Job ID = 2001531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:23:25 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 ) 2019-07-04T19:27:01 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:36:47 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 ) 2019-07-04T19:36:47 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 ) 2019-07-04T19:43:59 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 ) 2019-07-04T19:43:59 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 ) 2019-07-04T19:43:59 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 ) 2019-07-04T19:45:25 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 ) 2019-07-04T19:48:18 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 ) 2019-07-04T20:03:01 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 ) 2019-07-04T20:05:06 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 : 107,966,354 reads read : 107,966,354 reads written : 107,966,354 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: 00:00:00 Multiseed full-index search: 02:11:35 107966354 reads; of these: 107966354 (100.00%) were unpaired; of these: 1760908 (1.63%) aligned 0 times 88739314 (82.19%) aligned exactly 1 time 17466132 (16.18%) aligned >1 times 98.37% overall alignment rate Time searching: 02:11:37 Overall time: 02:11:37 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] 64982888 / 106205446 = 0.6119 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 07:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.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 07:47:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:47:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.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 07:47:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:47:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.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 07:47:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:47:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:47:22: 1000000 INFO @ Fri, 05 Jul 2019 07:47:22: 1000000 INFO @ Fri, 05 Jul 2019 07:47:23: 1000000 INFO @ Fri, 05 Jul 2019 07:47:29: 2000000 INFO @ Fri, 05 Jul 2019 07:47:29: 2000000 INFO @ Fri, 05 Jul 2019 07:47:30: 2000000 INFO @ Fri, 05 Jul 2019 07:47:36: 3000000 INFO @ Fri, 05 Jul 2019 07:47:37: 3000000 INFO @ Fri, 05 Jul 2019 07:47:37: 3000000 INFO @ Fri, 05 Jul 2019 07:47:44: 4000000 INFO @ Fri, 05 Jul 2019 07:47:44: 4000000 INFO @ Fri, 05 Jul 2019 07:47:45: 4000000 INFO @ Fri, 05 Jul 2019 07:47:51: 5000000 INFO @ Fri, 05 Jul 2019 07:47:51: 5000000 INFO @ Fri, 05 Jul 2019 07:47:52: 5000000 INFO @ Fri, 05 Jul 2019 07:47:58: 6000000 INFO @ Fri, 05 Jul 2019 07:47:59: 6000000 INFO @ Fri, 05 Jul 2019 07:48:00: 6000000 INFO @ Fri, 05 Jul 2019 07:48:05: 7000000 INFO @ Fri, 05 Jul 2019 07:48:06: 7000000 INFO @ Fri, 05 Jul 2019 07:48:07: 7000000 INFO @ Fri, 05 Jul 2019 07:48:13: 8000000 INFO @ Fri, 05 Jul 2019 07:48:14: 8000000 INFO @ Fri, 05 Jul 2019 07:48:15: 8000000 INFO @ Fri, 05 Jul 2019 07:48:20: 9000000 INFO @ Fri, 05 Jul 2019 07:48:21: 9000000 INFO @ Fri, 05 Jul 2019 07:48:22: 9000000 INFO @ Fri, 05 Jul 2019 07:48:27: 10000000 INFO @ Fri, 05 Jul 2019 07:48:29: 10000000 INFO @ Fri, 05 Jul 2019 07:48:30: 10000000 INFO @ Fri, 05 Jul 2019 07:48:35: 11000000 INFO @ Fri, 05 Jul 2019 07:48:36: 11000000 INFO @ Fri, 05 Jul 2019 07:48:37: 11000000 INFO @ Fri, 05 Jul 2019 07:48:42: 12000000 INFO @ Fri, 05 Jul 2019 07:48:44: 12000000 INFO @ Fri, 05 Jul 2019 07:48:45: 12000000 INFO @ Fri, 05 Jul 2019 07:48:49: 13000000 INFO @ Fri, 05 Jul 2019 07:48:51: 13000000 INFO @ Fri, 05 Jul 2019 07:48:52: 13000000 INFO @ Fri, 05 Jul 2019 07:48:57: 14000000 INFO @ Fri, 05 Jul 2019 07:48:59: 14000000 INFO @ Fri, 05 Jul 2019 07:48:59: 14000000 INFO @ Fri, 05 Jul 2019 07:49:04: 15000000 INFO @ Fri, 05 Jul 2019 07:49:06: 15000000 INFO @ Fri, 05 Jul 2019 07:49:06: 15000000 INFO @ Fri, 05 Jul 2019 07:49:11: 16000000 INFO @ Fri, 05 Jul 2019 07:49:12: 16000000 INFO @ Fri, 05 Jul 2019 07:49:13: 16000000 INFO @ Fri, 05 Jul 2019 07:49:19: 17000000 INFO @ Fri, 05 Jul 2019 07:49:19: 17000000 INFO @ Fri, 05 Jul 2019 07:49:21: 17000000 INFO @ Fri, 05 Jul 2019 07:49:26: 18000000 INFO @ Fri, 05 Jul 2019 07:49:26: 18000000 INFO @ Fri, 05 Jul 2019 07:49:28: 18000000 INFO @ Fri, 05 Jul 2019 07:49:33: 19000000 INFO @ Fri, 05 Jul 2019 07:49:33: 19000000 INFO @ Fri, 05 Jul 2019 07:49:35: 19000000 INFO @ Fri, 05 Jul 2019 07:49:39: 20000000 INFO @ Fri, 05 Jul 2019 07:49:40: 20000000 INFO @ Fri, 05 Jul 2019 07:49:42: 20000000 INFO @ Fri, 05 Jul 2019 07:49:46: 21000000 INFO @ Fri, 05 Jul 2019 07:49:48: 21000000 INFO @ Fri, 05 Jul 2019 07:49:49: 21000000 INFO @ Fri, 05 Jul 2019 07:49:53: 22000000 INFO @ Fri, 05 Jul 2019 07:49:55: 22000000 INFO @ Fri, 05 Jul 2019 07:49:56: 22000000 INFO @ Fri, 05 Jul 2019 07:49:59: 23000000 INFO @ Fri, 05 Jul 2019 07:50:02: 23000000 INFO @ Fri, 05 Jul 2019 07:50:03: 23000000 INFO @ Fri, 05 Jul 2019 07:50:06: 24000000 INFO @ Fri, 05 Jul 2019 07:50:09: 24000000 INFO @ Fri, 05 Jul 2019 07:50:10: 24000000 INFO @ Fri, 05 Jul 2019 07:50:14: 25000000 INFO @ Fri, 05 Jul 2019 07:50:16: 25000000 INFO @ Fri, 05 Jul 2019 07:50:16: 25000000 INFO @ Fri, 05 Jul 2019 07:50:23: 26000000 INFO @ Fri, 05 Jul 2019 07:50:23: 26000000 INFO @ Fri, 05 Jul 2019 07:50:24: 26000000 INFO @ Fri, 05 Jul 2019 07:50:30: 27000000 INFO @ Fri, 05 Jul 2019 07:50:31: 27000000 INFO @ Fri, 05 Jul 2019 07:50:31: 27000000 INFO @ Fri, 05 Jul 2019 07:50:36: 28000000 INFO @ Fri, 05 Jul 2019 07:50:38: 28000000 INFO @ Fri, 05 Jul 2019 07:50:38: 28000000 INFO @ Fri, 05 Jul 2019 07:50:43: 29000000 INFO @ Fri, 05 Jul 2019 07:50:45: 29000000 INFO @ Fri, 05 Jul 2019 07:50:45: 29000000 INFO @ Fri, 05 Jul 2019 07:50:50: 30000000 INFO @ Fri, 05 Jul 2019 07:50:53: 30000000 INFO @ Fri, 05 Jul 2019 07:50:53: 30000000 INFO @ Fri, 05 Jul 2019 07:50:58: 31000000 INFO @ Fri, 05 Jul 2019 07:51:00: 31000000 INFO @ Fri, 05 Jul 2019 07:51:00: 31000000 INFO @ Fri, 05 Jul 2019 07:51:05: 32000000 INFO @ Fri, 05 Jul 2019 07:51:07: 32000000 INFO @ Fri, 05 Jul 2019 07:51:07: 32000000 INFO @ Fri, 05 Jul 2019 07:51:12: 33000000 INFO @ Fri, 05 Jul 2019 07:51:13: 33000000 INFO @ Fri, 05 Jul 2019 07:51:14: 33000000 INFO @ Fri, 05 Jul 2019 07:51:19: 34000000 INFO @ Fri, 05 Jul 2019 07:51:20: 34000000 INFO @ Fri, 05 Jul 2019 07:51:22: 34000000 INFO @ Fri, 05 Jul 2019 07:51:26: 35000000 INFO @ Fri, 05 Jul 2019 07:51:27: 35000000 INFO @ Fri, 05 Jul 2019 07:51:29: 35000000 INFO @ Fri, 05 Jul 2019 07:51:33: 36000000 INFO @ Fri, 05 Jul 2019 07:51:33: 36000000 INFO @ Fri, 05 Jul 2019 07:51:36: 36000000 INFO @ Fri, 05 Jul 2019 07:51:40: 37000000 INFO @ Fri, 05 Jul 2019 07:51:40: 37000000 INFO @ Fri, 05 Jul 2019 07:51:43: 37000000 INFO @ Fri, 05 Jul 2019 07:51:47: 38000000 INFO @ Fri, 05 Jul 2019 07:51:47: 38000000 INFO @ Fri, 05 Jul 2019 07:51:51: 38000000 INFO @ Fri, 05 Jul 2019 07:51:53: 39000000 INFO @ Fri, 05 Jul 2019 07:51:54: 39000000 INFO @ Fri, 05 Jul 2019 07:51:58: 39000000 INFO @ Fri, 05 Jul 2019 07:52:00: 40000000 INFO @ Fri, 05 Jul 2019 07:52:01: 40000000 INFO @ Fri, 05 Jul 2019 07:52:05: 40000000 INFO @ Fri, 05 Jul 2019 07:52:07: 41000000 INFO @ Fri, 05 Jul 2019 07:52:09: 41000000 INFO @ Fri, 05 Jul 2019 07:52:09: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:52:09: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:52:09: #1 total tags in treatment: 41222558 INFO @ Fri, 05 Jul 2019 07:52:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:52:09: #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 07:52:10: #1 tags after filtering in treatment: 41222439 INFO @ Fri, 05 Jul 2019 07:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:52:10: #1 finished! INFO @ Fri, 05 Jul 2019 07:52:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:52:11: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:52:11: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:52:11: #1 total tags in treatment: 41222558 INFO @ Fri, 05 Jul 2019 07:52:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:52:11: #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 07:52:12: #1 tags after filtering in treatment: 41222439 INFO @ Fri, 05 Jul 2019 07:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:52:12: #1 finished! INFO @ Fri, 05 Jul 2019 07:52:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:52:12: 41000000 INFO @ Fri, 05 Jul 2019 07:52:14: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:52:14: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:52:14: #1 total tags in treatment: 41222558 INFO @ Fri, 05 Jul 2019 07:52:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:52:14: #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 07:52:15: #1 tags after filtering in treatment: 41222439 INFO @ Fri, 05 Jul 2019 07:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:52:15: #1 finished! INFO @ Fri, 05 Jul 2019 07:52:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:52:19: #2 number of paired peaks: 103374 INFO @ Fri, 05 Jul 2019 07:52:19: start model_add_line... INFO @ Fri, 05 Jul 2019 07:52:20: start X-correlation... INFO @ Fri, 05 Jul 2019 07:52:20: end of X-cor INFO @ Fri, 05 Jul 2019 07:52:20: #2 finished! INFO @ Fri, 05 Jul 2019 07:52:20: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 07:52:20: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 07:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20_model.r INFO @ Fri, 05 Jul 2019 07:52:21: #2 number of paired peaks: 103374 INFO @ Fri, 05 Jul 2019 07:52:21: start model_add_line... INFO @ Fri, 05 Jul 2019 07:52:22: start X-correlation... INFO @ Fri, 05 Jul 2019 07:52:22: end of X-cor INFO @ Fri, 05 Jul 2019 07:52:22: #2 finished! INFO @ Fri, 05 Jul 2019 07:52:22: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 07:52:22: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 07:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10_model.r INFO @ Fri, 05 Jul 2019 07:52:24: #2 number of paired peaks: 103374 INFO @ Fri, 05 Jul 2019 07:52:24: start model_add_line... INFO @ Fri, 05 Jul 2019 07:52:25: start X-correlation... INFO @ Fri, 05 Jul 2019 07:52:25: end of X-cor INFO @ Fri, 05 Jul 2019 07:52:25: #2 finished! INFO @ Fri, 05 Jul 2019 07:52:25: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 07:52:25: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 07:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05_model.r INFO @ Fri, 05 Jul 2019 07:52:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:52:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:52:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:54:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:54:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.20_summits.bed INFO @ Fri, 05 Jul 2019 07:55:40: Done! pass1 - making usageList (48 chroms): 4 millis pass2 - checking and writing primary data (5644 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.10_summits.bed INFO @ Fri, 05 Jul 2019 07:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:55:44: Done! pass1 - making usageList (108 chroms): 12 millis INFO @ Fri, 05 Jul 2019 07:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101875/ERX101875.05_summits.bed pass2 - checking and writing primary data (35785 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:55:45: Done! pass1 - making usageList (193 chroms): 22 millis pass2 - checking and writing primary data (108480 records, 4 fields): 132 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。