Job ID = 2001696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:47:40 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 ) 2019-07-05T00:03:04 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 ) 2019-07-05T00:03:04 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 ) 2019-07-05T00:06:52 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 ) 2019-07-05T00:11:39 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 ) 2019-07-05T00:14:48 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 ) 2019-07-05T00:40:34 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 : 116,445,351 reads read : 116,445,351 reads written : 116,445,351 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:17:47 116445351 reads; of these: 116445351 (100.00%) were unpaired; of these: 2004848 (1.72%) aligned 0 times 102958530 (88.42%) aligned exactly 1 time 11481973 (9.86%) aligned >1 times 98.28% overall alignment rate Time searching: 01:17:49 Overall time: 01:17:49 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 48 files... [bam_rmdupse_core] 78827700 / 114440503 = 0.6888 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 11:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.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 11:53:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.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 11:53:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.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 11:53:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:43: 1000000 INFO @ Fri, 05 Jul 2019 11:53:45: 1000000 INFO @ Fri, 05 Jul 2019 11:53:46: 1000000 INFO @ Fri, 05 Jul 2019 11:53:54: 2000000 INFO @ Fri, 05 Jul 2019 11:53:56: 2000000 INFO @ Fri, 05 Jul 2019 11:53:57: 2000000 INFO @ Fri, 05 Jul 2019 11:54:04: 3000000 INFO @ Fri, 05 Jul 2019 11:54:08: 3000000 INFO @ Fri, 05 Jul 2019 11:54:09: 3000000 INFO @ Fri, 05 Jul 2019 11:54:14: 4000000 INFO @ Fri, 05 Jul 2019 11:54:19: 4000000 INFO @ Fri, 05 Jul 2019 11:54:20: 4000000 INFO @ Fri, 05 Jul 2019 11:54:24: 5000000 INFO @ Fri, 05 Jul 2019 11:54:30: 5000000 INFO @ Fri, 05 Jul 2019 11:54:31: 5000000 INFO @ Fri, 05 Jul 2019 11:54:34: 6000000 INFO @ Fri, 05 Jul 2019 11:54:41: 6000000 INFO @ Fri, 05 Jul 2019 11:54:42: 6000000 INFO @ Fri, 05 Jul 2019 11:54:44: 7000000 INFO @ Fri, 05 Jul 2019 11:54:53: 7000000 INFO @ Fri, 05 Jul 2019 11:54:54: 7000000 INFO @ Fri, 05 Jul 2019 11:54:54: 8000000 INFO @ Fri, 05 Jul 2019 11:55:04: 8000000 INFO @ Fri, 05 Jul 2019 11:55:04: 9000000 INFO @ Fri, 05 Jul 2019 11:55:05: 8000000 INFO @ Fri, 05 Jul 2019 11:55:14: 10000000 INFO @ Fri, 05 Jul 2019 11:55:15: 9000000 INFO @ Fri, 05 Jul 2019 11:55:16: 9000000 INFO @ Fri, 05 Jul 2019 11:55:25: 11000000 INFO @ Fri, 05 Jul 2019 11:55:27: 10000000 INFO @ Fri, 05 Jul 2019 11:55:27: 10000000 INFO @ Fri, 05 Jul 2019 11:55:36: 12000000 INFO @ Fri, 05 Jul 2019 11:55:38: 11000000 INFO @ Fri, 05 Jul 2019 11:55:38: 11000000 INFO @ Fri, 05 Jul 2019 11:55:47: 13000000 INFO @ Fri, 05 Jul 2019 11:55:49: 12000000 INFO @ Fri, 05 Jul 2019 11:55:50: 12000000 INFO @ Fri, 05 Jul 2019 11:55:58: 14000000 INFO @ Fri, 05 Jul 2019 11:56:01: 13000000 INFO @ Fri, 05 Jul 2019 11:56:01: 13000000 INFO @ Fri, 05 Jul 2019 11:56:09: 15000000 INFO @ Fri, 05 Jul 2019 11:56:12: 14000000 INFO @ Fri, 05 Jul 2019 11:56:13: 14000000 INFO @ Fri, 05 Jul 2019 11:56:19: 16000000 INFO @ Fri, 05 Jul 2019 11:56:24: 15000000 INFO @ Fri, 05 Jul 2019 11:56:24: 15000000 INFO @ Fri, 05 Jul 2019 11:56:30: 17000000 INFO @ Fri, 05 Jul 2019 11:56:36: 16000000 INFO @ Fri, 05 Jul 2019 11:56:37: 16000000 INFO @ Fri, 05 Jul 2019 11:56:42: 18000000 INFO @ Fri, 05 Jul 2019 11:56:48: 17000000 INFO @ Fri, 05 Jul 2019 11:56:49: 17000000 INFO @ Fri, 05 Jul 2019 11:56:53: 19000000 INFO @ Fri, 05 Jul 2019 11:57:01: 18000000 INFO @ Fri, 05 Jul 2019 11:57:01: 18000000 INFO @ Fri, 05 Jul 2019 11:57:05: 20000000 INFO @ Fri, 05 Jul 2019 11:57:13: 19000000 INFO @ Fri, 05 Jul 2019 11:57:13: 19000000 INFO @ Fri, 05 Jul 2019 11:57:16: 21000000 INFO @ Fri, 05 Jul 2019 11:57:25: 20000000 INFO @ Fri, 05 Jul 2019 11:57:26: 20000000 INFO @ Fri, 05 Jul 2019 11:57:28: 22000000 INFO @ Fri, 05 Jul 2019 11:57:37: 21000000 INFO @ Fri, 05 Jul 2019 11:57:38: 21000000 INFO @ Fri, 05 Jul 2019 11:57:41: 23000000 INFO @ Fri, 05 Jul 2019 11:57:50: 22000000 INFO @ Fri, 05 Jul 2019 11:57:50: 22000000 INFO @ Fri, 05 Jul 2019 11:57:52: 24000000 INFO @ Fri, 05 Jul 2019 11:58:02: 23000000 INFO @ Fri, 05 Jul 2019 11:58:02: 23000000 INFO @ Fri, 05 Jul 2019 11:58:05: 25000000 INFO @ Fri, 05 Jul 2019 11:58:14: 24000000 INFO @ Fri, 05 Jul 2019 11:58:14: 24000000 INFO @ Fri, 05 Jul 2019 11:58:16: 26000000 INFO @ Fri, 05 Jul 2019 11:58:26: 27000000 INFO @ Fri, 05 Jul 2019 11:58:27: 25000000 INFO @ Fri, 05 Jul 2019 11:58:27: 25000000 INFO @ Fri, 05 Jul 2019 11:58:37: 28000000 INFO @ Fri, 05 Jul 2019 11:58:40: 26000000 INFO @ Fri, 05 Jul 2019 11:58:40: 26000000 INFO @ Fri, 05 Jul 2019 11:58:50: 29000000 INFO @ Fri, 05 Jul 2019 11:58:53: 27000000 INFO @ Fri, 05 Jul 2019 11:58:53: 27000000 INFO @ Fri, 05 Jul 2019 11:59:02: 30000000 INFO @ Fri, 05 Jul 2019 11:59:07: 28000000 INFO @ Fri, 05 Jul 2019 11:59:07: 28000000 INFO @ Fri, 05 Jul 2019 11:59:14: 31000000 INFO @ Fri, 05 Jul 2019 11:59:19: 29000000 INFO @ Fri, 05 Jul 2019 11:59:20: 29000000 INFO @ Fri, 05 Jul 2019 11:59:27: 32000000 INFO @ Fri, 05 Jul 2019 11:59:32: 30000000 INFO @ Fri, 05 Jul 2019 11:59:33: 30000000 INFO @ Fri, 05 Jul 2019 11:59:40: 33000000 INFO @ Fri, 05 Jul 2019 11:59:46: 31000000 INFO @ Fri, 05 Jul 2019 11:59:47: 31000000 INFO @ Fri, 05 Jul 2019 11:59:52: 34000000 INFO @ Fri, 05 Jul 2019 12:00:00: 32000000 INFO @ Fri, 05 Jul 2019 12:00:01: 32000000 INFO @ Fri, 05 Jul 2019 12:00:05: 35000000 INFO @ Fri, 05 Jul 2019 12:00:14: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:00:14: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:00:14: #1 total tags in treatment: 35612803 INFO @ Fri, 05 Jul 2019 12:00:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:00:14: #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 12:00:15: #1 tags after filtering in treatment: 35612601 INFO @ Fri, 05 Jul 2019 12:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:00:15: #1 finished! INFO @ Fri, 05 Jul 2019 12:00:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:00:15: 33000000 INFO @ Fri, 05 Jul 2019 12:00:15: 33000000 INFO @ Fri, 05 Jul 2019 12:00:26: #2 number of paired peaks: 67429 INFO @ Fri, 05 Jul 2019 12:00:26: start model_add_line... INFO @ Fri, 05 Jul 2019 12:00:27: start X-correlation... INFO @ Fri, 05 Jul 2019 12:00:27: end of X-cor INFO @ Fri, 05 Jul 2019 12:00:27: #2 finished! INFO @ Fri, 05 Jul 2019 12:00:27: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 12:00:27: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 12:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05_model.r INFO @ Fri, 05 Jul 2019 12:00:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:00:30: 34000000 INFO @ Fri, 05 Jul 2019 12:00:30: 34000000 INFO @ Fri, 05 Jul 2019 12:00:43: 35000000 INFO @ Fri, 05 Jul 2019 12:00:44: 35000000 INFO @ Fri, 05 Jul 2019 12:00:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:00:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:00:52: #1 total tags in treatment: 35612803 INFO @ Fri, 05 Jul 2019 12:00:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:00:52: #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 12:00:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:00:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:00:52: #1 total tags in treatment: 35612803 INFO @ Fri, 05 Jul 2019 12:00:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:00:52: #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 12:00:53: #1 tags after filtering in treatment: 35612601 INFO @ Fri, 05 Jul 2019 12:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:00:53: #1 finished! INFO @ Fri, 05 Jul 2019 12:00:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:00:53: #1 tags after filtering in treatment: 35612601 INFO @ Fri, 05 Jul 2019 12:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:00:53: #1 finished! INFO @ Fri, 05 Jul 2019 12:00:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:01:04: #2 number of paired peaks: 67429 INFO @ Fri, 05 Jul 2019 12:01:04: start model_add_line... INFO @ Fri, 05 Jul 2019 12:01:04: #2 number of paired peaks: 67429 INFO @ Fri, 05 Jul 2019 12:01:04: start model_add_line... INFO @ Fri, 05 Jul 2019 12:01:05: start X-correlation... INFO @ Fri, 05 Jul 2019 12:01:05: end of X-cor INFO @ Fri, 05 Jul 2019 12:01:05: #2 finished! INFO @ Fri, 05 Jul 2019 12:01:05: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 12:01:05: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 12:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20_model.r INFO @ Fri, 05 Jul 2019 12:01:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:01:05: start X-correlation... INFO @ Fri, 05 Jul 2019 12:01:05: end of X-cor INFO @ Fri, 05 Jul 2019 12:01:05: #2 finished! INFO @ Fri, 05 Jul 2019 12:01:05: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 12:01:05: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 12:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10_model.r INFO @ Fri, 05 Jul 2019 12:01:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:02:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:03:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:03:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.05_summits.bed INFO @ Fri, 05 Jul 2019 12:03:59: Done! pass1 - making usageList (168 chroms): 14 millis pass2 - checking and writing primary data (61644 records, 4 fields): 131 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.20_summits.bed INFO @ Fri, 05 Jul 2019 12:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:04:30: Done! INFO @ Fri, 05 Jul 2019 12:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10_peaks.narrowPeak pass1 - making usageList (124 chroms): 17 millis pass2 - checking and writing primary data (37605 records, 4 fields): 124 millis INFO @ Fri, 05 Jul 2019 12:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102006/ERX102006.10_summits.bed INFO @ Fri, 05 Jul 2019 12:04:31: Done! pass1 - making usageList (151 chroms): 19 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (49867 records, 4 fields): 157 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。