Job ID = 2640569 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:43:20 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 ) 2019-08-24T08:43:20 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 ) 2019-08-24T08:43:20 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 ) 2019-08-24T08:43:20 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 ) 2019-08-24T08:45:27 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 ) 2019-08-24T08:45:27 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 ) 2019-08-24T08:45:27 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 ) 2019-08-24T08:46:20 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 : 21,529,078 reads read : 43,058,156 reads written : 21,529,078 reads 0-length : 21,529,078 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: 00:14:56 21529078 reads; of these: 21529078 (100.00%) were unpaired; of these: 486164 (2.26%) aligned 0 times 16891188 (78.46%) aligned exactly 1 time 4151726 (19.28%) aligned >1 times 97.74% overall alignment rate Time searching: 00:14:59 Overall time: 00:14:59 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] 6841321 / 21042914 = 0.3251 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.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 18:09:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:22: 1000000 INFO @ Sat, 24 Aug 2019 18:09:28: 2000000 INFO @ Sat, 24 Aug 2019 18:09:35: 3000000 INFO @ Sat, 24 Aug 2019 18:09:42: 4000000 INFO @ Sat, 24 Aug 2019 18:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.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 18:09:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:49: 5000000 INFO @ Sat, 24 Aug 2019 18:09:52: 1000000 INFO @ Sat, 24 Aug 2019 18:09:56: 6000000 INFO @ Sat, 24 Aug 2019 18:09:59: 2000000 INFO @ Sat, 24 Aug 2019 18:10:03: 7000000 INFO @ Sat, 24 Aug 2019 18:10:07: 3000000 INFO @ Sat, 24 Aug 2019 18:10:10: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.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 18:10:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:10:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:10:14: 4000000 INFO @ Sat, 24 Aug 2019 18:10:17: 9000000 INFO @ Sat, 24 Aug 2019 18:10:22: 5000000 INFO @ Sat, 24 Aug 2019 18:10:23: 1000000 INFO @ Sat, 24 Aug 2019 18:10:24: 10000000 INFO @ Sat, 24 Aug 2019 18:10:30: 6000000 INFO @ Sat, 24 Aug 2019 18:10:31: 11000000 INFO @ Sat, 24 Aug 2019 18:10:32: 2000000 INFO @ Sat, 24 Aug 2019 18:10:37: 7000000 INFO @ Sat, 24 Aug 2019 18:10:38: 12000000 INFO @ Sat, 24 Aug 2019 18:10:40: 3000000 INFO @ Sat, 24 Aug 2019 18:10:45: 13000000 INFO @ Sat, 24 Aug 2019 18:10:46: 8000000 INFO @ Sat, 24 Aug 2019 18:10:50: 4000000 INFO @ Sat, 24 Aug 2019 18:10:52: 14000000 INFO @ Sat, 24 Aug 2019 18:10:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:10:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:10:53: #1 total tags in treatment: 14201593 INFO @ Sat, 24 Aug 2019 18:10:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:10:53: #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 18:10:54: #1 tags after filtering in treatment: 14201388 INFO @ Sat, 24 Aug 2019 18:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:10:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:10:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:10:54: 9000000 INFO @ Sat, 24 Aug 2019 18:10:57: #2 number of paired peaks: 60741 INFO @ Sat, 24 Aug 2019 18:10:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:10:58: start X-correlation... INFO @ Sat, 24 Aug 2019 18:10:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:10:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:10:58: #2 predicted fragment length is 170 bps INFO @ Sat, 24 Aug 2019 18:10:58: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 24 Aug 2019 18:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05_model.r INFO @ Sat, 24 Aug 2019 18:10:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:10:59: 5000000 INFO @ Sat, 24 Aug 2019 18:11:01: 10000000 INFO @ Sat, 24 Aug 2019 18:11:08: 6000000 INFO @ Sat, 24 Aug 2019 18:11:09: 11000000 INFO @ Sat, 24 Aug 2019 18:11:16: 12000000 INFO @ Sat, 24 Aug 2019 18:11:17: 7000000 INFO @ Sat, 24 Aug 2019 18:11:24: 13000000 INFO @ Sat, 24 Aug 2019 18:11:26: 8000000 INFO @ Sat, 24 Aug 2019 18:11:32: 14000000 INFO @ Sat, 24 Aug 2019 18:11:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:11:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:11:33: #1 total tags in treatment: 14201593 INFO @ Sat, 24 Aug 2019 18:11:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:11:33: #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 18:11:34: #1 tags after filtering in treatment: 14201388 INFO @ Sat, 24 Aug 2019 18:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:11:34: #1 finished! INFO @ Sat, 24 Aug 2019 18:11:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:11:35: 9000000 INFO @ Sat, 24 Aug 2019 18:11:38: #2 number of paired peaks: 60741 INFO @ Sat, 24 Aug 2019 18:11:38: start model_add_line... INFO @ Sat, 24 Aug 2019 18:11:38: start X-correlation... INFO @ Sat, 24 Aug 2019 18:11:38: end of X-cor INFO @ Sat, 24 Aug 2019 18:11:38: #2 finished! INFO @ Sat, 24 Aug 2019 18:11:38: #2 predicted fragment length is 170 bps INFO @ Sat, 24 Aug 2019 18:11:38: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 24 Aug 2019 18:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10_model.r INFO @ Sat, 24 Aug 2019 18:11:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:11:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:11:44: 10000000 INFO @ Sat, 24 Aug 2019 18:11:53: 11000000 INFO @ Sat, 24 Aug 2019 18:12:02: 12000000 INFO @ Sat, 24 Aug 2019 18:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:12:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.05_summits.bed INFO @ Sat, 24 Aug 2019 18:12:08: Done! pass1 - making usageList (91 chroms): 7 millis pass2 - checking and writing primary data (16440 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:12:11: 13000000 INFO @ Sat, 24 Aug 2019 18:12:19: 14000000 INFO @ Sat, 24 Aug 2019 18:12:21: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:12:21: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:12:21: #1 total tags in treatment: 14201593 INFO @ Sat, 24 Aug 2019 18:12:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:12:21: #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 18:12:22: #1 tags after filtering in treatment: 14201388 INFO @ Sat, 24 Aug 2019 18:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:12:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:12:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:12:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:12:25: #2 number of paired peaks: 60741 INFO @ Sat, 24 Aug 2019 18:12:25: start model_add_line... INFO @ Sat, 24 Aug 2019 18:12:26: start X-correlation... INFO @ Sat, 24 Aug 2019 18:12:26: end of X-cor INFO @ Sat, 24 Aug 2019 18:12:26: #2 finished! INFO @ Sat, 24 Aug 2019 18:12:26: #2 predicted fragment length is 170 bps INFO @ Sat, 24 Aug 2019 18:12:26: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 24 Aug 2019 18:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20_model.r INFO @ Sat, 24 Aug 2019 18:12:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.10_summits.bed INFO @ Sat, 24 Aug 2019 18:12:48: Done! pass1 - making usageList (71 chroms): 3 millis pass2 - checking and writing primary data (11730 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:13:12: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375015/SRX5375015.20_summits.bed INFO @ Sat, 24 Aug 2019 18:13:37: Done! pass1 - making usageList (46 chroms): 4 millis pass2 - checking and writing primary data (6497 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。