Job ID = 2640529 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:28:28 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 ) 2019-08-24T08:28:28 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 ) 2019-08-24T08:30:04 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 ) 2019-08-24T08:33:43 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 ) 2019-08-24T08:33:43 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 ) 2019-08-24T08:33:43 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 : 22,267,420 reads read : 44,534,840 reads written : 22,267,420 reads 0-length : 22,267,420 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: 00:13:40 22267420 reads; of these: 22267420 (100.00%) were unpaired; of these: 762346 (3.42%) aligned 0 times 18373062 (82.51%) aligned exactly 1 time 3132012 (14.07%) aligned >1 times 96.58% overall alignment rate Time searching: 00:13:43 Overall time: 00:13:43 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] 4648995 / 21505074 = 0.2162 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.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 17:55:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:55:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:55:51: 1000000 INFO @ Sat, 24 Aug 2019 17:55:57: 2000000 INFO @ Sat, 24 Aug 2019 17:56:04: 3000000 INFO @ Sat, 24 Aug 2019 17:56:10: 4000000 INFO @ Sat, 24 Aug 2019 17:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.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 17:56:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:56:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:56:17: 5000000 INFO @ Sat, 24 Aug 2019 17:56:21: 1000000 INFO @ Sat, 24 Aug 2019 17:56:23: 6000000 INFO @ Sat, 24 Aug 2019 17:56:28: 2000000 INFO @ Sat, 24 Aug 2019 17:56:30: 7000000 INFO @ Sat, 24 Aug 2019 17:56:36: 3000000 INFO @ Sat, 24 Aug 2019 17:56:36: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:56:43: 9000000 INFO @ Sat, 24 Aug 2019 17:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.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 17:56:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:56:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:56:43: 4000000 INFO @ Sat, 24 Aug 2019 17:56:49: 10000000 INFO @ Sat, 24 Aug 2019 17:56:49: 1000000 INFO @ Sat, 24 Aug 2019 17:56:50: 5000000 INFO @ Sat, 24 Aug 2019 17:56:55: 2000000 INFO @ Sat, 24 Aug 2019 17:56:56: 11000000 INFO @ Sat, 24 Aug 2019 17:56:58: 6000000 INFO @ Sat, 24 Aug 2019 17:57:01: 3000000 INFO @ Sat, 24 Aug 2019 17:57:02: 12000000 INFO @ Sat, 24 Aug 2019 17:57:05: 7000000 INFO @ Sat, 24 Aug 2019 17:57:08: 4000000 INFO @ Sat, 24 Aug 2019 17:57:09: 13000000 INFO @ Sat, 24 Aug 2019 17:57:13: 8000000 INFO @ Sat, 24 Aug 2019 17:57:14: 5000000 INFO @ Sat, 24 Aug 2019 17:57:17: 14000000 INFO @ Sat, 24 Aug 2019 17:57:20: 6000000 INFO @ Sat, 24 Aug 2019 17:57:20: 9000000 INFO @ Sat, 24 Aug 2019 17:57:23: 15000000 INFO @ Sat, 24 Aug 2019 17:57:26: 7000000 INFO @ Sat, 24 Aug 2019 17:57:27: 10000000 INFO @ Sat, 24 Aug 2019 17:57:30: 16000000 INFO @ Sat, 24 Aug 2019 17:57:32: 8000000 INFO @ Sat, 24 Aug 2019 17:57:35: 11000000 INFO @ Sat, 24 Aug 2019 17:57:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:57:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:57:36: #1 total tags in treatment: 16856079 INFO @ Sat, 24 Aug 2019 17:57:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:57:36: #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 17:57:36: #1 tags after filtering in treatment: 16855857 INFO @ Sat, 24 Aug 2019 17:57:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:57:36: #1 finished! INFO @ Sat, 24 Aug 2019 17:57:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:57:38: 9000000 INFO @ Sat, 24 Aug 2019 17:57:41: #2 number of paired peaks: 66658 INFO @ Sat, 24 Aug 2019 17:57:41: start model_add_line... INFO @ Sat, 24 Aug 2019 17:57:41: start X-correlation... INFO @ Sat, 24 Aug 2019 17:57:41: end of X-cor INFO @ Sat, 24 Aug 2019 17:57:41: #2 finished! INFO @ Sat, 24 Aug 2019 17:57:41: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 17:57:41: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 17:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05_model.r INFO @ Sat, 24 Aug 2019 17:57:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:57:42: 12000000 INFO @ Sat, 24 Aug 2019 17:57:44: 10000000 INFO @ Sat, 24 Aug 2019 17:57:49: 13000000 INFO @ Sat, 24 Aug 2019 17:57:50: 11000000 INFO @ Sat, 24 Aug 2019 17:57:56: 12000000 INFO @ Sat, 24 Aug 2019 17:57:57: 14000000 INFO @ Sat, 24 Aug 2019 17:58:02: 13000000 INFO @ Sat, 24 Aug 2019 17:58:04: 15000000 INFO @ Sat, 24 Aug 2019 17:58:08: 14000000 INFO @ Sat, 24 Aug 2019 17:58:12: 16000000 INFO @ Sat, 24 Aug 2019 17:58:14: 15000000 INFO @ Sat, 24 Aug 2019 17:58:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:58:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:58:18: #1 total tags in treatment: 16856079 INFO @ Sat, 24 Aug 2019 17:58:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:58:18: #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 17:58:19: #1 tags after filtering in treatment: 16855857 INFO @ Sat, 24 Aug 2019 17:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:58:19: #1 finished! INFO @ Sat, 24 Aug 2019 17:58:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:58:21: 16000000 INFO @ Sat, 24 Aug 2019 17:58:23: #2 number of paired peaks: 66658 INFO @ Sat, 24 Aug 2019 17:58:23: start model_add_line... INFO @ Sat, 24 Aug 2019 17:58:24: start X-correlation... INFO @ Sat, 24 Aug 2019 17:58:24: end of X-cor INFO @ Sat, 24 Aug 2019 17:58:24: #2 finished! INFO @ Sat, 24 Aug 2019 17:58:24: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 17:58:24: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 17:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10_model.r INFO @ Sat, 24 Aug 2019 17:58:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:58:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:58:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:58:26: #1 total tags in treatment: 16856079 INFO @ Sat, 24 Aug 2019 17:58:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:58:26: #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 17:58:27: #1 tags after filtering in treatment: 16855857 INFO @ Sat, 24 Aug 2019 17:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:58:27: #1 finished! INFO @ Sat, 24 Aug 2019 17:58:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:58:31: #2 number of paired peaks: 66658 INFO @ Sat, 24 Aug 2019 17:58:31: start model_add_line... INFO @ Sat, 24 Aug 2019 17:58:31: start X-correlation... INFO @ Sat, 24 Aug 2019 17:58:31: end of X-cor INFO @ Sat, 24 Aug 2019 17:58:31: #2 finished! INFO @ Sat, 24 Aug 2019 17:58:31: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 17:58:31: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 17:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20_model.r INFO @ Sat, 24 Aug 2019 17:58:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:58:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.05_summits.bed INFO @ Sat, 24 Aug 2019 17:59:07: Done! pass1 - making usageList (125 chroms): 15 millis pass2 - checking and writing primary data (41360 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:59:19: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:59:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.10_summits.bed INFO @ Sat, 24 Aug 2019 17:59:49: Done! pass1 - making usageList (106 chroms): 11 millis pass2 - checking and writing primary data (30341 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375005/SRX5375005.20_summits.bed INFO @ Sat, 24 Aug 2019 17:59:55: Done! pass1 - making usageList (81 chroms): 4 millis pass2 - checking and writing primary data (19050 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。