Job ID = 2640588 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:44 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 ) spots read : 50,913,975 reads read : 101,827,950 reads written : 50,913,975 reads 0-length : 50,913,975 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: 00:34:20 50913975 reads; of these: 50913975 (100.00%) were unpaired; of these: 1364068 (2.68%) aligned 0 times 39135021 (76.86%) aligned exactly 1 time 10414886 (20.46%) aligned >1 times 97.32% overall alignment rate Time searching: 00:34:23 Overall time: 00:34:23 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 24 files... [bam_rmdupse_core] 10377078 / 49549907 = 0.2094 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.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 18:57:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:57:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:57:49: 1000000 INFO @ Sat, 24 Aug 2019 18:57:57: 2000000 INFO @ Sat, 24 Aug 2019 18:58:05: 3000000 INFO @ Sat, 24 Aug 2019 18:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.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 18:58:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:58:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:58:14: 4000000 INFO @ Sat, 24 Aug 2019 18:58:17: 1000000 INFO @ Sat, 24 Aug 2019 18:58:22: 5000000 INFO @ Sat, 24 Aug 2019 18:58:24: 2000000 INFO @ Sat, 24 Aug 2019 18:58:30: 6000000 INFO @ Sat, 24 Aug 2019 18:58:31: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:58:38: 7000000 INFO @ Sat, 24 Aug 2019 18:58:38: 4000000 INFO @ Sat, 24 Aug 2019 18:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.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 18:58:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:58:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:58:45: 5000000 INFO @ Sat, 24 Aug 2019 18:58:46: 8000000 INFO @ Sat, 24 Aug 2019 18:58:48: 1000000 INFO @ Sat, 24 Aug 2019 18:58:54: 6000000 INFO @ Sat, 24 Aug 2019 18:58:55: 9000000 INFO @ Sat, 24 Aug 2019 18:58:57: 2000000 INFO @ Sat, 24 Aug 2019 18:59:02: 7000000 INFO @ Sat, 24 Aug 2019 18:59:03: 10000000 INFO @ Sat, 24 Aug 2019 18:59:05: 3000000 INFO @ Sat, 24 Aug 2019 18:59:11: 8000000 INFO @ Sat, 24 Aug 2019 18:59:12: 11000000 INFO @ Sat, 24 Aug 2019 18:59:14: 4000000 INFO @ Sat, 24 Aug 2019 18:59:20: 9000000 INFO @ Sat, 24 Aug 2019 18:59:20: 12000000 INFO @ Sat, 24 Aug 2019 18:59:23: 5000000 INFO @ Sat, 24 Aug 2019 18:59:28: 10000000 INFO @ Sat, 24 Aug 2019 18:59:29: 13000000 INFO @ Sat, 24 Aug 2019 18:59:31: 6000000 INFO @ Sat, 24 Aug 2019 18:59:36: 11000000 INFO @ Sat, 24 Aug 2019 18:59:37: 14000000 INFO @ Sat, 24 Aug 2019 18:59:39: 7000000 INFO @ Sat, 24 Aug 2019 18:59:44: 12000000 INFO @ Sat, 24 Aug 2019 18:59:46: 15000000 INFO @ Sat, 24 Aug 2019 18:59:47: 8000000 INFO @ Sat, 24 Aug 2019 18:59:53: 13000000 INFO @ Sat, 24 Aug 2019 18:59:54: 16000000 INFO @ Sat, 24 Aug 2019 18:59:55: 9000000 INFO @ Sat, 24 Aug 2019 19:00:01: 14000000 INFO @ Sat, 24 Aug 2019 19:00:03: 17000000 INFO @ Sat, 24 Aug 2019 19:00:03: 10000000 INFO @ Sat, 24 Aug 2019 19:00:09: 15000000 INFO @ Sat, 24 Aug 2019 19:00:11: 18000000 INFO @ Sat, 24 Aug 2019 19:00:11: 11000000 INFO @ Sat, 24 Aug 2019 19:00:17: 16000000 INFO @ Sat, 24 Aug 2019 19:00:19: 12000000 INFO @ Sat, 24 Aug 2019 19:00:19: 19000000 INFO @ Sat, 24 Aug 2019 19:00:25: 17000000 INFO @ Sat, 24 Aug 2019 19:00:27: 13000000 INFO @ Sat, 24 Aug 2019 19:00:28: 20000000 INFO @ Sat, 24 Aug 2019 19:00:34: 18000000 INFO @ Sat, 24 Aug 2019 19:00:36: 14000000 INFO @ Sat, 24 Aug 2019 19:00:36: 21000000 INFO @ Sat, 24 Aug 2019 19:00:41: 19000000 INFO @ Sat, 24 Aug 2019 19:00:44: 15000000 INFO @ Sat, 24 Aug 2019 19:00:44: 22000000 INFO @ Sat, 24 Aug 2019 19:00:49: 20000000 INFO @ Sat, 24 Aug 2019 19:00:52: 16000000 INFO @ Sat, 24 Aug 2019 19:00:52: 23000000 INFO @ Sat, 24 Aug 2019 19:00:57: 21000000 INFO @ Sat, 24 Aug 2019 19:01:00: 17000000 INFO @ Sat, 24 Aug 2019 19:01:01: 24000000 INFO @ Sat, 24 Aug 2019 19:01:06: 22000000 INFO @ Sat, 24 Aug 2019 19:01:08: 18000000 INFO @ Sat, 24 Aug 2019 19:01:09: 25000000 INFO @ Sat, 24 Aug 2019 19:01:14: 23000000 INFO @ Sat, 24 Aug 2019 19:01:16: 19000000 INFO @ Sat, 24 Aug 2019 19:01:17: 26000000 INFO @ Sat, 24 Aug 2019 19:01:22: 24000000 INFO @ Sat, 24 Aug 2019 19:01:25: 20000000 INFO @ Sat, 24 Aug 2019 19:01:25: 27000000 INFO @ Sat, 24 Aug 2019 19:01:30: 25000000 INFO @ Sat, 24 Aug 2019 19:01:33: 21000000 INFO @ Sat, 24 Aug 2019 19:01:34: 28000000 INFO @ Sat, 24 Aug 2019 19:01:38: 26000000 INFO @ Sat, 24 Aug 2019 19:01:41: 22000000 INFO @ Sat, 24 Aug 2019 19:01:43: 29000000 INFO @ Sat, 24 Aug 2019 19:01:46: 27000000 INFO @ Sat, 24 Aug 2019 19:01:49: 23000000 INFO @ Sat, 24 Aug 2019 19:01:51: 30000000 INFO @ Sat, 24 Aug 2019 19:01:54: 28000000 INFO @ Sat, 24 Aug 2019 19:01:57: 24000000 INFO @ Sat, 24 Aug 2019 19:01:59: 31000000 INFO @ Sat, 24 Aug 2019 19:02:03: 29000000 INFO @ Sat, 24 Aug 2019 19:02:05: 25000000 INFO @ Sat, 24 Aug 2019 19:02:07: 32000000 INFO @ Sat, 24 Aug 2019 19:02:10: 30000000 INFO @ Sat, 24 Aug 2019 19:02:12: 26000000 INFO @ Sat, 24 Aug 2019 19:02:15: 33000000 INFO @ Sat, 24 Aug 2019 19:02:17: 31000000 INFO @ Sat, 24 Aug 2019 19:02:20: 27000000 INFO @ Sat, 24 Aug 2019 19:02:23: 34000000 INFO @ Sat, 24 Aug 2019 19:02:24: 32000000 INFO @ Sat, 24 Aug 2019 19:02:27: 28000000 INFO @ Sat, 24 Aug 2019 19:02:31: 35000000 INFO @ Sat, 24 Aug 2019 19:02:31: 33000000 INFO @ Sat, 24 Aug 2019 19:02:34: 29000000 INFO @ Sat, 24 Aug 2019 19:02:38: 34000000 INFO @ Sat, 24 Aug 2019 19:02:39: 36000000 INFO @ Sat, 24 Aug 2019 19:02:42: 30000000 INFO @ Sat, 24 Aug 2019 19:02:45: 35000000 INFO @ Sat, 24 Aug 2019 19:02:47: 37000000 INFO @ Sat, 24 Aug 2019 19:02:49: 31000000 INFO @ Sat, 24 Aug 2019 19:02:53: 36000000 INFO @ Sat, 24 Aug 2019 19:02:55: 38000000 INFO @ Sat, 24 Aug 2019 19:02:56: 32000000 INFO @ Sat, 24 Aug 2019 19:03:00: 37000000 INFO @ Sat, 24 Aug 2019 19:03:03: 39000000 INFO @ Sat, 24 Aug 2019 19:03:03: 33000000 INFO @ Sat, 24 Aug 2019 19:03:04: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:04: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:04: #1 total tags in treatment: 39172829 INFO @ Sat, 24 Aug 2019 19:03:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:04: #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 19:03:05: #1 tags after filtering in treatment: 39172739 INFO @ Sat, 24 Aug 2019 19:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:05: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:07: 38000000 INFO @ Sat, 24 Aug 2019 19:03:10: 34000000 INFO @ Sat, 24 Aug 2019 19:03:12: #2 number of paired peaks: 46311 INFO @ Sat, 24 Aug 2019 19:03:12: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:12: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:12: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:12: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:12: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 19:03:12: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 19:03:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05_model.r INFO @ Sat, 24 Aug 2019 19:03:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:14: 39000000 INFO @ Sat, 24 Aug 2019 19:03:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:16: #1 total tags in treatment: 39172829 INFO @ Sat, 24 Aug 2019 19:03:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:16: #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 19:03:17: #1 tags after filtering in treatment: 39172739 INFO @ Sat, 24 Aug 2019 19:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:17: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:17: 35000000 INFO @ Sat, 24 Aug 2019 19:03:23: #2 number of paired peaks: 46311 INFO @ Sat, 24 Aug 2019 19:03:23: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:24: 36000000 INFO @ Sat, 24 Aug 2019 19:03:24: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:24: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:24: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:24: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 19:03:24: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 19:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10_model.r INFO @ Sat, 24 Aug 2019 19:03:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:31: 37000000 INFO @ Sat, 24 Aug 2019 19:03:38: 38000000 INFO @ Sat, 24 Aug 2019 19:03:45: 39000000 INFO @ Sat, 24 Aug 2019 19:03:47: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:47: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:47: #1 total tags in treatment: 39172829 INFO @ Sat, 24 Aug 2019 19:03:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:47: #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 19:03:48: #1 tags after filtering in treatment: 39172739 INFO @ Sat, 24 Aug 2019 19:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:48: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:54: #2 number of paired peaks: 46311 INFO @ Sat, 24 Aug 2019 19:03:54: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:55: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:55: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:55: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:55: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 19:03:55: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 19:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20_model.r INFO @ Sat, 24 Aug 2019 19:03:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:05:20: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:06:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.05_summits.bed INFO @ Sat, 24 Aug 2019 19:06:27: Done! pass1 - making usageList (114 chroms): 10 millis pass2 - checking and writing primary data (24615 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.10_summits.bed INFO @ Sat, 24 Aug 2019 19:06:36: Done! pass1 - making usageList (100 chroms): 6 millis pass2 - checking and writing primary data (19560 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:07:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:07:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:07:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375026/SRX5375026.20_summits.bed INFO @ Sat, 24 Aug 2019 19:07:07: Done! pass1 - making usageList (81 chroms): 6 millis pass2 - checking and writing primary data (14375 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。