Job ID = 2640472 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:07:51 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 ) 2019-08-24T08:07:51 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 ) 2019-08-24T08:07:51 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 ) 2019-08-24T08:07:51 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:09:15 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 ) 2019-08-24T08:09:15 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:12:39 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 ) 2019-08-24T08:12:39 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 ) 2019-08-24T08:13:38 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 ) 2019-08-24T08:13:38 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 ) 2019-08-24T08:13:43 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 ) 2019-08-24T08:14:59 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 ) 2019-08-24T08:21:52 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 ) 2019-08-24T08:21:52 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 : 24,479,071 reads read : 48,958,142 reads written : 24,479,071 reads 0-length : 24,479,071 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: 00:17:29 24479071 reads; of these: 24479071 (100.00%) were unpaired; of these: 1213424 (4.96%) aligned 0 times 17290262 (70.63%) aligned exactly 1 time 5975385 (24.41%) aligned >1 times 95.04% overall alignment rate Time searching: 00:17:32 Overall time: 00:17:32 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 12 files... [bam_rmdupse_core] 1559380 / 23265647 = 0.0670 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.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 @ Sat, 24 Aug 2019 17:47:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:47:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:47:46: 1000000 INFO @ Sat, 24 Aug 2019 17:47:56: 2000000 INFO @ Sat, 24 Aug 2019 17:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.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 @ Sat, 24 Aug 2019 17:48:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:48:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:48:06: 3000000 INFO @ Sat, 24 Aug 2019 17:48:16: 1000000 INFO @ Sat, 24 Aug 2019 17:48:16: 4000000 INFO @ Sat, 24 Aug 2019 17:48:27: 2000000 INFO @ Sat, 24 Aug 2019 17:48:27: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.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 @ Sat, 24 Aug 2019 17:48:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:48:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:48:37: 3000000 INFO @ Sat, 24 Aug 2019 17:48:38: 6000000 INFO @ Sat, 24 Aug 2019 17:48:45: 1000000 INFO @ Sat, 24 Aug 2019 17:48:47: 4000000 INFO @ Sat, 24 Aug 2019 17:48:47: 7000000 INFO @ Sat, 24 Aug 2019 17:48:55: 2000000 INFO @ Sat, 24 Aug 2019 17:48:56: 5000000 INFO @ Sat, 24 Aug 2019 17:48:57: 8000000 INFO @ Sat, 24 Aug 2019 17:49:04: 6000000 INFO @ Sat, 24 Aug 2019 17:49:05: 3000000 INFO @ Sat, 24 Aug 2019 17:49:07: 9000000 INFO @ Sat, 24 Aug 2019 17:49:12: 7000000 INFO @ Sat, 24 Aug 2019 17:49:15: 4000000 INFO @ Sat, 24 Aug 2019 17:49:17: 10000000 INFO @ Sat, 24 Aug 2019 17:49:20: 8000000 INFO @ Sat, 24 Aug 2019 17:49:24: 5000000 INFO @ Sat, 24 Aug 2019 17:49:27: 11000000 INFO @ Sat, 24 Aug 2019 17:49:29: 9000000 INFO @ Sat, 24 Aug 2019 17:49:34: 6000000 INFO @ Sat, 24 Aug 2019 17:49:37: 10000000 INFO @ Sat, 24 Aug 2019 17:49:37: 12000000 INFO @ Sat, 24 Aug 2019 17:49:44: 7000000 INFO @ Sat, 24 Aug 2019 17:49:45: 11000000 INFO @ Sat, 24 Aug 2019 17:49:47: 13000000 INFO @ Sat, 24 Aug 2019 17:49:53: 12000000 INFO @ Sat, 24 Aug 2019 17:49:53: 8000000 INFO @ Sat, 24 Aug 2019 17:49:57: 14000000 INFO @ Sat, 24 Aug 2019 17:50:01: 13000000 INFO @ Sat, 24 Aug 2019 17:50:03: 9000000 INFO @ Sat, 24 Aug 2019 17:50:07: 15000000 INFO @ Sat, 24 Aug 2019 17:50:09: 14000000 INFO @ Sat, 24 Aug 2019 17:50:13: 10000000 INFO @ Sat, 24 Aug 2019 17:50:17: 16000000 INFO @ Sat, 24 Aug 2019 17:50:18: 15000000 INFO @ Sat, 24 Aug 2019 17:50:22: 11000000 INFO @ Sat, 24 Aug 2019 17:50:26: 16000000 INFO @ Sat, 24 Aug 2019 17:50:27: 17000000 INFO @ Sat, 24 Aug 2019 17:50:32: 12000000 INFO @ Sat, 24 Aug 2019 17:50:34: 17000000 INFO @ Sat, 24 Aug 2019 17:50:37: 18000000 INFO @ Sat, 24 Aug 2019 17:50:42: 13000000 INFO @ Sat, 24 Aug 2019 17:50:42: 18000000 INFO @ Sat, 24 Aug 2019 17:50:47: 19000000 INFO @ Sat, 24 Aug 2019 17:50:50: 19000000 INFO @ Sat, 24 Aug 2019 17:50:51: 14000000 INFO @ Sat, 24 Aug 2019 17:50:57: 20000000 INFO @ Sat, 24 Aug 2019 17:50:59: 20000000 INFO @ Sat, 24 Aug 2019 17:51:01: 15000000 INFO @ Sat, 24 Aug 2019 17:51:07: 21000000 INFO @ Sat, 24 Aug 2019 17:51:08: 21000000 INFO @ Sat, 24 Aug 2019 17:51:10: 16000000 INFO @ Sat, 24 Aug 2019 17:51:13: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:51:13: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:51:13: #1 total tags in treatment: 21706267 INFO @ Sat, 24 Aug 2019 17:51:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:51:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:51:13: #1 tags after filtering in treatment: 21706126 INFO @ Sat, 24 Aug 2019 17:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:51:13: #1 finished! INFO @ Sat, 24 Aug 2019 17:51:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:51:15: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:51:15: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:51:15: #1 total tags in treatment: 21706267 INFO @ Sat, 24 Aug 2019 17:51:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:51:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:51:15: #1 tags after filtering in treatment: 21706126 INFO @ Sat, 24 Aug 2019 17:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:51:15: #1 finished! INFO @ Sat, 24 Aug 2019 17:51:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:51:16: #2 number of paired peaks: 16009 INFO @ Sat, 24 Aug 2019 17:51:16: start model_add_line... INFO @ Sat, 24 Aug 2019 17:51:17: start X-correlation... INFO @ Sat, 24 Aug 2019 17:51:17: end of X-cor INFO @ Sat, 24 Aug 2019 17:51:17: #2 finished! INFO @ Sat, 24 Aug 2019 17:51:17: #2 predicted fragment length is 133 bps INFO @ Sat, 24 Aug 2019 17:51:17: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 24 Aug 2019 17:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10_model.r INFO @ Sat, 24 Aug 2019 17:51:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:51:18: #2 number of paired peaks: 16009 INFO @ Sat, 24 Aug 2019 17:51:18: start model_add_line... INFO @ Sat, 24 Aug 2019 17:51:18: start X-correlation... INFO @ Sat, 24 Aug 2019 17:51:18: end of X-cor INFO @ Sat, 24 Aug 2019 17:51:18: #2 finished! INFO @ Sat, 24 Aug 2019 17:51:18: #2 predicted fragment length is 133 bps INFO @ Sat, 24 Aug 2019 17:51:18: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 24 Aug 2019 17:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05_model.r INFO @ Sat, 24 Aug 2019 17:51:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:51:20: 17000000 INFO @ Sat, 24 Aug 2019 17:51:29: 18000000 INFO @ Sat, 24 Aug 2019 17:51:39: 19000000 INFO @ Sat, 24 Aug 2019 17:51:48: 20000000 INFO @ Sat, 24 Aug 2019 17:51:58: 21000000 INFO @ Sat, 24 Aug 2019 17:52:04: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:52:04: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:52:04: #1 total tags in treatment: 21706267 INFO @ Sat, 24 Aug 2019 17:52:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:52:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:52:05: #1 tags after filtering in treatment: 21706126 INFO @ Sat, 24 Aug 2019 17:52:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:52:05: #1 finished! INFO @ Sat, 24 Aug 2019 17:52:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:52:08: #2 number of paired peaks: 16009 INFO @ Sat, 24 Aug 2019 17:52:08: start model_add_line... INFO @ Sat, 24 Aug 2019 17:52:08: start X-correlation... INFO @ Sat, 24 Aug 2019 17:52:08: end of X-cor INFO @ Sat, 24 Aug 2019 17:52:08: #2 finished! INFO @ Sat, 24 Aug 2019 17:52:08: #2 predicted fragment length is 133 bps INFO @ Sat, 24 Aug 2019 17:52:08: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 24 Aug 2019 17:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20_model.r INFO @ Sat, 24 Aug 2019 17:52:08: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:52:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:52:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:52:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.10_summits.bed INFO @ Sat, 24 Aug 2019 17:52:59: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (5672 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.05_summits.bed INFO @ Sat, 24 Aug 2019 17:53:02: Done! pass1 - making usageList (66 chroms): 5 millis pass2 - checking and writing primary data (9741 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374987/SRX5374987.20_summits.bed INFO @ Sat, 24 Aug 2019 17:53:50: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (2831 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。