Job ID = 2001569 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:04:57 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 ) 2019-07-04T20:04:57 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 ) 2019-07-04T20:04:57 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 ) 2019-07-04T20:05:42 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 ) 2019-07-04T20:05:42 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 ) 2019-07-04T20:07:37 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 ) 2019-07-04T20:11:04 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 ) 2019-07-04T20:11:04 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 ) 2019-07-04T20:12:49 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 ) 2019-07-04T20:18:26 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 ) 2019-07-04T20:46:47 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 ) spots read : 109,169,437 reads read : 109,169,437 reads written : 109,169,437 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:06:03 109169437 reads; of these: 109169437 (100.00%) were unpaired; of these: 1816461 (1.66%) aligned 0 times 96361890 (88.27%) aligned exactly 1 time 10991086 (10.07%) aligned >1 times 98.34% overall alignment rate Time searching: 01:06:04 Overall time: 01:06:04 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] 66350027 / 107352976 = 0.6181 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 07:37:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.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 07:37:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:37:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:37:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.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 07:37:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:37:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.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 07:37:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:37:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:37:23: 1000000 INFO @ Fri, 05 Jul 2019 07:37:23: 1000000 INFO @ Fri, 05 Jul 2019 07:37:26: 1000000 INFO @ Fri, 05 Jul 2019 07:37:31: 2000000 INFO @ Fri, 05 Jul 2019 07:37:32: 2000000 INFO @ Fri, 05 Jul 2019 07:37:36: 2000000 INFO @ Fri, 05 Jul 2019 07:37:39: 3000000 INFO @ Fri, 05 Jul 2019 07:37:40: 3000000 INFO @ Fri, 05 Jul 2019 07:37:46: 3000000 INFO @ Fri, 05 Jul 2019 07:37:47: 4000000 INFO @ Fri, 05 Jul 2019 07:37:48: 4000000 INFO @ Fri, 05 Jul 2019 07:37:55: 5000000 INFO @ Fri, 05 Jul 2019 07:37:56: 4000000 INFO @ Fri, 05 Jul 2019 07:37:57: 5000000 INFO @ Fri, 05 Jul 2019 07:38:03: 6000000 INFO @ Fri, 05 Jul 2019 07:38:05: 6000000 INFO @ Fri, 05 Jul 2019 07:38:06: 5000000 INFO @ Fri, 05 Jul 2019 07:38:10: 7000000 INFO @ Fri, 05 Jul 2019 07:38:13: 7000000 INFO @ Fri, 05 Jul 2019 07:38:16: 6000000 INFO @ Fri, 05 Jul 2019 07:38:19: 8000000 INFO @ Fri, 05 Jul 2019 07:38:22: 8000000 INFO @ Fri, 05 Jul 2019 07:38:26: 7000000 INFO @ Fri, 05 Jul 2019 07:38:27: 9000000 INFO @ Fri, 05 Jul 2019 07:38:30: 9000000 INFO @ Fri, 05 Jul 2019 07:38:34: 10000000 INFO @ Fri, 05 Jul 2019 07:38:36: 8000000 INFO @ Fri, 05 Jul 2019 07:38:38: 10000000 INFO @ Fri, 05 Jul 2019 07:38:43: 11000000 INFO @ Fri, 05 Jul 2019 07:38:46: 9000000 INFO @ Fri, 05 Jul 2019 07:38:46: 11000000 INFO @ Fri, 05 Jul 2019 07:38:51: 12000000 INFO @ Fri, 05 Jul 2019 07:38:55: 12000000 INFO @ Fri, 05 Jul 2019 07:38:56: 10000000 INFO @ Fri, 05 Jul 2019 07:38:59: 13000000 INFO @ Fri, 05 Jul 2019 07:39:03: 13000000 INFO @ Fri, 05 Jul 2019 07:39:06: 11000000 INFO @ Fri, 05 Jul 2019 07:39:06: 14000000 INFO @ Fri, 05 Jul 2019 07:39:11: 14000000 INFO @ Fri, 05 Jul 2019 07:39:14: 15000000 INFO @ Fri, 05 Jul 2019 07:39:16: 12000000 INFO @ Fri, 05 Jul 2019 07:39:19: 15000000 INFO @ Fri, 05 Jul 2019 07:39:22: 16000000 INFO @ Fri, 05 Jul 2019 07:39:26: 13000000 INFO @ Fri, 05 Jul 2019 07:39:27: 16000000 INFO @ Fri, 05 Jul 2019 07:39:30: 17000000 INFO @ Fri, 05 Jul 2019 07:39:36: 14000000 INFO @ Fri, 05 Jul 2019 07:39:36: 17000000 INFO @ Fri, 05 Jul 2019 07:39:38: 18000000 INFO @ Fri, 05 Jul 2019 07:39:44: 18000000 INFO @ Fri, 05 Jul 2019 07:39:45: 15000000 INFO @ Fri, 05 Jul 2019 07:39:46: 19000000 INFO @ Fri, 05 Jul 2019 07:39:52: 19000000 INFO @ Fri, 05 Jul 2019 07:39:54: 20000000 INFO @ Fri, 05 Jul 2019 07:39:55: 16000000 INFO @ Fri, 05 Jul 2019 07:40:01: 20000000 INFO @ Fri, 05 Jul 2019 07:40:01: 21000000 INFO @ Fri, 05 Jul 2019 07:40:05: 17000000 INFO @ Fri, 05 Jul 2019 07:40:09: 21000000 INFO @ Fri, 05 Jul 2019 07:40:09: 22000000 INFO @ Fri, 05 Jul 2019 07:40:15: 18000000 INFO @ Fri, 05 Jul 2019 07:40:17: 22000000 INFO @ Fri, 05 Jul 2019 07:40:18: 23000000 INFO @ Fri, 05 Jul 2019 07:40:25: 19000000 INFO @ Fri, 05 Jul 2019 07:40:26: 23000000 INFO @ Fri, 05 Jul 2019 07:40:28: 24000000 INFO @ Fri, 05 Jul 2019 07:40:35: 24000000 INFO @ Fri, 05 Jul 2019 07:40:36: 20000000 INFO @ Fri, 05 Jul 2019 07:40:40: 25000000 INFO @ Fri, 05 Jul 2019 07:40:44: 25000000 INFO @ Fri, 05 Jul 2019 07:40:46: 21000000 INFO @ Fri, 05 Jul 2019 07:40:49: 26000000 INFO @ Fri, 05 Jul 2019 07:40:52: 26000000 INFO @ Fri, 05 Jul 2019 07:40:56: 22000000 INFO @ Fri, 05 Jul 2019 07:40:57: 27000000 INFO @ Fri, 05 Jul 2019 07:41:00: 27000000 INFO @ Fri, 05 Jul 2019 07:41:06: 23000000 INFO @ Fri, 05 Jul 2019 07:41:06: 28000000 INFO @ Fri, 05 Jul 2019 07:41:08: 28000000 INFO @ Fri, 05 Jul 2019 07:41:15: 29000000 INFO @ Fri, 05 Jul 2019 07:41:15: 24000000 INFO @ Fri, 05 Jul 2019 07:41:16: 29000000 INFO @ Fri, 05 Jul 2019 07:41:23: 30000000 INFO @ Fri, 05 Jul 2019 07:41:24: 30000000 INFO @ Fri, 05 Jul 2019 07:41:25: 25000000 INFO @ Fri, 05 Jul 2019 07:41:30: 31000000 INFO @ Fri, 05 Jul 2019 07:41:33: 31000000 INFO @ Fri, 05 Jul 2019 07:41:34: 26000000 INFO @ Fri, 05 Jul 2019 07:41:38: 32000000 INFO @ Fri, 05 Jul 2019 07:41:41: 32000000 INFO @ Fri, 05 Jul 2019 07:41:44: 27000000 INFO @ Fri, 05 Jul 2019 07:41:47: 33000000 INFO @ Fri, 05 Jul 2019 07:41:50: 33000000 INFO @ Fri, 05 Jul 2019 07:41:54: 28000000 INFO @ Fri, 05 Jul 2019 07:41:54: 34000000 INFO @ Fri, 05 Jul 2019 07:41:59: 34000000 INFO @ Fri, 05 Jul 2019 07:42:03: 35000000 INFO @ Fri, 05 Jul 2019 07:42:03: 29000000 INFO @ Fri, 05 Jul 2019 07:42:08: 35000000 INFO @ Fri, 05 Jul 2019 07:42:11: 36000000 INFO @ Fri, 05 Jul 2019 07:42:13: 30000000 INFO @ Fri, 05 Jul 2019 07:42:16: 36000000 INFO @ Fri, 05 Jul 2019 07:42:18: 37000000 INFO @ Fri, 05 Jul 2019 07:42:22: 31000000 INFO @ Fri, 05 Jul 2019 07:42:24: 37000000 INFO @ Fri, 05 Jul 2019 07:42:26: 38000000 INFO @ Fri, 05 Jul 2019 07:42:32: 38000000 INFO @ Fri, 05 Jul 2019 07:42:32: 32000000 INFO @ Fri, 05 Jul 2019 07:42:34: 39000000 INFO @ Fri, 05 Jul 2019 07:42:40: 39000000 INFO @ Fri, 05 Jul 2019 07:42:43: 40000000 INFO @ Fri, 05 Jul 2019 07:42:43: 33000000 INFO @ Fri, 05 Jul 2019 07:42:50: 40000000 INFO @ Fri, 05 Jul 2019 07:42:50: 41000000 INFO @ Fri, 05 Jul 2019 07:42:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:42:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:42:51: #1 total tags in treatment: 41002949 INFO @ Fri, 05 Jul 2019 07:42:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:42:51: #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 07:42:52: #1 tags after filtering in treatment: 41002754 INFO @ Fri, 05 Jul 2019 07:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:42:52: #1 finished! INFO @ Fri, 05 Jul 2019 07:42:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:42:53: 34000000 INFO @ Fri, 05 Jul 2019 07:42:58: 41000000 INFO @ Fri, 05 Jul 2019 07:42:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:42:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:42:58: #1 total tags in treatment: 41002949 INFO @ Fri, 05 Jul 2019 07:42:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:42:58: #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 07:42:59: #1 tags after filtering in treatment: 41002754 INFO @ Fri, 05 Jul 2019 07:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:42:59: #1 finished! INFO @ Fri, 05 Jul 2019 07:42:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:43:03: #2 number of paired peaks: 98372 INFO @ Fri, 05 Jul 2019 07:43:03: start model_add_line... INFO @ Fri, 05 Jul 2019 07:43:03: 35000000 INFO @ Fri, 05 Jul 2019 07:43:04: start X-correlation... INFO @ Fri, 05 Jul 2019 07:43:04: end of X-cor INFO @ Fri, 05 Jul 2019 07:43:04: #2 finished! INFO @ Fri, 05 Jul 2019 07:43:04: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 07:43:04: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 07:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10_model.r INFO @ Fri, 05 Jul 2019 07:43:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:43:10: #2 number of paired peaks: 98372 INFO @ Fri, 05 Jul 2019 07:43:10: start model_add_line... INFO @ Fri, 05 Jul 2019 07:43:11: start X-correlation... INFO @ Fri, 05 Jul 2019 07:43:11: end of X-cor INFO @ Fri, 05 Jul 2019 07:43:11: #2 finished! INFO @ Fri, 05 Jul 2019 07:43:11: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 07:43:11: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 07:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05_model.r INFO @ Fri, 05 Jul 2019 07:43:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:43:12: 36000000 INFO @ Fri, 05 Jul 2019 07:43:22: 37000000 INFO @ Fri, 05 Jul 2019 07:43:31: 38000000 INFO @ Fri, 05 Jul 2019 07:43:41: 39000000 INFO @ Fri, 05 Jul 2019 07:43:50: 40000000 INFO @ Fri, 05 Jul 2019 07:43:59: 41000000 INFO @ Fri, 05 Jul 2019 07:44:00: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:44:00: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:44:00: #1 total tags in treatment: 41002949 INFO @ Fri, 05 Jul 2019 07:44:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:44:00: #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 07:44:01: #1 tags after filtering in treatment: 41002754 INFO @ Fri, 05 Jul 2019 07:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:44:01: #1 finished! INFO @ Fri, 05 Jul 2019 07:44:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:44:12: #2 number of paired peaks: 98372 INFO @ Fri, 05 Jul 2019 07:44:12: start model_add_line... INFO @ Fri, 05 Jul 2019 07:44:13: start X-correlation... INFO @ Fri, 05 Jul 2019 07:44:13: end of X-cor INFO @ Fri, 05 Jul 2019 07:44:13: #2 finished! INFO @ Fri, 05 Jul 2019 07:44:13: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 07:44:13: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 07:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20_model.r INFO @ Fri, 05 Jul 2019 07:44:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:45:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:45:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.10_summits.bed INFO @ Fri, 05 Jul 2019 07:46:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:46:15: Done! pass1 - making usageList (166 chroms): 14 millis pass2 - checking and writing primary data (64744 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.05_summits.bed INFO @ Fri, 05 Jul 2019 07:46:22: Done! pass1 - making usageList (186 chroms): 21 millis pass2 - checking and writing primary data (84174 records, 4 fields): 115 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 07:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101912/ERX101912.20_summits.bed INFO @ Fri, 05 Jul 2019 07:47:20: Done! pass1 - making usageList (140 chroms): 15 millis pass2 - checking and writing primary data (45204 records, 4 fields): 69 millis CompletedMACS2peakCalling BigWig に変換しました。