Job ID = 2001661 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:02:40 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 ) 2019-07-04T23:07:13 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 ) 2019-07-04T23:08:10 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 ) 2019-07-04T23:08:45 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T23:09:28 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T23:10:07 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 ) 2019-07-04T23:15:22 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 ) 2019-07-04T23:15:53 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 ) 2019-07-04T23:17:31 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 ) 2019-07-04T23:30:18 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 ) 2019-07-04T23:35:41 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 117,499,547 reads read : 117,499,547 reads written : 117,499,547 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:06:37 117499547 reads; of these: 117499547 (100.00%) were unpaired; of these: 2067611 (1.76%) aligned 0 times 103678324 (88.24%) aligned exactly 1 time 11753612 (10.00%) aligned >1 times 98.24% overall alignment rate Time searching: 01:06:41 Overall time: 01:06:41 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 48 files... [bam_rmdupse_core] 77495764 / 115431936 = 0.6714 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, 05 Jul 2019 10:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.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 @ Fri, 05 Jul 2019 10:36:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:36:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.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 @ Fri, 05 Jul 2019 10:36:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:36:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.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 @ Fri, 05 Jul 2019 10:36:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:36:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:36:51: 1000000 INFO @ Fri, 05 Jul 2019 10:36:51: 1000000 INFO @ Fri, 05 Jul 2019 10:36:52: 1000000 INFO @ Fri, 05 Jul 2019 10:36:58: 2000000 INFO @ Fri, 05 Jul 2019 10:36:58: 2000000 INFO @ Fri, 05 Jul 2019 10:36:59: 2000000 INFO @ Fri, 05 Jul 2019 10:37:05: 3000000 INFO @ Fri, 05 Jul 2019 10:37:05: 3000000 INFO @ Fri, 05 Jul 2019 10:37:06: 3000000 INFO @ Fri, 05 Jul 2019 10:37:12: 4000000 INFO @ Fri, 05 Jul 2019 10:37:13: 4000000 INFO @ Fri, 05 Jul 2019 10:37:13: 4000000 INFO @ Fri, 05 Jul 2019 10:37:19: 5000000 INFO @ Fri, 05 Jul 2019 10:37:20: 5000000 INFO @ Fri, 05 Jul 2019 10:37:20: 5000000 INFO @ Fri, 05 Jul 2019 10:37:26: 6000000 INFO @ Fri, 05 Jul 2019 10:37:27: 6000000 INFO @ Fri, 05 Jul 2019 10:37:27: 6000000 INFO @ Fri, 05 Jul 2019 10:37:34: 7000000 INFO @ Fri, 05 Jul 2019 10:37:34: 7000000 INFO @ Fri, 05 Jul 2019 10:37:35: 7000000 INFO @ Fri, 05 Jul 2019 10:37:41: 8000000 INFO @ Fri, 05 Jul 2019 10:37:42: 8000000 INFO @ Fri, 05 Jul 2019 10:37:42: 8000000 INFO @ Fri, 05 Jul 2019 10:37:48: 9000000 INFO @ Fri, 05 Jul 2019 10:37:49: 9000000 INFO @ Fri, 05 Jul 2019 10:37:49: 9000000 INFO @ Fri, 05 Jul 2019 10:37:55: 10000000 INFO @ Fri, 05 Jul 2019 10:37:57: 10000000 INFO @ Fri, 05 Jul 2019 10:37:57: 10000000 INFO @ Fri, 05 Jul 2019 10:38:02: 11000000 INFO @ Fri, 05 Jul 2019 10:38:04: 11000000 INFO @ Fri, 05 Jul 2019 10:38:05: 11000000 INFO @ Fri, 05 Jul 2019 10:38:09: 12000000 INFO @ Fri, 05 Jul 2019 10:38:11: 12000000 INFO @ Fri, 05 Jul 2019 10:38:13: 12000000 INFO @ Fri, 05 Jul 2019 10:38:17: 13000000 INFO @ Fri, 05 Jul 2019 10:38:18: 13000000 INFO @ Fri, 05 Jul 2019 10:38:20: 13000000 INFO @ Fri, 05 Jul 2019 10:38:24: 14000000 INFO @ Fri, 05 Jul 2019 10:38:25: 14000000 INFO @ Fri, 05 Jul 2019 10:38:28: 14000000 INFO @ Fri, 05 Jul 2019 10:38:31: 15000000 INFO @ Fri, 05 Jul 2019 10:38:32: 15000000 INFO @ Fri, 05 Jul 2019 10:38:36: 15000000 INFO @ Fri, 05 Jul 2019 10:38:38: 16000000 INFO @ Fri, 05 Jul 2019 10:38:40: 16000000 INFO @ Fri, 05 Jul 2019 10:38:44: 16000000 INFO @ Fri, 05 Jul 2019 10:38:45: 17000000 INFO @ Fri, 05 Jul 2019 10:38:47: 17000000 INFO @ Fri, 05 Jul 2019 10:38:52: 17000000 INFO @ Fri, 05 Jul 2019 10:38:52: 18000000 INFO @ Fri, 05 Jul 2019 10:38:54: 18000000 INFO @ Fri, 05 Jul 2019 10:38:59: 19000000 INFO @ Fri, 05 Jul 2019 10:38:59: 18000000 INFO @ Fri, 05 Jul 2019 10:39:01: 19000000 INFO @ Fri, 05 Jul 2019 10:39:06: 20000000 INFO @ Fri, 05 Jul 2019 10:39:07: 19000000 INFO @ Fri, 05 Jul 2019 10:39:08: 20000000 INFO @ Fri, 05 Jul 2019 10:39:13: 21000000 INFO @ Fri, 05 Jul 2019 10:39:15: 20000000 INFO @ Fri, 05 Jul 2019 10:39:16: 21000000 INFO @ Fri, 05 Jul 2019 10:39:21: 22000000 INFO @ Fri, 05 Jul 2019 10:39:23: 22000000 INFO @ Fri, 05 Jul 2019 10:39:23: 21000000 INFO @ Fri, 05 Jul 2019 10:39:28: 23000000 INFO @ Fri, 05 Jul 2019 10:39:30: 23000000 INFO @ Fri, 05 Jul 2019 10:39:31: 22000000 INFO @ Fri, 05 Jul 2019 10:39:35: 24000000 INFO @ Fri, 05 Jul 2019 10:39:37: 24000000 INFO @ Fri, 05 Jul 2019 10:39:38: 23000000 INFO @ Fri, 05 Jul 2019 10:39:42: 25000000 INFO @ Fri, 05 Jul 2019 10:39:44: 25000000 INFO @ Fri, 05 Jul 2019 10:39:46: 24000000 INFO @ Fri, 05 Jul 2019 10:39:49: 26000000 INFO @ Fri, 05 Jul 2019 10:39:51: 26000000 INFO @ Fri, 05 Jul 2019 10:39:54: 25000000 INFO @ Fri, 05 Jul 2019 10:39:56: 27000000 INFO @ Fri, 05 Jul 2019 10:39:58: 27000000 INFO @ Fri, 05 Jul 2019 10:40:02: 26000000 INFO @ Fri, 05 Jul 2019 10:40:03: 28000000 INFO @ Fri, 05 Jul 2019 10:40:06: 28000000 INFO @ Fri, 05 Jul 2019 10:40:09: 27000000 INFO @ Fri, 05 Jul 2019 10:40:10: 29000000 INFO @ Fri, 05 Jul 2019 10:40:13: 29000000 INFO @ Fri, 05 Jul 2019 10:40:17: 30000000 INFO @ Fri, 05 Jul 2019 10:40:17: 28000000 INFO @ Fri, 05 Jul 2019 10:40:20: 30000000 INFO @ Fri, 05 Jul 2019 10:40:24: 31000000 INFO @ Fri, 05 Jul 2019 10:40:25: 29000000 INFO @ Fri, 05 Jul 2019 10:40:27: 31000000 INFO @ Fri, 05 Jul 2019 10:40:31: 32000000 INFO @ Fri, 05 Jul 2019 10:40:32: 30000000 INFO @ Fri, 05 Jul 2019 10:40:34: 32000000 INFO @ Fri, 05 Jul 2019 10:40:38: 33000000 INFO @ Fri, 05 Jul 2019 10:40:39: 31000000 INFO @ Fri, 05 Jul 2019 10:40:41: 33000000 INFO @ Fri, 05 Jul 2019 10:40:45: 34000000 INFO @ Fri, 05 Jul 2019 10:40:46: 32000000 INFO @ Fri, 05 Jul 2019 10:40:48: 34000000 INFO @ Fri, 05 Jul 2019 10:40:52: 35000000 INFO @ Fri, 05 Jul 2019 10:40:53: 33000000 INFO @ Fri, 05 Jul 2019 10:40:55: 35000000 INFO @ Fri, 05 Jul 2019 10:41:00: 36000000 INFO @ Fri, 05 Jul 2019 10:41:00: 34000000 INFO @ Fri, 05 Jul 2019 10:41:03: 36000000 INFO @ Fri, 05 Jul 2019 10:41:07: 37000000 INFO @ Fri, 05 Jul 2019 10:41:08: 35000000 INFO @ Fri, 05 Jul 2019 10:41:11: 37000000 INFO @ Fri, 05 Jul 2019 10:41:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 10:41:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 10:41:15: #1 total tags in treatment: 37936172 INFO @ Fri, 05 Jul 2019 10:41:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:41:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:41:16: #1 tags after filtering in treatment: 37935977 INFO @ Fri, 05 Jul 2019 10:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:41:16: #1 finished! INFO @ Fri, 05 Jul 2019 10:41:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:41:16: 36000000 INFO @ Fri, 05 Jul 2019 10:41:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 10:41:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 10:41:18: #1 total tags in treatment: 37936172 INFO @ Fri, 05 Jul 2019 10:41:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:41:19: #1 tags after filtering in treatment: 37935977 INFO @ Fri, 05 Jul 2019 10:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:41:19: #1 finished! INFO @ Fri, 05 Jul 2019 10:41:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:41:24: #2 number of paired peaks: 72023 INFO @ Fri, 05 Jul 2019 10:41:24: start model_add_line... INFO @ Fri, 05 Jul 2019 10:41:25: 37000000 INFO @ Fri, 05 Jul 2019 10:41:25: start X-correlation... INFO @ Fri, 05 Jul 2019 10:41:25: end of X-cor INFO @ Fri, 05 Jul 2019 10:41:25: #2 finished! INFO @ Fri, 05 Jul 2019 10:41:25: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 10:41:25: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 10:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05_model.r INFO @ Fri, 05 Jul 2019 10:41:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:41:27: #2 number of paired peaks: 72023 INFO @ Fri, 05 Jul 2019 10:41:27: start model_add_line... INFO @ Fri, 05 Jul 2019 10:41:28: start X-correlation... INFO @ Fri, 05 Jul 2019 10:41:28: end of X-cor INFO @ Fri, 05 Jul 2019 10:41:28: #2 finished! INFO @ Fri, 05 Jul 2019 10:41:28: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 10:41:28: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 10:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10_model.r INFO @ Fri, 05 Jul 2019 10:41:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:41:33: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 10:41:33: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 10:41:33: #1 total tags in treatment: 37936172 INFO @ Fri, 05 Jul 2019 10:41:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:41:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:41:34: #1 tags after filtering in treatment: 37935977 INFO @ Fri, 05 Jul 2019 10:41:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:41:34: #1 finished! INFO @ Fri, 05 Jul 2019 10:41:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:41:43: #2 number of paired peaks: 72023 INFO @ Fri, 05 Jul 2019 10:41:43: start model_add_line... INFO @ Fri, 05 Jul 2019 10:41:44: start X-correlation... INFO @ Fri, 05 Jul 2019 10:41:44: end of X-cor INFO @ Fri, 05 Jul 2019 10:41:44: #2 finished! INFO @ Fri, 05 Jul 2019 10:41:44: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 10:41:44: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 10:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20_model.r INFO @ Fri, 05 Jul 2019 10:41:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:43:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:43:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:43:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.05_summits.bed INFO @ Fri, 05 Jul 2019 10:44:15: Done! INFO @ Fri, 05 Jul 2019 10:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10_peaks.xls pass1 - making usageList (168 chroms): 19 millis INFO @ Fri, 05 Jul 2019 10:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10_peaks.narrowPeak pass2 - checking and writing primary data (62825 records, 4 fields): 86 millis INFO @ Fri, 05 Jul 2019 10:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.10_summits.bed INFO @ Fri, 05 Jul 2019 10:44:17: Done! pass1 - making usageList (148 chroms): 10 millis pass2 - checking and writing primary data (50990 records, 4 fields): 69 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101976/ERX101976.20_summits.bed INFO @ Fri, 05 Jul 2019 10:44:28: Done! pass1 - making usageList (121 chroms): 8 millis pass2 - checking and writing primary data (37932 records, 4 fields): 62 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。