Job ID = 2001664 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T22:42:41 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 ) 2019-07-04T22:42:41 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 ) 2019-07-04T22:42:41 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 ) 2019-07-04T22:42:41 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 ) 2019-07-04T22:52:15 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 ) 2019-07-04T23:09:28 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 ) 2019-07-04T23:09:44 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 ) 2019-07-04T23:09:44 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 ) 2019-07-04T23:13:19 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 ) 2019-07-04T23:14:55 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 ) 2019-07-04T23:18:16 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 : 109,287,477 reads read : 109,287,477 reads written : 109,287,477 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: 00:50:46 109287477 reads; of these: 109287477 (100.00%) were unpaired; of these: 2067022 (1.89%) aligned 0 times 96722544 (88.50%) aligned exactly 1 time 10497911 (9.61%) aligned >1 times 98.11% overall alignment rate Time searching: 00:50:49 Overall time: 00:50:49 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] 75283817 / 107220455 = 0.7021 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 09:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.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 09:53:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.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 09:53:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.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 09:53:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:48: 1000000 INFO @ Fri, 05 Jul 2019 09:53:48: 1000000 INFO @ Fri, 05 Jul 2019 09:53:49: 1000000 INFO @ Fri, 05 Jul 2019 09:53:57: 2000000 INFO @ Fri, 05 Jul 2019 09:53:57: 2000000 INFO @ Fri, 05 Jul 2019 09:53:58: 2000000 INFO @ Fri, 05 Jul 2019 09:54:05: 3000000 INFO @ Fri, 05 Jul 2019 09:54:06: 3000000 INFO @ Fri, 05 Jul 2019 09:54:08: 3000000 INFO @ Fri, 05 Jul 2019 09:54:13: 4000000 INFO @ Fri, 05 Jul 2019 09:54:15: 4000000 INFO @ Fri, 05 Jul 2019 09:54:17: 4000000 INFO @ Fri, 05 Jul 2019 09:54:20: 5000000 INFO @ Fri, 05 Jul 2019 09:54:23: 5000000 INFO @ Fri, 05 Jul 2019 09:54:27: 5000000 INFO @ Fri, 05 Jul 2019 09:54:28: 6000000 INFO @ Fri, 05 Jul 2019 09:54:31: 6000000 INFO @ Fri, 05 Jul 2019 09:54:35: 7000000 INFO @ Fri, 05 Jul 2019 09:54:36: 6000000 INFO @ Fri, 05 Jul 2019 09:54:40: 7000000 INFO @ Fri, 05 Jul 2019 09:54:43: 8000000 INFO @ Fri, 05 Jul 2019 09:54:46: 7000000 INFO @ Fri, 05 Jul 2019 09:54:48: 8000000 INFO @ Fri, 05 Jul 2019 09:54:50: 9000000 INFO @ Fri, 05 Jul 2019 09:54:55: 8000000 INFO @ Fri, 05 Jul 2019 09:54:56: 9000000 INFO @ Fri, 05 Jul 2019 09:54:58: 10000000 INFO @ Fri, 05 Jul 2019 09:55:05: 10000000 INFO @ Fri, 05 Jul 2019 09:55:05: 9000000 INFO @ Fri, 05 Jul 2019 09:55:05: 11000000 INFO @ Fri, 05 Jul 2019 09:55:13: 12000000 INFO @ Fri, 05 Jul 2019 09:55:13: 11000000 INFO @ Fri, 05 Jul 2019 09:55:14: 10000000 INFO @ Fri, 05 Jul 2019 09:55:20: 13000000 INFO @ Fri, 05 Jul 2019 09:55:21: 12000000 INFO @ Fri, 05 Jul 2019 09:55:24: 11000000 INFO @ Fri, 05 Jul 2019 09:55:28: 14000000 INFO @ Fri, 05 Jul 2019 09:55:29: 13000000 INFO @ Fri, 05 Jul 2019 09:55:32: 12000000 INFO @ Fri, 05 Jul 2019 09:55:35: 15000000 INFO @ Fri, 05 Jul 2019 09:55:37: 14000000 INFO @ Fri, 05 Jul 2019 09:55:41: 13000000 INFO @ Fri, 05 Jul 2019 09:55:42: 16000000 INFO @ Fri, 05 Jul 2019 09:55:46: 15000000 INFO @ Fri, 05 Jul 2019 09:55:50: 17000000 INFO @ Fri, 05 Jul 2019 09:55:51: 14000000 INFO @ Fri, 05 Jul 2019 09:55:54: 16000000 INFO @ Fri, 05 Jul 2019 09:55:57: 18000000 INFO @ Fri, 05 Jul 2019 09:56:00: 15000000 INFO @ Fri, 05 Jul 2019 09:56:02: 17000000 INFO @ Fri, 05 Jul 2019 09:56:05: 19000000 INFO @ Fri, 05 Jul 2019 09:56:09: 16000000 INFO @ Fri, 05 Jul 2019 09:56:10: 18000000 INFO @ Fri, 05 Jul 2019 09:56:12: 20000000 INFO @ Fri, 05 Jul 2019 09:56:19: 17000000 INFO @ Fri, 05 Jul 2019 09:56:19: 19000000 INFO @ Fri, 05 Jul 2019 09:56:20: 21000000 INFO @ Fri, 05 Jul 2019 09:56:27: 22000000 INFO @ Fri, 05 Jul 2019 09:56:27: 20000000 INFO @ Fri, 05 Jul 2019 09:56:28: 18000000 INFO @ Fri, 05 Jul 2019 09:56:34: 23000000 INFO @ Fri, 05 Jul 2019 09:56:35: 21000000 INFO @ Fri, 05 Jul 2019 09:56:37: 19000000 INFO @ Fri, 05 Jul 2019 09:56:42: 24000000 INFO @ Fri, 05 Jul 2019 09:56:43: 22000000 INFO @ Fri, 05 Jul 2019 09:56:47: 20000000 INFO @ Fri, 05 Jul 2019 09:56:49: 25000000 INFO @ Fri, 05 Jul 2019 09:56:51: 23000000 INFO @ Fri, 05 Jul 2019 09:56:56: 21000000 INFO @ Fri, 05 Jul 2019 09:56:56: 26000000 INFO @ Fri, 05 Jul 2019 09:56:59: 24000000 INFO @ Fri, 05 Jul 2019 09:57:04: 27000000 INFO @ Fri, 05 Jul 2019 09:57:05: 22000000 INFO @ Fri, 05 Jul 2019 09:57:07: 25000000 INFO @ Fri, 05 Jul 2019 09:57:11: 28000000 INFO @ Fri, 05 Jul 2019 09:57:14: 23000000 INFO @ Fri, 05 Jul 2019 09:57:15: 26000000 INFO @ Fri, 05 Jul 2019 09:57:18: 29000000 INFO @ Fri, 05 Jul 2019 09:57:23: 24000000 INFO @ Fri, 05 Jul 2019 09:57:24: 27000000 INFO @ Fri, 05 Jul 2019 09:57:26: 30000000 INFO @ Fri, 05 Jul 2019 09:57:32: 28000000 INFO @ Fri, 05 Jul 2019 09:57:32: 25000000 INFO @ Fri, 05 Jul 2019 09:57:33: 31000000 INFO @ Fri, 05 Jul 2019 09:57:40: 29000000 INFO @ Fri, 05 Jul 2019 09:57:41: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:57:41: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:57:41: #1 total tags in treatment: 31936638 INFO @ Fri, 05 Jul 2019 09:57:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:57:41: #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 09:57:41: 26000000 INFO @ Fri, 05 Jul 2019 09:57:41: #1 tags after filtering in treatment: 31936414 INFO @ Fri, 05 Jul 2019 09:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:57:41: #1 finished! INFO @ Fri, 05 Jul 2019 09:57:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:57:48: 30000000 INFO @ Fri, 05 Jul 2019 09:57:48: #2 number of paired peaks: 61097 INFO @ Fri, 05 Jul 2019 09:57:48: start model_add_line... INFO @ Fri, 05 Jul 2019 09:57:49: 27000000 INFO @ Fri, 05 Jul 2019 09:57:49: start X-correlation... INFO @ Fri, 05 Jul 2019 09:57:49: end of X-cor INFO @ Fri, 05 Jul 2019 09:57:49: #2 finished! INFO @ Fri, 05 Jul 2019 09:57:49: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 09:57:49: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 09:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20_model.r INFO @ Fri, 05 Jul 2019 09:57:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:57:56: 31000000 INFO @ Fri, 05 Jul 2019 09:57:57: 28000000 INFO @ Fri, 05 Jul 2019 09:58:04: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:58:04: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:58:04: #1 total tags in treatment: 31936638 INFO @ Fri, 05 Jul 2019 09:58:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:58:04: #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 09:58:05: #1 tags after filtering in treatment: 31936414 INFO @ Fri, 05 Jul 2019 09:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:58:05: #1 finished! INFO @ Fri, 05 Jul 2019 09:58:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:58:06: 29000000 INFO @ Fri, 05 Jul 2019 09:58:12: #2 number of paired peaks: 61097 INFO @ Fri, 05 Jul 2019 09:58:12: start model_add_line... INFO @ Fri, 05 Jul 2019 09:58:12: start X-correlation... INFO @ Fri, 05 Jul 2019 09:58:12: end of X-cor INFO @ Fri, 05 Jul 2019 09:58:12: #2 finished! INFO @ Fri, 05 Jul 2019 09:58:12: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 09:58:12: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 09:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10_model.r INFO @ Fri, 05 Jul 2019 09:58:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:58:16: 30000000 INFO @ Fri, 05 Jul 2019 09:58:25: 31000000 INFO @ Fri, 05 Jul 2019 09:58:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:58:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:58:34: #1 total tags in treatment: 31936638 INFO @ Fri, 05 Jul 2019 09:58:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:58:34: #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 09:58:35: #1 tags after filtering in treatment: 31936414 INFO @ Fri, 05 Jul 2019 09:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:58:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:58:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:58:42: #2 number of paired peaks: 61097 INFO @ Fri, 05 Jul 2019 09:58:42: start model_add_line... INFO @ Fri, 05 Jul 2019 09:58:42: start X-correlation... INFO @ Fri, 05 Jul 2019 09:58:42: end of X-cor INFO @ Fri, 05 Jul 2019 09:58:42: #2 finished! INFO @ Fri, 05 Jul 2019 09:58:42: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 09:58:42: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 09:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05_model.r INFO @ Fri, 05 Jul 2019 09:58:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:59:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:59:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.20_summits.bed INFO @ Fri, 05 Jul 2019 10:00:09: Done! pass1 - making usageList (116 chroms): 10 millis pass2 - checking and writing primary data (35073 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:00:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.10_summits.bed INFO @ Fri, 05 Jul 2019 10:00:34: Done! pass1 - making usageList (138 chroms): 12 millis pass2 - checking and writing primary data (45148 records, 4 fields): 100 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:01:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:01:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101979/ERX101979.05_summits.bed INFO @ Fri, 05 Jul 2019 10:01:08: Done! pass1 - making usageList (157 chroms): 13 millis pass2 - checking and writing primary data (55213 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。