Job ID = 2001543 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:46:26 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 ) 2019-07-04T19:53:51 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 ) 2019-07-04T20:03:05 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 ) 2019-07-04T20:03:43 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 ) 2019-07-04T20:04:55 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 ) 2019-07-04T20:05:42 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 ) 2019-07-04T20:11:04 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 ) 2019-07-04T20:12:37 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 ) 2019-07-04T20:12:49 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 : 105,977,109 reads read : 105,977,109 reads written : 105,977,109 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: 01:05:57 105977109 reads; of these: 105977109 (100.00%) were unpaired; of these: 1967034 (1.86%) aligned 0 times 92897382 (87.66%) aligned exactly 1 time 11112693 (10.49%) aligned >1 times 98.14% overall alignment rate Time searching: 01:06:00 Overall time: 01:06:00 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 44 files... [bam_rmdupse_core] 62191096 / 104010075 = 0.5979 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 06:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.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 06:57:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.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 06:57:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.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 06:57:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:25: 1000000 INFO @ Fri, 05 Jul 2019 06:57:25: 1000000 INFO @ Fri, 05 Jul 2019 06:57:26: 1000000 INFO @ Fri, 05 Jul 2019 06:57:34: 2000000 INFO @ Fri, 05 Jul 2019 06:57:35: 2000000 INFO @ Fri, 05 Jul 2019 06:57:35: 2000000 INFO @ Fri, 05 Jul 2019 06:57:42: 3000000 INFO @ Fri, 05 Jul 2019 06:57:44: 3000000 INFO @ Fri, 05 Jul 2019 06:57:45: 3000000 INFO @ Fri, 05 Jul 2019 06:57:50: 4000000 INFO @ Fri, 05 Jul 2019 06:57:53: 4000000 INFO @ Fri, 05 Jul 2019 06:57:54: 4000000 INFO @ Fri, 05 Jul 2019 06:57:58: 5000000 INFO @ Fri, 05 Jul 2019 06:58:03: 5000000 INFO @ Fri, 05 Jul 2019 06:58:03: 5000000 INFO @ Fri, 05 Jul 2019 06:58:07: 6000000 INFO @ Fri, 05 Jul 2019 06:58:12: 6000000 INFO @ Fri, 05 Jul 2019 06:58:12: 6000000 INFO @ Fri, 05 Jul 2019 06:58:15: 7000000 INFO @ Fri, 05 Jul 2019 06:58:21: 7000000 INFO @ Fri, 05 Jul 2019 06:58:22: 7000000 INFO @ Fri, 05 Jul 2019 06:58:23: 8000000 INFO @ Fri, 05 Jul 2019 06:58:30: 8000000 INFO @ Fri, 05 Jul 2019 06:58:31: 8000000 INFO @ Fri, 05 Jul 2019 06:58:32: 9000000 INFO @ Fri, 05 Jul 2019 06:58:39: 9000000 INFO @ Fri, 05 Jul 2019 06:58:40: 10000000 INFO @ Fri, 05 Jul 2019 06:58:40: 9000000 INFO @ Fri, 05 Jul 2019 06:58:49: 11000000 INFO @ Fri, 05 Jul 2019 06:58:49: 10000000 INFO @ Fri, 05 Jul 2019 06:58:49: 10000000 INFO @ Fri, 05 Jul 2019 06:58:57: 12000000 INFO @ Fri, 05 Jul 2019 06:58:58: 11000000 INFO @ Fri, 05 Jul 2019 06:58:59: 11000000 INFO @ Fri, 05 Jul 2019 06:59:06: 13000000 INFO @ Fri, 05 Jul 2019 06:59:07: 12000000 INFO @ Fri, 05 Jul 2019 06:59:08: 12000000 INFO @ Fri, 05 Jul 2019 06:59:14: 14000000 INFO @ Fri, 05 Jul 2019 06:59:16: 13000000 INFO @ Fri, 05 Jul 2019 06:59:17: 13000000 INFO @ Fri, 05 Jul 2019 06:59:23: 15000000 INFO @ Fri, 05 Jul 2019 06:59:25: 14000000 INFO @ Fri, 05 Jul 2019 06:59:27: 14000000 INFO @ Fri, 05 Jul 2019 06:59:31: 16000000 INFO @ Fri, 05 Jul 2019 06:59:35: 15000000 INFO @ Fri, 05 Jul 2019 06:59:36: 15000000 INFO @ Fri, 05 Jul 2019 06:59:40: 17000000 INFO @ Fri, 05 Jul 2019 06:59:44: 16000000 INFO @ Fri, 05 Jul 2019 06:59:45: 16000000 INFO @ Fri, 05 Jul 2019 06:59:49: 18000000 INFO @ Fri, 05 Jul 2019 06:59:53: 17000000 INFO @ Fri, 05 Jul 2019 06:59:54: 17000000 INFO @ Fri, 05 Jul 2019 06:59:57: 19000000 INFO @ Fri, 05 Jul 2019 07:00:02: 18000000 INFO @ Fri, 05 Jul 2019 07:00:04: 18000000 INFO @ Fri, 05 Jul 2019 07:00:06: 20000000 INFO @ Fri, 05 Jul 2019 07:00:11: 19000000 INFO @ Fri, 05 Jul 2019 07:00:13: 19000000 INFO @ Fri, 05 Jul 2019 07:00:14: 21000000 INFO @ Fri, 05 Jul 2019 07:00:20: 20000000 INFO @ Fri, 05 Jul 2019 07:00:22: 20000000 INFO @ Fri, 05 Jul 2019 07:00:23: 22000000 INFO @ Fri, 05 Jul 2019 07:00:29: 21000000 INFO @ Fri, 05 Jul 2019 07:00:31: 23000000 INFO @ Fri, 05 Jul 2019 07:00:31: 21000000 INFO @ Fri, 05 Jul 2019 07:00:38: 22000000 INFO @ Fri, 05 Jul 2019 07:00:39: 24000000 INFO @ Fri, 05 Jul 2019 07:00:40: 22000000 INFO @ Fri, 05 Jul 2019 07:00:47: 23000000 INFO @ Fri, 05 Jul 2019 07:00:48: 25000000 INFO @ Fri, 05 Jul 2019 07:00:49: 23000000 INFO @ Fri, 05 Jul 2019 07:00:56: 26000000 INFO @ Fri, 05 Jul 2019 07:00:56: 24000000 INFO @ Fri, 05 Jul 2019 07:00:58: 24000000 INFO @ Fri, 05 Jul 2019 07:01:04: 27000000 INFO @ Fri, 05 Jul 2019 07:01:05: 25000000 INFO @ Fri, 05 Jul 2019 07:01:07: 25000000 INFO @ Fri, 05 Jul 2019 07:01:12: 28000000 INFO @ Fri, 05 Jul 2019 07:01:14: 26000000 INFO @ Fri, 05 Jul 2019 07:01:16: 26000000 INFO @ Fri, 05 Jul 2019 07:01:21: 29000000 INFO @ Fri, 05 Jul 2019 07:01:23: 27000000 INFO @ Fri, 05 Jul 2019 07:01:25: 27000000 INFO @ Fri, 05 Jul 2019 07:01:29: 30000000 INFO @ Fri, 05 Jul 2019 07:01:31: 28000000 INFO @ Fri, 05 Jul 2019 07:01:34: 28000000 INFO @ Fri, 05 Jul 2019 07:01:37: 31000000 INFO @ Fri, 05 Jul 2019 07:01:40: 29000000 INFO @ Fri, 05 Jul 2019 07:01:43: 29000000 INFO @ Fri, 05 Jul 2019 07:01:46: 32000000 INFO @ Fri, 05 Jul 2019 07:01:49: 30000000 INFO @ Fri, 05 Jul 2019 07:01:52: 30000000 INFO @ Fri, 05 Jul 2019 07:01:54: 33000000 INFO @ Fri, 05 Jul 2019 07:01:58: 31000000 INFO @ Fri, 05 Jul 2019 07:02:02: 31000000 INFO @ Fri, 05 Jul 2019 07:02:02: 34000000 INFO @ Fri, 05 Jul 2019 07:02:06: 32000000 INFO @ Fri, 05 Jul 2019 07:02:10: 35000000 INFO @ Fri, 05 Jul 2019 07:02:11: 32000000 INFO @ Fri, 05 Jul 2019 07:02:15: 33000000 INFO @ Fri, 05 Jul 2019 07:02:18: 36000000 INFO @ Fri, 05 Jul 2019 07:02:20: 33000000 INFO @ Fri, 05 Jul 2019 07:02:24: 34000000 INFO @ Fri, 05 Jul 2019 07:02:26: 37000000 INFO @ Fri, 05 Jul 2019 07:02:29: 34000000 INFO @ Fri, 05 Jul 2019 07:02:32: 35000000 INFO @ Fri, 05 Jul 2019 07:02:34: 38000000 INFO @ Fri, 05 Jul 2019 07:02:38: 35000000 INFO @ Fri, 05 Jul 2019 07:02:41: 36000000 INFO @ Fri, 05 Jul 2019 07:02:42: 39000000 INFO @ Fri, 05 Jul 2019 07:02:47: 36000000 INFO @ Fri, 05 Jul 2019 07:02:50: 37000000 INFO @ Fri, 05 Jul 2019 07:02:50: 40000000 INFO @ Fri, 05 Jul 2019 07:02:56: 37000000 INFO @ Fri, 05 Jul 2019 07:02:58: 41000000 INFO @ Fri, 05 Jul 2019 07:02:59: 38000000 INFO @ Fri, 05 Jul 2019 07:03:05: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:03:05: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:03:05: #1 total tags in treatment: 41818979 INFO @ Fri, 05 Jul 2019 07:03:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:03:05: #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 07:03:06: 38000000 INFO @ Fri, 05 Jul 2019 07:03:06: #1 tags after filtering in treatment: 41818775 INFO @ Fri, 05 Jul 2019 07:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:03:06: #1 finished! INFO @ Fri, 05 Jul 2019 07:03:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:03:07: 39000000 INFO @ Fri, 05 Jul 2019 07:03:15: 39000000 INFO @ Fri, 05 Jul 2019 07:03:16: 40000000 INFO @ Fri, 05 Jul 2019 07:03:19: #2 number of paired peaks: 108032 INFO @ Fri, 05 Jul 2019 07:03:19: start model_add_line... INFO @ Fri, 05 Jul 2019 07:03:20: start X-correlation... INFO @ Fri, 05 Jul 2019 07:03:20: end of X-cor INFO @ Fri, 05 Jul 2019 07:03:20: #2 finished! INFO @ Fri, 05 Jul 2019 07:03:20: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 07:03:20: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 07:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20_model.r INFO @ Fri, 05 Jul 2019 07:03:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:03:24: 40000000 INFO @ Fri, 05 Jul 2019 07:03:25: 41000000 INFO @ Fri, 05 Jul 2019 07:03:33: 41000000 INFO @ Fri, 05 Jul 2019 07:03:33: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:03:33: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:03:33: #1 total tags in treatment: 41818979 INFO @ Fri, 05 Jul 2019 07:03:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:03:33: #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 07:03:34: #1 tags after filtering in treatment: 41818775 INFO @ Fri, 05 Jul 2019 07:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:03:34: #1 finished! INFO @ Fri, 05 Jul 2019 07:03:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:03:40: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:03:40: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:03:40: #1 total tags in treatment: 41818979 INFO @ Fri, 05 Jul 2019 07:03:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:03:40: #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 07:03:41: #1 tags after filtering in treatment: 41818775 INFO @ Fri, 05 Jul 2019 07:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:03:41: #1 finished! INFO @ Fri, 05 Jul 2019 07:03:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:03:46: #2 number of paired peaks: 108032 INFO @ Fri, 05 Jul 2019 07:03:46: start model_add_line... INFO @ Fri, 05 Jul 2019 07:03:47: start X-correlation... INFO @ Fri, 05 Jul 2019 07:03:47: end of X-cor INFO @ Fri, 05 Jul 2019 07:03:47: #2 finished! INFO @ Fri, 05 Jul 2019 07:03:47: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 07:03:47: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 07:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05_model.r INFO @ Fri, 05 Jul 2019 07:03:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:03:53: #2 number of paired peaks: 108032 INFO @ Fri, 05 Jul 2019 07:03:53: start model_add_line... INFO @ Fri, 05 Jul 2019 07:03:55: start X-correlation... INFO @ Fri, 05 Jul 2019 07:03:55: end of X-cor INFO @ Fri, 05 Jul 2019 07:03:55: #2 finished! INFO @ Fri, 05 Jul 2019 07:03:55: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 07:03:55: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 07:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10_model.r INFO @ Fri, 05 Jul 2019 07:03:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:03:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:05:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:06:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:06:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.20_summits.bed INFO @ Fri, 05 Jul 2019 07:07:07: Done! pass1 - making usageList (134 chroms): 14 millis pass2 - checking and writing primary data (44565 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.05_summits.bed INFO @ Fri, 05 Jul 2019 07:07:22: Done! pass1 - making usageList (189 chroms): 23 millis pass2 - checking and writing primary data (88129 records, 4 fields): 129 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101886/ERX101886.10_summits.bed INFO @ Fri, 05 Jul 2019 07:07:31: Done! pass1 - making usageList (161 chroms): 15 millis pass2 - checking and writing primary data (65322 records, 4 fields): 94 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。