Job ID = 2001645 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:53:55 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 ) 2019-07-04T22:05:28 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 ) 2019-07-04T22:09:10 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 ) 2019-07-04T22:10:49 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 ) 2019-07-04T22:10:54 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 ) 2019-07-04T22:11:59 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 ) 2019-07-04T22:12:44 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 ) 2019-07-04T22:13:02 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 ) 2019-07-04T22:13:33 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 ) 2019-07-04T22:24:45 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 : 120,868,851 reads read : 120,868,851 reads written : 120,868,851 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: 00:00:01 Multiseed full-index search: 00:57:45 120868851 reads; of these: 120868851 (100.00%) were unpaired; of these: 2112385 (1.75%) aligned 0 times 106160955 (87.83%) aligned exactly 1 time 12595511 (10.42%) aligned >1 times 98.25% overall alignment rate Time searching: 00:57:48 Overall time: 00:57:48 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 52 files... [bam_rmdupse_core] 77752070 / 118756466 = 0.6547 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 09:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.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 09:15:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:15:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.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 09:15:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:15:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.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 09:15:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:15:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:15:45: 1000000 INFO @ Fri, 05 Jul 2019 09:15:47: 1000000 INFO @ Fri, 05 Jul 2019 09:15:48: 1000000 INFO @ Fri, 05 Jul 2019 09:15:53: 2000000 INFO @ Fri, 05 Jul 2019 09:15:56: 2000000 INFO @ Fri, 05 Jul 2019 09:15:58: 2000000 INFO @ Fri, 05 Jul 2019 09:16:00: 3000000 INFO @ Fri, 05 Jul 2019 09:16:06: 3000000 INFO @ Fri, 05 Jul 2019 09:16:08: 4000000 INFO @ Fri, 05 Jul 2019 09:16:08: 3000000 INFO @ Fri, 05 Jul 2019 09:16:15: 4000000 INFO @ Fri, 05 Jul 2019 09:16:16: 5000000 INFO @ Fri, 05 Jul 2019 09:16:18: 4000000 INFO @ Fri, 05 Jul 2019 09:16:23: 6000000 INFO @ Fri, 05 Jul 2019 09:16:25: 5000000 INFO @ Fri, 05 Jul 2019 09:16:29: 5000000 INFO @ Fri, 05 Jul 2019 09:16:31: 7000000 INFO @ Fri, 05 Jul 2019 09:16:35: 6000000 INFO @ Fri, 05 Jul 2019 09:16:39: 8000000 INFO @ Fri, 05 Jul 2019 09:16:40: 6000000 INFO @ Fri, 05 Jul 2019 09:16:44: 7000000 INFO @ Fri, 05 Jul 2019 09:16:46: 9000000 INFO @ Fri, 05 Jul 2019 09:16:51: 7000000 INFO @ Fri, 05 Jul 2019 09:16:52: 8000000 INFO @ Fri, 05 Jul 2019 09:16:54: 10000000 INFO @ Fri, 05 Jul 2019 09:17:01: 8000000 INFO @ Fri, 05 Jul 2019 09:17:01: 9000000 INFO @ Fri, 05 Jul 2019 09:17:02: 11000000 INFO @ Fri, 05 Jul 2019 09:17:10: 12000000 INFO @ Fri, 05 Jul 2019 09:17:10: 10000000 INFO @ Fri, 05 Jul 2019 09:17:12: 9000000 INFO @ Fri, 05 Jul 2019 09:17:17: 13000000 INFO @ Fri, 05 Jul 2019 09:17:19: 11000000 INFO @ Fri, 05 Jul 2019 09:17:22: 10000000 INFO @ Fri, 05 Jul 2019 09:17:25: 14000000 INFO @ Fri, 05 Jul 2019 09:17:27: 12000000 INFO @ Fri, 05 Jul 2019 09:17:32: 11000000 INFO @ Fri, 05 Jul 2019 09:17:34: 15000000 INFO @ Fri, 05 Jul 2019 09:17:36: 13000000 INFO @ Fri, 05 Jul 2019 09:17:41: 12000000 INFO @ Fri, 05 Jul 2019 09:17:41: 16000000 INFO @ Fri, 05 Jul 2019 09:17:44: 14000000 INFO @ Fri, 05 Jul 2019 09:17:49: 17000000 INFO @ Fri, 05 Jul 2019 09:17:51: 13000000 INFO @ Fri, 05 Jul 2019 09:17:52: 15000000 INFO @ Fri, 05 Jul 2019 09:17:57: 18000000 INFO @ Fri, 05 Jul 2019 09:18:01: 16000000 INFO @ Fri, 05 Jul 2019 09:18:02: 14000000 INFO @ Fri, 05 Jul 2019 09:18:05: 19000000 INFO @ Fri, 05 Jul 2019 09:18:10: 17000000 INFO @ Fri, 05 Jul 2019 09:18:12: 15000000 INFO @ Fri, 05 Jul 2019 09:18:12: 20000000 INFO @ Fri, 05 Jul 2019 09:18:18: 18000000 INFO @ Fri, 05 Jul 2019 09:18:20: 21000000 INFO @ Fri, 05 Jul 2019 09:18:22: 16000000 INFO @ Fri, 05 Jul 2019 09:18:27: 19000000 INFO @ Fri, 05 Jul 2019 09:18:28: 22000000 INFO @ Fri, 05 Jul 2019 09:18:33: 17000000 INFO @ Fri, 05 Jul 2019 09:18:35: 23000000 INFO @ Fri, 05 Jul 2019 09:18:35: 20000000 INFO @ Fri, 05 Jul 2019 09:18:43: 18000000 INFO @ Fri, 05 Jul 2019 09:18:43: 24000000 INFO @ Fri, 05 Jul 2019 09:18:44: 21000000 INFO @ Fri, 05 Jul 2019 09:18:51: 25000000 INFO @ Fri, 05 Jul 2019 09:18:52: 22000000 INFO @ Fri, 05 Jul 2019 09:18:53: 19000000 INFO @ Fri, 05 Jul 2019 09:18:59: 26000000 INFO @ Fri, 05 Jul 2019 09:19:01: 23000000 INFO @ Fri, 05 Jul 2019 09:19:03: 20000000 INFO @ Fri, 05 Jul 2019 09:19:07: 27000000 INFO @ Fri, 05 Jul 2019 09:19:09: 24000000 INFO @ Fri, 05 Jul 2019 09:19:13: 21000000 INFO @ Fri, 05 Jul 2019 09:19:14: 28000000 INFO @ Fri, 05 Jul 2019 09:19:17: 25000000 INFO @ Fri, 05 Jul 2019 09:19:22: 29000000 INFO @ Fri, 05 Jul 2019 09:19:23: 22000000 INFO @ Fri, 05 Jul 2019 09:19:26: 26000000 INFO @ Fri, 05 Jul 2019 09:19:30: 30000000 INFO @ Fri, 05 Jul 2019 09:19:32: 23000000 INFO @ Fri, 05 Jul 2019 09:19:34: 27000000 INFO @ Fri, 05 Jul 2019 09:19:37: 31000000 INFO @ Fri, 05 Jul 2019 09:19:42: 24000000 INFO @ Fri, 05 Jul 2019 09:19:42: 28000000 INFO @ Fri, 05 Jul 2019 09:19:45: 32000000 INFO @ Fri, 05 Jul 2019 09:19:51: 29000000 INFO @ Fri, 05 Jul 2019 09:19:52: 25000000 INFO @ Fri, 05 Jul 2019 09:19:52: 33000000 INFO @ Fri, 05 Jul 2019 09:19:59: 30000000 INFO @ Fri, 05 Jul 2019 09:20:00: 34000000 INFO @ Fri, 05 Jul 2019 09:20:01: 26000000 INFO @ Fri, 05 Jul 2019 09:20:07: 31000000 INFO @ Fri, 05 Jul 2019 09:20:08: 35000000 INFO @ Fri, 05 Jul 2019 09:20:12: 27000000 INFO @ Fri, 05 Jul 2019 09:20:15: 36000000 INFO @ Fri, 05 Jul 2019 09:20:16: 32000000 INFO @ Fri, 05 Jul 2019 09:20:22: 28000000 INFO @ Fri, 05 Jul 2019 09:20:23: 37000000 INFO @ Fri, 05 Jul 2019 09:20:24: 33000000 INFO @ Fri, 05 Jul 2019 09:20:31: 38000000 INFO @ Fri, 05 Jul 2019 09:20:32: 34000000 INFO @ Fri, 05 Jul 2019 09:20:33: 29000000 INFO @ Fri, 05 Jul 2019 09:20:38: 39000000 INFO @ Fri, 05 Jul 2019 09:20:41: 35000000 INFO @ Fri, 05 Jul 2019 09:20:43: 30000000 INFO @ Fri, 05 Jul 2019 09:20:46: 40000000 INFO @ Fri, 05 Jul 2019 09:20:49: 36000000 INFO @ Fri, 05 Jul 2019 09:20:53: 31000000 INFO @ Fri, 05 Jul 2019 09:20:54: 41000000 INFO @ Fri, 05 Jul 2019 09:20:54: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:20:54: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:20:54: #1 total tags in treatment: 41004396 INFO @ Fri, 05 Jul 2019 09:20:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:20:54: #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 09:20:55: #1 tags after filtering in treatment: 41004221 INFO @ Fri, 05 Jul 2019 09:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:20:55: #1 finished! INFO @ Fri, 05 Jul 2019 09:20:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:20:57: 37000000 INFO @ Fri, 05 Jul 2019 09:21:02: 32000000 INFO @ Fri, 05 Jul 2019 09:21:05: #2 number of paired peaks: 83152 INFO @ Fri, 05 Jul 2019 09:21:05: start model_add_line... INFO @ Fri, 05 Jul 2019 09:21:05: 38000000 INFO @ Fri, 05 Jul 2019 09:21:06: start X-correlation... INFO @ Fri, 05 Jul 2019 09:21:06: end of X-cor INFO @ Fri, 05 Jul 2019 09:21:06: #2 finished! INFO @ Fri, 05 Jul 2019 09:21:06: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:21:06: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 09:21:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20_model.r INFO @ Fri, 05 Jul 2019 09:21:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:21:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:21:13: 33000000 INFO @ Fri, 05 Jul 2019 09:21:14: 39000000 INFO @ Fri, 05 Jul 2019 09:21:22: 40000000 INFO @ Fri, 05 Jul 2019 09:21:23: 34000000 INFO @ Fri, 05 Jul 2019 09:21:30: 41000000 INFO @ Fri, 05 Jul 2019 09:21:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:21:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:21:31: #1 total tags in treatment: 41004396 INFO @ Fri, 05 Jul 2019 09:21:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:21:31: #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 09:21:32: #1 tags after filtering in treatment: 41004221 INFO @ Fri, 05 Jul 2019 09:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:21:32: #1 finished! INFO @ Fri, 05 Jul 2019 09:21:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:21:33: 35000000 INFO @ Fri, 05 Jul 2019 09:21:42: #2 number of paired peaks: 83152 INFO @ Fri, 05 Jul 2019 09:21:42: start model_add_line... INFO @ Fri, 05 Jul 2019 09:21:43: start X-correlation... INFO @ Fri, 05 Jul 2019 09:21:43: end of X-cor INFO @ Fri, 05 Jul 2019 09:21:43: #2 finished! INFO @ Fri, 05 Jul 2019 09:21:43: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:21:43: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 09:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10_model.r INFO @ Fri, 05 Jul 2019 09:21:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:21:44: 36000000 INFO @ Fri, 05 Jul 2019 09:21:54: 37000000 INFO @ Fri, 05 Jul 2019 09:22:04: 38000000 INFO @ Fri, 05 Jul 2019 09:22:14: 39000000 INFO @ Fri, 05 Jul 2019 09:22:24: 40000000 INFO @ Fri, 05 Jul 2019 09:22:34: 41000000 INFO @ Fri, 05 Jul 2019 09:22:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:22:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:22:35: #1 total tags in treatment: 41004396 INFO @ Fri, 05 Jul 2019 09:22:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:22:35: #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 09:22:36: #1 tags after filtering in treatment: 41004221 INFO @ Fri, 05 Jul 2019 09:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:22:36: #1 finished! INFO @ Fri, 05 Jul 2019 09:22:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:22:46: #2 number of paired peaks: 83152 INFO @ Fri, 05 Jul 2019 09:22:46: start model_add_line... INFO @ Fri, 05 Jul 2019 09:22:47: start X-correlation... INFO @ Fri, 05 Jul 2019 09:22:47: end of X-cor INFO @ Fri, 05 Jul 2019 09:22:47: #2 finished! INFO @ Fri, 05 Jul 2019 09:22:47: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:22:47: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 05 Jul 2019 09:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05_model.r INFO @ Fri, 05 Jul 2019 09:22:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:23:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:23:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.20_summits.bed INFO @ Fri, 05 Jul 2019 09:24:13: Done! pass1 - making usageList (128 chroms): 14 millis pass2 - checking and writing primary data (39065 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:24:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.10_summits.bed INFO @ Fri, 05 Jul 2019 09:24:52: Done! pass1 - making usageList (157 chroms): 11 millis pass2 - checking and writing primary data (54203 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101960/ERX101960.05_summits.bed INFO @ Fri, 05 Jul 2019 09:25:57: Done! pass1 - making usageList (174 chroms): 17 millis pass2 - checking and writing primary data (68049 records, 4 fields): 99 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。