Job ID = 2640564 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:42:26 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 ) 2019-08-24T08:42:26 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 ) 2019-08-24T08:42:42 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 ) 2019-08-24T08:43:09 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 ) 2019-08-24T08:43:09 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 ) spots read : 21,270,433 reads read : 42,540,866 reads written : 21,270,433 reads 0-length : 21,270,433 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: 00:00:00 Multiseed full-index search: 00:14:02 21270433 reads; of these: 21270433 (100.00%) were unpaired; of these: 627128 (2.95%) aligned 0 times 16823105 (79.09%) aligned exactly 1 time 3820200 (17.96%) aligned >1 times 97.05% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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 12 files... [bam_rmdupse_core] 5346295 / 20643305 = 0.2590 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.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 @ Sat, 24 Aug 2019 18:04:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:04:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:04:47: 1000000 INFO @ Sat, 24 Aug 2019 18:04:54: 2000000 INFO @ Sat, 24 Aug 2019 18:05:01: 3000000 INFO @ Sat, 24 Aug 2019 18:05:08: 4000000 INFO @ Sat, 24 Aug 2019 18:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.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 @ Sat, 24 Aug 2019 18:05:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:14: 5000000 INFO @ Sat, 24 Aug 2019 18:05:17: 1000000 INFO @ Sat, 24 Aug 2019 18:05:21: 6000000 INFO @ Sat, 24 Aug 2019 18:05:24: 2000000 INFO @ Sat, 24 Aug 2019 18:05:28: 7000000 INFO @ Sat, 24 Aug 2019 18:05:31: 3000000 INFO @ Sat, 24 Aug 2019 18:05:35: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:05:37: 4000000 INFO @ Sat, 24 Aug 2019 18:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.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 @ Sat, 24 Aug 2019 18:05:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:42: 9000000 INFO @ Sat, 24 Aug 2019 18:05:44: 5000000 INFO @ Sat, 24 Aug 2019 18:05:47: 1000000 INFO @ Sat, 24 Aug 2019 18:05:49: 10000000 INFO @ Sat, 24 Aug 2019 18:05:51: 6000000 INFO @ Sat, 24 Aug 2019 18:05:55: 2000000 INFO @ Sat, 24 Aug 2019 18:05:56: 11000000 INFO @ Sat, 24 Aug 2019 18:05:58: 7000000 INFO @ Sat, 24 Aug 2019 18:06:03: 12000000 INFO @ Sat, 24 Aug 2019 18:06:03: 3000000 INFO @ Sat, 24 Aug 2019 18:06:06: 8000000 INFO @ Sat, 24 Aug 2019 18:06:10: 13000000 INFO @ Sat, 24 Aug 2019 18:06:11: 4000000 INFO @ Sat, 24 Aug 2019 18:06:13: 9000000 INFO @ Sat, 24 Aug 2019 18:06:17: 14000000 INFO @ Sat, 24 Aug 2019 18:06:19: 5000000 INFO @ Sat, 24 Aug 2019 18:06:20: 10000000 INFO @ Sat, 24 Aug 2019 18:06:24: 15000000 INFO @ Sat, 24 Aug 2019 18:06:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:06:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:06:26: #1 total tags in treatment: 15297010 INFO @ Sat, 24 Aug 2019 18:06:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:06:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:06:27: 11000000 INFO @ Sat, 24 Aug 2019 18:06:27: #1 tags after filtering in treatment: 15296802 INFO @ Sat, 24 Aug 2019 18:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:06:27: #1 finished! INFO @ Sat, 24 Aug 2019 18:06:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:06:27: 6000000 INFO @ Sat, 24 Aug 2019 18:06:31: #2 number of paired peaks: 68553 INFO @ Sat, 24 Aug 2019 18:06:31: start model_add_line... INFO @ Sat, 24 Aug 2019 18:06:31: start X-correlation... INFO @ Sat, 24 Aug 2019 18:06:31: end of X-cor INFO @ Sat, 24 Aug 2019 18:06:31: #2 finished! INFO @ Sat, 24 Aug 2019 18:06:31: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:06:31: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05_model.r INFO @ Sat, 24 Aug 2019 18:06:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:06:33: 12000000 INFO @ Sat, 24 Aug 2019 18:06:35: 7000000 INFO @ Sat, 24 Aug 2019 18:06:40: 13000000 INFO @ Sat, 24 Aug 2019 18:06:43: 8000000 INFO @ Sat, 24 Aug 2019 18:06:47: 14000000 INFO @ Sat, 24 Aug 2019 18:06:51: 9000000 INFO @ Sat, 24 Aug 2019 18:06:54: 15000000 INFO @ Sat, 24 Aug 2019 18:06:57: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:06:57: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:06:57: #1 total tags in treatment: 15297010 INFO @ Sat, 24 Aug 2019 18:06:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:06:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:06:57: #1 tags after filtering in treatment: 15296802 INFO @ Sat, 24 Aug 2019 18:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:06:57: #1 finished! INFO @ Sat, 24 Aug 2019 18:06:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:06:59: 10000000 INFO @ Sat, 24 Aug 2019 18:07:01: #2 number of paired peaks: 68553 INFO @ Sat, 24 Aug 2019 18:07:01: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:02: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:07:02: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10_model.r INFO @ Sat, 24 Aug 2019 18:07:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:06: 11000000 INFO @ Sat, 24 Aug 2019 18:07:14: 12000000 INFO @ Sat, 24 Aug 2019 18:07:22: 13000000 INFO @ Sat, 24 Aug 2019 18:07:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:07:29: 14000000 INFO @ Sat, 24 Aug 2019 18:07:38: 15000000 INFO @ Sat, 24 Aug 2019 18:07:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:07:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:07:40: #1 total tags in treatment: 15297010 INFO @ Sat, 24 Aug 2019 18:07:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:07:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:07:41: #1 tags after filtering in treatment: 15296802 INFO @ Sat, 24 Aug 2019 18:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:07:41: #1 finished! INFO @ Sat, 24 Aug 2019 18:07:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:07:45: #2 number of paired peaks: 68553 INFO @ Sat, 24 Aug 2019 18:07:45: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:45: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:45: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:45: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:45: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:07:45: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:07:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20_model.r INFO @ Sat, 24 Aug 2019 18:07:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.05_summits.bed INFO @ Sat, 24 Aug 2019 18:07:51: Done! pass1 - making usageList (92 chroms): 8 millis pass2 - checking and writing primary data (17399 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:07:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.10_summits.bed INFO @ Sat, 24 Aug 2019 18:08:19: Done! pass1 - making usageList (73 chroms): 7 millis pass2 - checking and writing primary data (12649 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:08:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375013/SRX5375013.20_summits.bed INFO @ Sat, 24 Aug 2019 18:09:03: Done! pass1 - making usageList (52 chroms): 4 millis pass2 - checking and writing primary data (7729 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。