Job ID = 2003228 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T03:07:51 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 ) 2019-07-05T03:07:51 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 ) 2019-07-05T03:07:51 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 ) 2019-07-05T03:07:51 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 ) 2019-07-05T03:09:55 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 ) 2019-07-05T03:09:55 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 ) 2019-07-05T03:13:55 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 ) 2019-07-05T03:14:49 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 ) 2019-07-05T03:15:50 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 ) 2019-07-05T03:15:50 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 : 41,923,807 reads read : 41,923,807 reads written : 41,923,807 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: 00:16:43 41923807 reads; of these: 41923807 (100.00%) were unpaired; of these: 5630031 (13.43%) aligned 0 times 26615642 (63.49%) aligned exactly 1 time 9678134 (23.09%) aligned >1 times 86.57% overall alignment rate Time searching: 00:16:45 Overall time: 00:16:45 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] 1014884 / 36293776 = 0.0280 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 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.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 13:05:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:05:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.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 13:05:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:05:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.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 13:05:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:05:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:05:10: 1000000 INFO @ Fri, 05 Jul 2019 13:05:10: 1000000 INFO @ Fri, 05 Jul 2019 13:05:11: 1000000 INFO @ Fri, 05 Jul 2019 13:05:17: 2000000 INFO @ Fri, 05 Jul 2019 13:05:18: 2000000 INFO @ Fri, 05 Jul 2019 13:05:20: 2000000 INFO @ Fri, 05 Jul 2019 13:05:25: 3000000 INFO @ Fri, 05 Jul 2019 13:05:26: 3000000 INFO @ Fri, 05 Jul 2019 13:05:28: 3000000 INFO @ Fri, 05 Jul 2019 13:05:33: 4000000 INFO @ Fri, 05 Jul 2019 13:05:34: 4000000 INFO @ Fri, 05 Jul 2019 13:05:37: 4000000 INFO @ Fri, 05 Jul 2019 13:05:41: 5000000 INFO @ Fri, 05 Jul 2019 13:05:42: 5000000 INFO @ Fri, 05 Jul 2019 13:05:46: 5000000 INFO @ Fri, 05 Jul 2019 13:05:49: 6000000 INFO @ Fri, 05 Jul 2019 13:05:50: 6000000 INFO @ Fri, 05 Jul 2019 13:05:54: 6000000 INFO @ Fri, 05 Jul 2019 13:05:57: 7000000 INFO @ Fri, 05 Jul 2019 13:05:58: 7000000 INFO @ Fri, 05 Jul 2019 13:06:03: 7000000 INFO @ Fri, 05 Jul 2019 13:06:05: 8000000 INFO @ Fri, 05 Jul 2019 13:06:05: 8000000 INFO @ Fri, 05 Jul 2019 13:06:12: 8000000 INFO @ Fri, 05 Jul 2019 13:06:13: 9000000 INFO @ Fri, 05 Jul 2019 13:06:13: 9000000 INFO @ Fri, 05 Jul 2019 13:06:20: 10000000 INFO @ Fri, 05 Jul 2019 13:06:20: 9000000 INFO @ Fri, 05 Jul 2019 13:06:21: 10000000 INFO @ Fri, 05 Jul 2019 13:06:28: 11000000 INFO @ Fri, 05 Jul 2019 13:06:29: 10000000 INFO @ Fri, 05 Jul 2019 13:06:29: 11000000 INFO @ Fri, 05 Jul 2019 13:06:37: 12000000 INFO @ Fri, 05 Jul 2019 13:06:37: 12000000 INFO @ Fri, 05 Jul 2019 13:06:38: 11000000 INFO @ Fri, 05 Jul 2019 13:06:45: 13000000 INFO @ Fri, 05 Jul 2019 13:06:46: 13000000 INFO @ Fri, 05 Jul 2019 13:06:49: 12000000 INFO @ Fri, 05 Jul 2019 13:06:54: 14000000 INFO @ Fri, 05 Jul 2019 13:06:54: 14000000 INFO @ Fri, 05 Jul 2019 13:07:00: 13000000 INFO @ Fri, 05 Jul 2019 13:07:02: 15000000 INFO @ Fri, 05 Jul 2019 13:07:02: 15000000 INFO @ Fri, 05 Jul 2019 13:07:08: 14000000 INFO @ Fri, 05 Jul 2019 13:07:10: 16000000 INFO @ Fri, 05 Jul 2019 13:07:10: 16000000 INFO @ Fri, 05 Jul 2019 13:07:17: 15000000 INFO @ Fri, 05 Jul 2019 13:07:18: 17000000 INFO @ Fri, 05 Jul 2019 13:07:18: 17000000 INFO @ Fri, 05 Jul 2019 13:07:25: 18000000 INFO @ Fri, 05 Jul 2019 13:07:26: 16000000 INFO @ Fri, 05 Jul 2019 13:07:26: 18000000 INFO @ Fri, 05 Jul 2019 13:07:34: 19000000 INFO @ Fri, 05 Jul 2019 13:07:35: 17000000 INFO @ Fri, 05 Jul 2019 13:07:35: 19000000 INFO @ Fri, 05 Jul 2019 13:07:41: 20000000 INFO @ Fri, 05 Jul 2019 13:07:44: 18000000 INFO @ Fri, 05 Jul 2019 13:07:45: 20000000 INFO @ Fri, 05 Jul 2019 13:07:49: 21000000 INFO @ Fri, 05 Jul 2019 13:07:53: 19000000 INFO @ Fri, 05 Jul 2019 13:07:53: 21000000 INFO @ Fri, 05 Jul 2019 13:07:57: 22000000 INFO @ Fri, 05 Jul 2019 13:08:01: 22000000 INFO @ Fri, 05 Jul 2019 13:08:01: 20000000 INFO @ Fri, 05 Jul 2019 13:08:04: 23000000 INFO @ Fri, 05 Jul 2019 13:08:09: 23000000 INFO @ Fri, 05 Jul 2019 13:08:10: 21000000 INFO @ Fri, 05 Jul 2019 13:08:12: 24000000 INFO @ Fri, 05 Jul 2019 13:08:17: 24000000 INFO @ Fri, 05 Jul 2019 13:08:19: 22000000 INFO @ Fri, 05 Jul 2019 13:08:20: 25000000 INFO @ Fri, 05 Jul 2019 13:08:25: 25000000 INFO @ Fri, 05 Jul 2019 13:08:28: 26000000 INFO @ Fri, 05 Jul 2019 13:08:28: 23000000 INFO @ Fri, 05 Jul 2019 13:08:34: 26000000 INFO @ Fri, 05 Jul 2019 13:08:36: 27000000 INFO @ Fri, 05 Jul 2019 13:08:37: 24000000 INFO @ Fri, 05 Jul 2019 13:08:42: 27000000 INFO @ Fri, 05 Jul 2019 13:08:44: 28000000 INFO @ Fri, 05 Jul 2019 13:08:46: 25000000 INFO @ Fri, 05 Jul 2019 13:08:50: 28000000 INFO @ Fri, 05 Jul 2019 13:08:52: 29000000 INFO @ Fri, 05 Jul 2019 13:08:55: 26000000 INFO @ Fri, 05 Jul 2019 13:08:58: 29000000 INFO @ Fri, 05 Jul 2019 13:08:59: 30000000 INFO @ Fri, 05 Jul 2019 13:09:04: 27000000 INFO @ Fri, 05 Jul 2019 13:09:06: 30000000 INFO @ Fri, 05 Jul 2019 13:09:07: 31000000 INFO @ Fri, 05 Jul 2019 13:09:13: 28000000 INFO @ Fri, 05 Jul 2019 13:09:14: 31000000 INFO @ Fri, 05 Jul 2019 13:09:15: 32000000 INFO @ Fri, 05 Jul 2019 13:09:22: 32000000 INFO @ Fri, 05 Jul 2019 13:09:22: 29000000 INFO @ Fri, 05 Jul 2019 13:09:23: 33000000 INFO @ Fri, 05 Jul 2019 13:09:30: 33000000 INFO @ Fri, 05 Jul 2019 13:09:30: 34000000 INFO @ Fri, 05 Jul 2019 13:09:31: 30000000 INFO @ Fri, 05 Jul 2019 13:09:38: 34000000 INFO @ Fri, 05 Jul 2019 13:09:38: 35000000 INFO @ Fri, 05 Jul 2019 13:09:40: 31000000 INFO @ Fri, 05 Jul 2019 13:09:41: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:09:41: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:09:41: #1 total tags in treatment: 35278892 INFO @ Fri, 05 Jul 2019 13:09:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:09:41: #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 13:09:42: #1 tags after filtering in treatment: 35278808 INFO @ Fri, 05 Jul 2019 13:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:09:42: #1 finished! INFO @ Fri, 05 Jul 2019 13:09:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:09:46: #2 number of paired peaks: 4633 INFO @ Fri, 05 Jul 2019 13:09:46: start model_add_line... INFO @ Fri, 05 Jul 2019 13:09:46: 35000000 INFO @ Fri, 05 Jul 2019 13:09:46: start X-correlation... INFO @ Fri, 05 Jul 2019 13:09:46: end of X-cor INFO @ Fri, 05 Jul 2019 13:09:46: #2 finished! INFO @ Fri, 05 Jul 2019 13:09:46: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 13:09:46: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 05 Jul 2019 13:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20_model.r WARNING @ Fri, 05 Jul 2019 13:09:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:09:46: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 05 Jul 2019 13:09:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:09:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:09:48: 32000000 INFO @ Fri, 05 Jul 2019 13:09:49: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:09:49: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:09:49: #1 total tags in treatment: 35278892 INFO @ Fri, 05 Jul 2019 13:09:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:09:49: #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 13:09:49: #1 tags after filtering in treatment: 35278808 INFO @ Fri, 05 Jul 2019 13:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:09:49: #1 finished! INFO @ Fri, 05 Jul 2019 13:09:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:09:53: #2 number of paired peaks: 4633 INFO @ Fri, 05 Jul 2019 13:09:53: start model_add_line... INFO @ Fri, 05 Jul 2019 13:09:54: start X-correlation... INFO @ Fri, 05 Jul 2019 13:09:54: end of X-cor INFO @ Fri, 05 Jul 2019 13:09:54: #2 finished! INFO @ Fri, 05 Jul 2019 13:09:54: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 13:09:54: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 05 Jul 2019 13:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05_model.r WARNING @ Fri, 05 Jul 2019 13:09:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:09:54: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 05 Jul 2019 13:09:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:09:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:09:57: 33000000 INFO @ Fri, 05 Jul 2019 13:10:06: 34000000 INFO @ Fri, 05 Jul 2019 13:10:15: 35000000 INFO @ Fri, 05 Jul 2019 13:10:18: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:10:18: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:10:18: #1 total tags in treatment: 35278892 INFO @ Fri, 05 Jul 2019 13:10:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:10:18: #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 13:10:19: #1 tags after filtering in treatment: 35278808 INFO @ Fri, 05 Jul 2019 13:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:10:19: #1 finished! INFO @ Fri, 05 Jul 2019 13:10:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:10:23: #2 number of paired peaks: 4633 INFO @ Fri, 05 Jul 2019 13:10:23: start model_add_line... INFO @ Fri, 05 Jul 2019 13:10:23: start X-correlation... INFO @ Fri, 05 Jul 2019 13:10:23: end of X-cor INFO @ Fri, 05 Jul 2019 13:10:23: #2 finished! INFO @ Fri, 05 Jul 2019 13:10:23: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 13:10:23: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 05 Jul 2019 13:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10_model.r WARNING @ Fri, 05 Jul 2019 13:10:23: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:10:23: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 05 Jul 2019 13:10:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:10:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:11:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:11:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:12:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.20_summits.bed INFO @ Fri, 05 Jul 2019 13:12:31: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.05_summits.bed INFO @ Fri, 05 Jul 2019 13:12:43: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (2725 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181520/SRX181520.10_summits.bed INFO @ Fri, 05 Jul 2019 13:13:08: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (1297 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。