Job ID = 2001169 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:22:19 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 ) 2019-07-04T19:36:47 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 ) 2019-07-04T19:44:22 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 ) 2019-07-04T19:46:09 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 ) 2019-07-04T19:53:44 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 : 115,066,223 reads read : 115,066,223 reads written : 115,066,223 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:03:25 115066223 reads; of these: 115066223 (100.00%) were unpaired; of these: 2112604 (1.84%) aligned 0 times 101474845 (88.19%) aligned exactly 1 time 11478774 (9.98%) aligned >1 times 98.16% overall alignment rate Time searching: 01:03:27 Overall time: 01:03:27 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] 77342846 / 112953619 = 0.6847 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 06:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.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 06:32:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:32:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.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 06:33:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:33:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.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 06:33:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:33:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:33:11: 1000000 INFO @ Fri, 05 Jul 2019 06:33:11: 1000000 INFO @ Fri, 05 Jul 2019 06:33:13: 1000000 INFO @ Fri, 05 Jul 2019 06:33:22: 2000000 INFO @ Fri, 05 Jul 2019 06:33:23: 2000000 INFO @ Fri, 05 Jul 2019 06:33:24: 2000000 INFO @ Fri, 05 Jul 2019 06:33:33: 3000000 INFO @ Fri, 05 Jul 2019 06:33:33: 3000000 INFO @ Fri, 05 Jul 2019 06:33:35: 3000000 INFO @ Fri, 05 Jul 2019 06:33:44: 4000000 INFO @ Fri, 05 Jul 2019 06:33:44: 4000000 INFO @ Fri, 05 Jul 2019 06:33:46: 4000000 INFO @ Fri, 05 Jul 2019 06:33:55: 5000000 INFO @ Fri, 05 Jul 2019 06:33:55: 5000000 INFO @ Fri, 05 Jul 2019 06:33:57: 5000000 INFO @ Fri, 05 Jul 2019 06:34:06: 6000000 INFO @ Fri, 05 Jul 2019 06:34:06: 6000000 INFO @ Fri, 05 Jul 2019 06:34:08: 6000000 INFO @ Fri, 05 Jul 2019 06:34:16: 7000000 INFO @ Fri, 05 Jul 2019 06:34:17: 7000000 INFO @ Fri, 05 Jul 2019 06:34:19: 7000000 INFO @ Fri, 05 Jul 2019 06:34:27: 8000000 INFO @ Fri, 05 Jul 2019 06:34:28: 8000000 INFO @ Fri, 05 Jul 2019 06:34:30: 8000000 INFO @ Fri, 05 Jul 2019 06:34:38: 9000000 INFO @ Fri, 05 Jul 2019 06:34:38: 9000000 INFO @ Fri, 05 Jul 2019 06:34:41: 9000000 INFO @ Fri, 05 Jul 2019 06:34:49: 10000000 INFO @ Fri, 05 Jul 2019 06:34:49: 10000000 INFO @ Fri, 05 Jul 2019 06:34:52: 10000000 INFO @ Fri, 05 Jul 2019 06:35:00: 11000000 INFO @ Fri, 05 Jul 2019 06:35:00: 11000000 INFO @ Fri, 05 Jul 2019 06:35:03: 11000000 INFO @ Fri, 05 Jul 2019 06:35:11: 12000000 INFO @ Fri, 05 Jul 2019 06:35:11: 12000000 INFO @ Fri, 05 Jul 2019 06:35:14: 12000000 INFO @ Fri, 05 Jul 2019 06:35:23: 13000000 INFO @ Fri, 05 Jul 2019 06:35:25: 13000000 INFO @ Fri, 05 Jul 2019 06:35:26: 13000000 INFO @ Fri, 05 Jul 2019 06:35:35: 14000000 INFO @ Fri, 05 Jul 2019 06:35:38: 14000000 INFO @ Fri, 05 Jul 2019 06:35:39: 14000000 INFO @ Fri, 05 Jul 2019 06:35:47: 15000000 INFO @ Fri, 05 Jul 2019 06:35:51: 15000000 INFO @ Fri, 05 Jul 2019 06:35:52: 15000000 INFO @ Fri, 05 Jul 2019 06:35:59: 16000000 INFO @ Fri, 05 Jul 2019 06:36:03: 16000000 INFO @ Fri, 05 Jul 2019 06:36:05: 16000000 INFO @ Fri, 05 Jul 2019 06:36:10: 17000000 INFO @ Fri, 05 Jul 2019 06:36:15: 17000000 INFO @ Fri, 05 Jul 2019 06:36:18: 17000000 INFO @ Fri, 05 Jul 2019 06:36:24: 18000000 INFO @ Fri, 05 Jul 2019 06:36:26: 18000000 INFO @ Fri, 05 Jul 2019 06:36:31: 18000000 INFO @ Fri, 05 Jul 2019 06:36:37: 19000000 INFO @ Fri, 05 Jul 2019 06:36:38: 19000000 INFO @ Fri, 05 Jul 2019 06:36:44: 19000000 INFO @ Fri, 05 Jul 2019 06:36:50: 20000000 INFO @ Fri, 05 Jul 2019 06:36:51: 20000000 INFO @ Fri, 05 Jul 2019 06:36:59: 20000000 INFO @ Fri, 05 Jul 2019 06:37:02: 21000000 INFO @ Fri, 05 Jul 2019 06:37:03: 21000000 INFO @ Fri, 05 Jul 2019 06:37:13: 21000000 INFO @ Fri, 05 Jul 2019 06:37:14: 22000000 INFO @ Fri, 05 Jul 2019 06:37:16: 22000000 INFO @ Fri, 05 Jul 2019 06:37:24: 22000000 INFO @ Fri, 05 Jul 2019 06:37:25: 23000000 INFO @ Fri, 05 Jul 2019 06:37:29: 23000000 INFO @ Fri, 05 Jul 2019 06:37:36: 23000000 INFO @ Fri, 05 Jul 2019 06:37:37: 24000000 INFO @ Fri, 05 Jul 2019 06:37:40: 24000000 INFO @ Fri, 05 Jul 2019 06:37:48: 24000000 INFO @ Fri, 05 Jul 2019 06:37:48: 25000000 INFO @ Fri, 05 Jul 2019 06:37:52: 25000000 INFO @ Fri, 05 Jul 2019 06:37:59: 25000000 INFO @ Fri, 05 Jul 2019 06:37:59: 26000000 INFO @ Fri, 05 Jul 2019 06:38:02: 26000000 INFO @ Fri, 05 Jul 2019 06:38:10: 26000000 INFO @ Fri, 05 Jul 2019 06:38:10: 27000000 INFO @ Fri, 05 Jul 2019 06:38:13: 27000000 INFO @ Fri, 05 Jul 2019 06:38:21: 28000000 INFO @ Fri, 05 Jul 2019 06:38:21: 27000000 INFO @ Fri, 05 Jul 2019 06:38:24: 28000000 INFO @ Fri, 05 Jul 2019 06:38:32: 29000000 INFO @ Fri, 05 Jul 2019 06:38:33: 28000000 INFO @ Fri, 05 Jul 2019 06:38:35: 29000000 INFO @ Fri, 05 Jul 2019 06:38:43: 30000000 INFO @ Fri, 05 Jul 2019 06:38:44: 29000000 INFO @ Fri, 05 Jul 2019 06:38:46: 30000000 INFO @ Fri, 05 Jul 2019 06:38:55: 31000000 INFO @ Fri, 05 Jul 2019 06:38:55: 30000000 INFO @ Fri, 05 Jul 2019 06:38:58: 31000000 INFO @ Fri, 05 Jul 2019 06:39:06: 32000000 INFO @ Fri, 05 Jul 2019 06:39:07: 31000000 INFO @ Fri, 05 Jul 2019 06:39:09: 32000000 INFO @ Fri, 05 Jul 2019 06:39:18: 33000000 INFO @ Fri, 05 Jul 2019 06:39:18: 32000000 INFO @ Fri, 05 Jul 2019 06:39:20: 33000000 INFO @ Fri, 05 Jul 2019 06:39:29: 34000000 INFO @ Fri, 05 Jul 2019 06:39:30: 33000000 INFO @ Fri, 05 Jul 2019 06:39:32: 34000000 INFO @ Fri, 05 Jul 2019 06:39:41: 34000000 INFO @ Fri, 05 Jul 2019 06:39:41: 35000000 INFO @ Fri, 05 Jul 2019 06:39:43: 35000000 INFO @ Fri, 05 Jul 2019 06:39:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 06:39:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 06:39:48: #1 total tags in treatment: 35610773 INFO @ Fri, 05 Jul 2019 06:39:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:39:48: #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 06:39:49: #1 tags after filtering in treatment: 35610588 INFO @ Fri, 05 Jul 2019 06:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:39:49: #1 finished! INFO @ Fri, 05 Jul 2019 06:39:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:39:50: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 06:39:50: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 06:39:50: #1 total tags in treatment: 35610773 INFO @ Fri, 05 Jul 2019 06:39:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:39:50: #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 06:39:51: #1 tags after filtering in treatment: 35610588 INFO @ Fri, 05 Jul 2019 06:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:39:51: #1 finished! INFO @ Fri, 05 Jul 2019 06:39:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:39:52: 35000000 INFO @ Fri, 05 Jul 2019 06:39:59: #2 number of paired peaks: 68084 INFO @ Fri, 05 Jul 2019 06:39:59: start model_add_line... INFO @ Fri, 05 Jul 2019 06:39:59: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 06:39:59: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 06:39:59: #1 total tags in treatment: 35610773 INFO @ Fri, 05 Jul 2019 06:39:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:39:59: #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 06:39:59: start X-correlation... INFO @ Fri, 05 Jul 2019 06:39:59: end of X-cor INFO @ Fri, 05 Jul 2019 06:39:59: #2 finished! INFO @ Fri, 05 Jul 2019 06:39:59: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:39:59: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05_model.r INFO @ Fri, 05 Jul 2019 06:40:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:40:00: #2 number of paired peaks: 68084 INFO @ Fri, 05 Jul 2019 06:40:00: start model_add_line... INFO @ Fri, 05 Jul 2019 06:40:00: #1 tags after filtering in treatment: 35610588 INFO @ Fri, 05 Jul 2019 06:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:40:00: #1 finished! INFO @ Fri, 05 Jul 2019 06:40:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:40:01: start X-correlation... INFO @ Fri, 05 Jul 2019 06:40:01: end of X-cor INFO @ Fri, 05 Jul 2019 06:40:01: #2 finished! INFO @ Fri, 05 Jul 2019 06:40:01: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:40:01: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20_model.r INFO @ Fri, 05 Jul 2019 06:40:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:40:09: #2 number of paired peaks: 68084 INFO @ Fri, 05 Jul 2019 06:40:09: start model_add_line... INFO @ Fri, 05 Jul 2019 06:40:10: start X-correlation... INFO @ Fri, 05 Jul 2019 06:40:10: end of X-cor INFO @ Fri, 05 Jul 2019 06:40:10: #2 finished! INFO @ Fri, 05 Jul 2019 06:40:10: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:40:10: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10_model.r INFO @ Fri, 05 Jul 2019 06:40:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:41:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:41:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.20_summits.bed INFO @ Fri, 05 Jul 2019 06:43:04: Done! pass1 - making usageList (123 chroms): 8 millis pass2 - checking and writing primary data (37900 records, 4 fields): 77 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.05_summits.bed INFO @ Fri, 05 Jul 2019 06:43:08: Done! pass1 - making usageList (174 chroms): 18 millis INFO @ Fri, 05 Jul 2019 06:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10_peaks.xls pass2 - checking and writing primary data (61918 records, 4 fields): 18857 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:43:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101858/ERX101858.10_summits.bed INFO @ Fri, 05 Jul 2019 06:43:29: Done! pass1 - making usageList (150 chroms): 11 millis pass2 - checking and writing primary data (50046 records, 4 fields): 74 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。