Job ID = 2001166 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:25:24 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 ) 2019-07-04T19:25:24 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 ) 2019-07-04T19:30:10 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 ) 2019-07-04T19:33:54 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:47:37 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 ) spots read : 111,901,991 reads read : 111,901,991 reads written : 111,901,991 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: 01:06:47 111901991 reads; of these: 111901991 (100.00%) were unpaired; of these: 2025339 (1.81%) aligned 0 times 97695258 (87.30%) aligned exactly 1 time 12181394 (10.89%) aligned >1 times 98.19% overall alignment rate Time searching: 01:06:50 Overall time: 01:06:50 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] 60822050 / 109876652 = 0.5535 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 06:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.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 06:32:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:32:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.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 06:32:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:32:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.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 06:32:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:32:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:32:42: 1000000 INFO @ Fri, 05 Jul 2019 06:32:44: 1000000 INFO @ Fri, 05 Jul 2019 06:32:45: 1000000 INFO @ Fri, 05 Jul 2019 06:32:52: 2000000 INFO @ Fri, 05 Jul 2019 06:32:56: 2000000 INFO @ Fri, 05 Jul 2019 06:32:57: 2000000 INFO @ Fri, 05 Jul 2019 06:33:04: 3000000 INFO @ Fri, 05 Jul 2019 06:33:07: 3000000 INFO @ Fri, 05 Jul 2019 06:33:09: 3000000 INFO @ Fri, 05 Jul 2019 06:33:15: 4000000 INFO @ Fri, 05 Jul 2019 06:33:18: 4000000 INFO @ Fri, 05 Jul 2019 06:33:18: 4000000 INFO @ Fri, 05 Jul 2019 06:33:26: 5000000 INFO @ Fri, 05 Jul 2019 06:33:28: 5000000 INFO @ Fri, 05 Jul 2019 06:33:29: 5000000 INFO @ Fri, 05 Jul 2019 06:33:36: 6000000 INFO @ Fri, 05 Jul 2019 06:33:39: 6000000 INFO @ Fri, 05 Jul 2019 06:33:40: 6000000 INFO @ Fri, 05 Jul 2019 06:33:47: 7000000 INFO @ Fri, 05 Jul 2019 06:33:49: 7000000 INFO @ Fri, 05 Jul 2019 06:33:52: 7000000 INFO @ Fri, 05 Jul 2019 06:33:58: 8000000 INFO @ Fri, 05 Jul 2019 06:33:58: 8000000 INFO @ Fri, 05 Jul 2019 06:34:03: 8000000 INFO @ Fri, 05 Jul 2019 06:34:08: 9000000 INFO @ Fri, 05 Jul 2019 06:34:09: 9000000 INFO @ Fri, 05 Jul 2019 06:34:13: 9000000 INFO @ Fri, 05 Jul 2019 06:34:19: 10000000 INFO @ Fri, 05 Jul 2019 06:34:21: 10000000 INFO @ Fri, 05 Jul 2019 06:34:22: 10000000 INFO @ Fri, 05 Jul 2019 06:34:30: 11000000 INFO @ Fri, 05 Jul 2019 06:34:31: 11000000 INFO @ Fri, 05 Jul 2019 06:34:31: 11000000 INFO @ Fri, 05 Jul 2019 06:34:39: 12000000 INFO @ Fri, 05 Jul 2019 06:34:41: 12000000 INFO @ Fri, 05 Jul 2019 06:34:42: 12000000 INFO @ Fri, 05 Jul 2019 06:34:49: 13000000 INFO @ Fri, 05 Jul 2019 06:34:52: 13000000 INFO @ Fri, 05 Jul 2019 06:34:53: 13000000 INFO @ Fri, 05 Jul 2019 06:34:58: 14000000 INFO @ Fri, 05 Jul 2019 06:35:02: 14000000 INFO @ Fri, 05 Jul 2019 06:35:03: 14000000 INFO @ Fri, 05 Jul 2019 06:35:10: 15000000 INFO @ Fri, 05 Jul 2019 06:35:13: 15000000 INFO @ Fri, 05 Jul 2019 06:35:14: 15000000 INFO @ Fri, 05 Jul 2019 06:35:23: 16000000 INFO @ Fri, 05 Jul 2019 06:35:25: 16000000 INFO @ Fri, 05 Jul 2019 06:35:26: 16000000 INFO @ Fri, 05 Jul 2019 06:35:36: 17000000 INFO @ Fri, 05 Jul 2019 06:35:36: 17000000 INFO @ Fri, 05 Jul 2019 06:35:37: 17000000 INFO @ Fri, 05 Jul 2019 06:35:47: 18000000 INFO @ Fri, 05 Jul 2019 06:35:49: 18000000 INFO @ Fri, 05 Jul 2019 06:35:49: 18000000 INFO @ Fri, 05 Jul 2019 06:35:58: 19000000 INFO @ Fri, 05 Jul 2019 06:36:01: 19000000 INFO @ Fri, 05 Jul 2019 06:36:01: 19000000 INFO @ Fri, 05 Jul 2019 06:36:09: 20000000 INFO @ Fri, 05 Jul 2019 06:36:13: 20000000 INFO @ Fri, 05 Jul 2019 06:36:13: 20000000 INFO @ Fri, 05 Jul 2019 06:36:21: 21000000 INFO @ Fri, 05 Jul 2019 06:36:24: 21000000 INFO @ Fri, 05 Jul 2019 06:36:25: 21000000 INFO @ Fri, 05 Jul 2019 06:36:34: 22000000 INFO @ Fri, 05 Jul 2019 06:36:36: 22000000 INFO @ Fri, 05 Jul 2019 06:36:37: 22000000 INFO @ Fri, 05 Jul 2019 06:36:46: 23000000 INFO @ Fri, 05 Jul 2019 06:36:49: 23000000 INFO @ Fri, 05 Jul 2019 06:36:50: 23000000 INFO @ Fri, 05 Jul 2019 06:37:00: 24000000 INFO @ Fri, 05 Jul 2019 06:37:01: 24000000 INFO @ Fri, 05 Jul 2019 06:37:02: 24000000 INFO @ Fri, 05 Jul 2019 06:37:12: 25000000 INFO @ Fri, 05 Jul 2019 06:37:13: 25000000 INFO @ Fri, 05 Jul 2019 06:37:15: 25000000 INFO @ Fri, 05 Jul 2019 06:37:23: 26000000 INFO @ Fri, 05 Jul 2019 06:37:24: 26000000 INFO @ Fri, 05 Jul 2019 06:37:26: 26000000 INFO @ Fri, 05 Jul 2019 06:37:35: 27000000 INFO @ Fri, 05 Jul 2019 06:37:36: 27000000 INFO @ Fri, 05 Jul 2019 06:37:38: 27000000 INFO @ Fri, 05 Jul 2019 06:37:46: 28000000 INFO @ Fri, 05 Jul 2019 06:37:48: 28000000 INFO @ Fri, 05 Jul 2019 06:37:50: 28000000 INFO @ Fri, 05 Jul 2019 06:37:56: 29000000 INFO @ Fri, 05 Jul 2019 06:38:01: 29000000 INFO @ Fri, 05 Jul 2019 06:38:02: 29000000 INFO @ Fri, 05 Jul 2019 06:38:06: 30000000 INFO @ Fri, 05 Jul 2019 06:38:13: 30000000 INFO @ Fri, 05 Jul 2019 06:38:14: 30000000 INFO @ Fri, 05 Jul 2019 06:38:16: 31000000 INFO @ Fri, 05 Jul 2019 06:38:25: 31000000 INFO @ Fri, 05 Jul 2019 06:38:26: 31000000 INFO @ Fri, 05 Jul 2019 06:38:26: 32000000 INFO @ Fri, 05 Jul 2019 06:38:37: 32000000 INFO @ Fri, 05 Jul 2019 06:38:37: 33000000 INFO @ Fri, 05 Jul 2019 06:38:38: 32000000 INFO @ Fri, 05 Jul 2019 06:38:49: 33000000 INFO @ Fri, 05 Jul 2019 06:38:49: 33000000 INFO @ Fri, 05 Jul 2019 06:38:49: 34000000 INFO @ Fri, 05 Jul 2019 06:39:00: 34000000 INFO @ Fri, 05 Jul 2019 06:39:01: 34000000 INFO @ Fri, 05 Jul 2019 06:39:01: 35000000 INFO @ Fri, 05 Jul 2019 06:39:11: 35000000 INFO @ Fri, 05 Jul 2019 06:39:12: 35000000 INFO @ Fri, 05 Jul 2019 06:39:13: 36000000 INFO @ Fri, 05 Jul 2019 06:39:23: 36000000 INFO @ Fri, 05 Jul 2019 06:39:23: 36000000 INFO @ Fri, 05 Jul 2019 06:39:25: 37000000 INFO @ Fri, 05 Jul 2019 06:39:33: 37000000 INFO @ Fri, 05 Jul 2019 06:39:35: 37000000 INFO @ Fri, 05 Jul 2019 06:39:37: 38000000 INFO @ Fri, 05 Jul 2019 06:39:43: 38000000 INFO @ Fri, 05 Jul 2019 06:39:47: 38000000 INFO @ Fri, 05 Jul 2019 06:39:49: 39000000 INFO @ Fri, 05 Jul 2019 06:39:52: 39000000 INFO @ Fri, 05 Jul 2019 06:39:58: 39000000 INFO @ Fri, 05 Jul 2019 06:40:01: 40000000 INFO @ Fri, 05 Jul 2019 06:40:02: 40000000 INFO @ Fri, 05 Jul 2019 06:40:09: 40000000 INFO @ Fri, 05 Jul 2019 06:40:12: 41000000 INFO @ Fri, 05 Jul 2019 06:40:12: 41000000 INFO @ Fri, 05 Jul 2019 06:40:19: 41000000 INFO @ Fri, 05 Jul 2019 06:40:22: 42000000 INFO @ Fri, 05 Jul 2019 06:40:23: 42000000 INFO @ Fri, 05 Jul 2019 06:40:31: 42000000 INFO @ Fri, 05 Jul 2019 06:40:32: 43000000 INFO @ Fri, 05 Jul 2019 06:40:34: 43000000 INFO @ Fri, 05 Jul 2019 06:40:41: 43000000 INFO @ Fri, 05 Jul 2019 06:40:41: 44000000 INFO @ Fri, 05 Jul 2019 06:40:45: 44000000 INFO @ Fri, 05 Jul 2019 06:40:51: 44000000 INFO @ Fri, 05 Jul 2019 06:40:51: 45000000 INFO @ Fri, 05 Jul 2019 06:40:55: 45000000 INFO @ Fri, 05 Jul 2019 06:41:01: 45000000 INFO @ Fri, 05 Jul 2019 06:41:02: 46000000 INFO @ Fri, 05 Jul 2019 06:41:05: 46000000 INFO @ Fri, 05 Jul 2019 06:41:11: 46000000 INFO @ Fri, 05 Jul 2019 06:41:12: 47000000 INFO @ Fri, 05 Jul 2019 06:41:16: 47000000 INFO @ Fri, 05 Jul 2019 06:41:21: 47000000 INFO @ Fri, 05 Jul 2019 06:41:23: 48000000 INFO @ Fri, 05 Jul 2019 06:41:26: 48000000 INFO @ Fri, 05 Jul 2019 06:41:31: 48000000 INFO @ Fri, 05 Jul 2019 06:41:33: 49000000 INFO @ Fri, 05 Jul 2019 06:41:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:41:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:41:35: #1 total tags in treatment: 49054602 INFO @ Fri, 05 Jul 2019 06:41:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:41:35: #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 06:41:36: #1 tags after filtering in treatment: 49054435 INFO @ Fri, 05 Jul 2019 06:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:41:36: #1 finished! INFO @ Fri, 05 Jul 2019 06:41:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:41:37: 49000000 INFO @ Fri, 05 Jul 2019 06:41:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:41:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:41:38: #1 total tags in treatment: 49054602 INFO @ Fri, 05 Jul 2019 06:41:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:41:38: #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 06:41:39: #1 tags after filtering in treatment: 49054435 INFO @ Fri, 05 Jul 2019 06:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:41:39: #1 finished! INFO @ Fri, 05 Jul 2019 06:41:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:41:41: 49000000 INFO @ Fri, 05 Jul 2019 06:41:42: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:41:42: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:41:42: #1 total tags in treatment: 49054602 INFO @ Fri, 05 Jul 2019 06:41:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:41:42: #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 06:41:43: #1 tags after filtering in treatment: 49054435 INFO @ Fri, 05 Jul 2019 06:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:41:43: #1 finished! INFO @ Fri, 05 Jul 2019 06:41:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:41:50: #2 number of paired peaks: 107802 INFO @ Fri, 05 Jul 2019 06:41:50: start model_add_line... INFO @ Fri, 05 Jul 2019 06:41:51: start X-correlation... INFO @ Fri, 05 Jul 2019 06:41:51: end of X-cor INFO @ Fri, 05 Jul 2019 06:41:51: #2 finished! INFO @ Fri, 05 Jul 2019 06:41:51: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 06:41:51: #2 alternative fragment length(s) may be 3,132 bps INFO @ Fri, 05 Jul 2019 06:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20_model.r INFO @ Fri, 05 Jul 2019 06:41:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:41:53: #2 number of paired peaks: 107802 INFO @ Fri, 05 Jul 2019 06:41:53: start model_add_line... INFO @ Fri, 05 Jul 2019 06:41:54: start X-correlation... INFO @ Fri, 05 Jul 2019 06:41:54: end of X-cor INFO @ Fri, 05 Jul 2019 06:41:54: #2 finished! INFO @ Fri, 05 Jul 2019 06:41:54: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 06:41:54: #2 alternative fragment length(s) may be 3,132 bps INFO @ Fri, 05 Jul 2019 06:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05_model.r INFO @ Fri, 05 Jul 2019 06:41:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:41:57: #2 number of paired peaks: 107802 INFO @ Fri, 05 Jul 2019 06:41:57: start model_add_line... INFO @ Fri, 05 Jul 2019 06:41:59: start X-correlation... INFO @ Fri, 05 Jul 2019 06:41:59: end of X-cor INFO @ Fri, 05 Jul 2019 06:41:59: #2 finished! INFO @ Fri, 05 Jul 2019 06:41:59: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 06:41:59: #2 alternative fragment length(s) may be 3,132 bps INFO @ Fri, 05 Jul 2019 06:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10_model.r INFO @ Fri, 05 Jul 2019 06:41:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:44:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:44:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:44:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:46:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.20_summits.bed INFO @ Fri, 05 Jul 2019 06:46:18: Done! pass1 - making usageList (132 chroms): 10 millis pass2 - checking and writing primary data (45674 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.05_summits.bed INFO @ Fri, 05 Jul 2019 06:46:24: Done! pass1 - making usageList (182 chroms): 18 millis pass2 - checking and writing primary data (88749 records, 4 fields): 124 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:46:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:46:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101855/ERX101855.10_summits.bed INFO @ Fri, 05 Jul 2019 06:46:31: Done! pass1 - making usageList (162 chroms): 14 millis pass2 - checking and writing primary data (66456 records, 4 fields): 104 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。