ Sat, 24 Aug 2019 18:52:54: 20000000 INFO @ Sat, 24 Aug 2019 18:52:57: 19000000 INFO @ Sat, 24 Aug 2019 18:53:01: 13000000 INFO @ Sat, 24 Aug 2019 18:53:01: 21000000 INFO @ Sat, 24 Aug 2019 18:53:06: 20000000 INFO @ Sat, 24 Aug 2019 18:53:08: 22000000 INFO @ Sat, 24 Aug 2019 18:53:10: 14000000 INFO @ Sat, 24 Aug 2019 18:53:15: 21000000 INFO @ Sat, 24 Aug 2019 18:53:16: 23000000 INFO @ Sat, 24 Aug 2019 18:53:19: 15000000 INFO @ Sat, 24 Aug 2019 18:53:23: 24000000 INFO @ Sat, 24 Aug 2019 18:53:24: 22000000 INFO @ Sat, 24 Aug 2019 18:53:28: 16000000 INFO @ Sat, 24 Aug 2019 18:53:30: 25000000 INFO @ Sat, 24 Aug 2019 18:53:34: 23000000 INFO @ Sat, 24 Aug 2019 18:53:37: 26000000 INFO @ Sat, 24 Aug 2019 18:53:38: 17000000 INFO @ Sat, 24 Aug 2019 18:53:43: 24000000 INFO @ Sat, 24 Aug 2019 18:53:44: 27000000 INFO @ Sat, 24 Aug 2019 18:53:47: 18000000 INFO @ Sat, 24 Aug 2019 18:53:52: 28000000 INFO @ Sat, 24 Aug 2019 18:53:52: 25000000 INFO @ Sat, 24 Aug 2019 18:53:56: 19000000 INFO @ Sat, 24 Aug 2019 18:53:59: 29000000 INFO @ Sat, 24 Aug 2019 18:54:01: 26000000 INFO @ Sat, 24 Aug 2019 18:54:05: 20000000 INFO @ Sat, 24 Aug 2019 18:54:06: 30000000 INFO @ Sat, 24 Aug 2019 18:54:10: 27000000 INFO @ Sat, 24 Aug 2019 18:54:13: 31000000 INFO @ Sat, 24 Aug 2019 18:54:14: 21000000 INFO @ Sat, 24 Aug 2019 18:54:19: 28000000 INFO @ Sat, 24 Aug 2019 18:54:21: 32000000 INFO @ Sat, 24 Aug 2019 18:54:23: 22000000 INFO @ Sat, 24 Aug 2019 18:54:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:54:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:54:25: #1 total tags in treatment: 32553670 INFO @ Sat, 24 Aug 2019 18:54:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:54:25: #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 18:54:26: #1 tags after filtering in treatment: 32553551 INFO @ Sat, 24 Aug 2019 18:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:54:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:54:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:54:28: 29000000 INFO @ Sat, 24 Aug 2019 18:54:32: 23000000 INFO @ Sat, 24 Aug 2019 18:54:33: #2 number of paired peaks: 77518 INFO @ Sat, 24 Aug 2019 18:54:33: start model_add_line... INFO @ Sat, 24 Aug 2019 18:54:33: start X-correlation... INFO @ Sat, 24 Aug 2019 18:54:33: end of X-cor INFO @ Sat, 24 Aug 2019 18:54:33: #2 finished! INFO @ Sat, 24 Aug 2019 18:54:33: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:54:33: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10_model.r INFO @ Sat, 24 Aug 2019 18:54:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:37: 30000000 INFO @ Sat, 24 Aug 2019 18:54:42: 24000000 INFO @ Sat, 24 Aug 2019 18:54:47: 31000000 INFO @ Sat, 24 Aug 2019 18:54:51: 25000000 INFO @ Sat, 24 Aug 2019 18:54:56: 32000000 INFO @ Sat, 24 Aug 2019 18:55:00: 26000000 INFO @ Sat, 24 Aug 2019 18:55:02: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:55:02: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:55:02: #1 total tags in treatment: 32553670 INFO @ Sat, 24 Aug 2019 18:55:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:55:02: #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 18:55:02: #1 tags after filtering in treatment: 32553551 INFO @ Sat, 24 Aug 2019 18:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:55:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:55:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:55:09: 27000000 INFO @ Sat, 24 Aug 2019 18:55:09: #2 number of paired peaks: 77518 INFO @ Sat, 24 Aug 2019 18:55:09: start model_add_line... INFO @ Sat, 24 Aug 2019 18:55:10: start X-correlation... INFO @ Sat, 24 Aug 2019 18:55:10: end of X-cor INFO @ Sat, 24 Aug 2019 18:55:10: #2 finished! INFO @ Sat, 24 Aug 2019 18:55:10: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:55:10: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05_model.r INFO @ Sat, 24 Aug 2019 18:55:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:55:18: 28000000 INFO @ Sat, 24 Aug 2019 18:55:26: 29000000 INFO @ Sat, 24 Aug 2019 18:55:37: 30000000 INFO @ Sat, 24 Aug 2019 18:55:46: 31000000 INFO @ Sat, 24 Aug 2019 18:55:55: 32000000 INFO @ Sat, 24 Aug 2019 18:56:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:56:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:56:00: #1 total tags in treatment: 32553670 INFO @ Sat, 24 Aug 2019 18:56:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:00: #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 18:56:01: #1 tags after filtering in treatment: 32553551 INFO @ Sat, 24 Aug 2019 18:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:08: #2 number of paired peaks: 77518 INFO @ Sat, 24 Aug 2019 18:56:08: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:09: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:09: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:09: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:09: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:56:09: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20_model.r INFO @ Sat, 24 Aug 2019 18:56:09: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:56:23: #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 18:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.10_summits.bed INFO @ Sat, 24 Aug 2019 18:57:23: Done! pass1 - making usageList (95 chroms): 6 millis pass2 - checking and writing primary data (16671 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.05_summits.bed INFO @ Sat, 24 Aug 2019 18:57:58: Done! pass1 - making usageList (119 chroms): 7 millis pass2 - checking and writing primary data (21406 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:58:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375027/SRX5375027.20_summits.bed INFO @ Sat, 24 Aug 2019 18:58:57: Done! pass1 - making usageList (77 chroms): 5 millis pass2 - checking and writing primary data (11988 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。