Job ID = 2001648 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 ) 2019-07-04T21:53:56 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 ) 2019-07-04T22:04:58 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 ) 2019-07-04T22:06:33 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 ) 2019-07-04T22:06:33 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 ) 2019-07-04T22:12:15 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 ) spots read : 76,934,029 reads read : 76,934,029 reads written : 76,934,029 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:45:15 76934029 reads; of these: 76934029 (100.00%) were unpaired; of these: 2112575 (2.75%) aligned 0 times 66796050 (86.82%) aligned exactly 1 time 8025404 (10.43%) aligned >1 times 97.25% overall alignment rate Time searching: 00:45:16 Overall time: 00:45:16 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 32 files... [bam_rmdupse_core] 40962287 / 74821454 = 0.5475 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 08:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.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 08:33:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:33:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.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 08:33:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:33:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.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 08:33:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:33:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:33:17: 1000000 INFO @ Fri, 05 Jul 2019 08:33:19: 1000000 INFO @ Fri, 05 Jul 2019 08:33:21: 1000000 INFO @ Fri, 05 Jul 2019 08:33:24: 2000000 INFO @ Fri, 05 Jul 2019 08:33:27: 2000000 INFO @ Fri, 05 Jul 2019 08:33:29: 2000000 INFO @ Fri, 05 Jul 2019 08:33:30: 3000000 INFO @ Fri, 05 Jul 2019 08:33:35: 3000000 INFO @ Fri, 05 Jul 2019 08:33:37: 4000000 INFO @ Fri, 05 Jul 2019 08:33:38: 3000000 INFO @ Fri, 05 Jul 2019 08:33:42: 4000000 INFO @ Fri, 05 Jul 2019 08:33:43: 5000000 INFO @ Fri, 05 Jul 2019 08:33:46: 4000000 INFO @ Fri, 05 Jul 2019 08:33:50: 5000000 INFO @ Fri, 05 Jul 2019 08:33:50: 6000000 INFO @ Fri, 05 Jul 2019 08:33:54: 5000000 INFO @ Fri, 05 Jul 2019 08:33:57: 6000000 INFO @ Fri, 05 Jul 2019 08:33:57: 7000000 INFO @ Fri, 05 Jul 2019 08:34:03: 6000000 INFO @ Fri, 05 Jul 2019 08:34:04: 8000000 INFO @ Fri, 05 Jul 2019 08:34:04: 7000000 INFO @ Fri, 05 Jul 2019 08:34:10: 9000000 INFO @ Fri, 05 Jul 2019 08:34:12: 8000000 INFO @ Fri, 05 Jul 2019 08:34:12: 7000000 INFO @ Fri, 05 Jul 2019 08:34:17: 10000000 INFO @ Fri, 05 Jul 2019 08:34:19: 9000000 INFO @ Fri, 05 Jul 2019 08:34:21: 8000000 INFO @ Fri, 05 Jul 2019 08:34:23: 11000000 INFO @ Fri, 05 Jul 2019 08:34:26: 10000000 INFO @ Fri, 05 Jul 2019 08:34:30: 12000000 INFO @ Fri, 05 Jul 2019 08:34:30: 9000000 INFO @ Fri, 05 Jul 2019 08:34:34: 11000000 INFO @ Fri, 05 Jul 2019 08:34:36: 13000000 INFO @ Fri, 05 Jul 2019 08:34:39: 10000000 INFO @ Fri, 05 Jul 2019 08:34:41: 12000000 INFO @ Fri, 05 Jul 2019 08:34:43: 14000000 INFO @ Fri, 05 Jul 2019 08:34:47: 11000000 INFO @ Fri, 05 Jul 2019 08:34:48: 13000000 INFO @ Fri, 05 Jul 2019 08:34:49: 15000000 INFO @ Fri, 05 Jul 2019 08:34:55: 14000000 INFO @ Fri, 05 Jul 2019 08:34:56: 12000000 INFO @ Fri, 05 Jul 2019 08:34:56: 16000000 INFO @ Fri, 05 Jul 2019 08:35:02: 15000000 INFO @ Fri, 05 Jul 2019 08:35:02: 17000000 INFO @ Fri, 05 Jul 2019 08:35:04: 13000000 INFO @ Fri, 05 Jul 2019 08:35:09: 18000000 INFO @ Fri, 05 Jul 2019 08:35:10: 16000000 INFO @ Fri, 05 Jul 2019 08:35:13: 14000000 INFO @ Fri, 05 Jul 2019 08:35:16: 19000000 INFO @ Fri, 05 Jul 2019 08:35:17: 17000000 INFO @ Fri, 05 Jul 2019 08:35:21: 15000000 INFO @ Fri, 05 Jul 2019 08:35:22: 20000000 INFO @ Fri, 05 Jul 2019 08:35:24: 18000000 INFO @ Fri, 05 Jul 2019 08:35:29: 21000000 INFO @ Fri, 05 Jul 2019 08:35:30: 16000000 INFO @ Fri, 05 Jul 2019 08:35:31: 19000000 INFO @ Fri, 05 Jul 2019 08:35:35: 22000000 INFO @ Fri, 05 Jul 2019 08:35:38: 17000000 INFO @ Fri, 05 Jul 2019 08:35:39: 20000000 INFO @ Fri, 05 Jul 2019 08:35:42: 23000000 INFO @ Fri, 05 Jul 2019 08:35:46: 21000000 INFO @ Fri, 05 Jul 2019 08:35:47: 18000000 INFO @ Fri, 05 Jul 2019 08:35:48: 24000000 INFO @ Fri, 05 Jul 2019 08:35:53: 22000000 INFO @ Fri, 05 Jul 2019 08:35:55: 19000000 INFO @ Fri, 05 Jul 2019 08:35:56: 25000000 INFO @ Fri, 05 Jul 2019 08:36:00: 23000000 INFO @ Fri, 05 Jul 2019 08:36:03: 26000000 INFO @ Fri, 05 Jul 2019 08:36:03: 20000000 INFO @ Fri, 05 Jul 2019 08:36:08: 24000000 INFO @ Fri, 05 Jul 2019 08:36:10: 27000000 INFO @ Fri, 05 Jul 2019 08:36:11: 21000000 INFO @ Fri, 05 Jul 2019 08:36:15: 25000000 INFO @ Fri, 05 Jul 2019 08:36:17: 28000000 INFO @ Fri, 05 Jul 2019 08:36:19: 22000000 INFO @ Fri, 05 Jul 2019 08:36:23: 26000000 INFO @ Fri, 05 Jul 2019 08:36:23: 29000000 INFO @ Fri, 05 Jul 2019 08:36:27: 23000000 INFO @ Fri, 05 Jul 2019 08:36:30: 30000000 INFO @ Fri, 05 Jul 2019 08:36:30: 27000000 INFO @ Fri, 05 Jul 2019 08:36:36: 24000000 INFO @ Fri, 05 Jul 2019 08:36:37: 31000000 INFO @ Fri, 05 Jul 2019 08:36:38: 28000000 INFO @ Fri, 05 Jul 2019 08:36:43: 32000000 INFO @ Fri, 05 Jul 2019 08:36:45: 25000000 INFO @ Fri, 05 Jul 2019 08:36:45: 29000000 INFO @ Fri, 05 Jul 2019 08:36:50: 33000000 INFO @ Fri, 05 Jul 2019 08:36:52: 30000000 INFO @ Fri, 05 Jul 2019 08:36:53: 26000000 INFO @ Fri, 05 Jul 2019 08:36:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:36:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:36:56: #1 total tags in treatment: 33859167 INFO @ Fri, 05 Jul 2019 08:36:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:36:56: #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 08:36:57: #1 tags after filtering in treatment: 33858964 INFO @ Fri, 05 Jul 2019 08:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:36:57: #1 finished! INFO @ Fri, 05 Jul 2019 08:36:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:37:00: 31000000 INFO @ Fri, 05 Jul 2019 08:37:01: 27000000 INFO @ Fri, 05 Jul 2019 08:37:07: 32000000 INFO @ Fri, 05 Jul 2019 08:37:07: #2 number of paired peaks: 110305 INFO @ Fri, 05 Jul 2019 08:37:07: start model_add_line... INFO @ Fri, 05 Jul 2019 08:37:08: start X-correlation... INFO @ Fri, 05 Jul 2019 08:37:08: end of X-cor INFO @ Fri, 05 Jul 2019 08:37:08: #2 finished! INFO @ Fri, 05 Jul 2019 08:37:08: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 08:37:08: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 08:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05_model.r INFO @ Fri, 05 Jul 2019 08:37:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:37:10: 28000000 INFO @ Fri, 05 Jul 2019 08:37:14: 33000000 INFO @ Fri, 05 Jul 2019 08:37:19: 29000000 INFO @ Fri, 05 Jul 2019 08:37:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:37:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:37:21: #1 total tags in treatment: 33859167 INFO @ Fri, 05 Jul 2019 08:37:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:37:21: #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 08:37:22: #1 tags after filtering in treatment: 33858964 INFO @ Fri, 05 Jul 2019 08:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:37:22: #1 finished! INFO @ Fri, 05 Jul 2019 08:37:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:37:27: 30000000 INFO @ Fri, 05 Jul 2019 08:37:32: #2 number of paired peaks: 110305 INFO @ Fri, 05 Jul 2019 08:37:32: start model_add_line... INFO @ Fri, 05 Jul 2019 08:37:33: start X-correlation... INFO @ Fri, 05 Jul 2019 08:37:33: end of X-cor INFO @ Fri, 05 Jul 2019 08:37:33: #2 finished! INFO @ Fri, 05 Jul 2019 08:37:33: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 08:37:33: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 08:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10_model.r INFO @ Fri, 05 Jul 2019 08:37:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:37:36: 31000000 INFO @ Fri, 05 Jul 2019 08:37:44: 32000000 INFO @ Fri, 05 Jul 2019 08:37:52: 33000000 INFO @ Fri, 05 Jul 2019 08:37:59: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:37:59: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:37:59: #1 total tags in treatment: 33859167 INFO @ Fri, 05 Jul 2019 08:37:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:37:59: #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 08:38:00: #1 tags after filtering in treatment: 33858964 INFO @ Fri, 05 Jul 2019 08:38:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:38:00: #1 finished! INFO @ Fri, 05 Jul 2019 08:38:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:38:10: #2 number of paired peaks: 110305 INFO @ Fri, 05 Jul 2019 08:38:10: start model_add_line... INFO @ Fri, 05 Jul 2019 08:38:11: start X-correlation... INFO @ Fri, 05 Jul 2019 08:38:11: end of X-cor INFO @ Fri, 05 Jul 2019 08:38:11: #2 finished! INFO @ Fri, 05 Jul 2019 08:38:11: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 08:38:11: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 08:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20_model.r INFO @ Fri, 05 Jul 2019 08:38:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:38:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:39:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.05_summits.bed INFO @ Fri, 05 Jul 2019 08:39:46: Done! pass1 - making usageList (175 chroms): 19 millis pass2 - checking and writing primary data (77767 records, 4 fields): 104 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:39:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:40:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:40:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.10_summits.bed INFO @ Fri, 05 Jul 2019 08:40:14: Done! pass1 - making usageList (155 chroms): 17 millis pass2 - checking and writing primary data (57063 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101963/ERX101963.20_summits.bed INFO @ Fri, 05 Jul 2019 08:40:52: Done! pass1 - making usageList (119 chroms): 10 millis pass2 - checking and writing primary data (33864 records, 4 fields): 48 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。