Job ID = 2640484 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:14:46 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 ) 2019-08-24T08:14:46 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 : 19,401,558 reads read : 38,803,116 reads written : 19,401,558 reads 0-length : 19,401,558 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: 00:14:01 19401558 reads; of these: 19401558 (100.00%) were unpaired; of these: 400236 (2.06%) aligned 0 times 16154915 (83.27%) aligned exactly 1 time 2846407 (14.67%) aligned >1 times 97.94% 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 8 files... [bam_rmdupse_core] 2118707 / 19001322 = 0.1115 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.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 17:39:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:39:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:39:12: 1000000 INFO @ Sat, 24 Aug 2019 17:39:18: 2000000 INFO @ Sat, 24 Aug 2019 17:39:24: 3000000 INFO @ Sat, 24 Aug 2019 17:39:31: 4000000 INFO @ Sat, 24 Aug 2019 17:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.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 17:39:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:39:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:39:37: 5000000 INFO @ Sat, 24 Aug 2019 17:39:42: 1000000 INFO @ Sat, 24 Aug 2019 17:39:44: 6000000 INFO @ Sat, 24 Aug 2019 17:39:49: 2000000 INFO @ Sat, 24 Aug 2019 17:39:51: 7000000 INFO @ Sat, 24 Aug 2019 17:39:57: 3000000 INFO @ Sat, 24 Aug 2019 17:39:58: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:40:04: 4000000 INFO @ Sat, 24 Aug 2019 17:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.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 17:40:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:40:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:40:05: 9000000 INFO @ Sat, 24 Aug 2019 17:40:11: 5000000 INFO @ Sat, 24 Aug 2019 17:40:12: 10000000 INFO @ Sat, 24 Aug 2019 17:40:14: 1000000 INFO @ Sat, 24 Aug 2019 17:40:18: 6000000 INFO @ Sat, 24 Aug 2019 17:40:19: 11000000 INFO @ Sat, 24 Aug 2019 17:40:22: 2000000 INFO @ Sat, 24 Aug 2019 17:40:25: 7000000 INFO @ Sat, 24 Aug 2019 17:40:26: 12000000 INFO @ Sat, 24 Aug 2019 17:40:31: 3000000 INFO @ Sat, 24 Aug 2019 17:40:32: 8000000 INFO @ Sat, 24 Aug 2019 17:40:32: 13000000 INFO @ Sat, 24 Aug 2019 17:40:39: 14000000 INFO @ Sat, 24 Aug 2019 17:40:39: 9000000 INFO @ Sat, 24 Aug 2019 17:40:39: 4000000 INFO @ Sat, 24 Aug 2019 17:40:45: 15000000 INFO @ Sat, 24 Aug 2019 17:40:46: 10000000 INFO @ Sat, 24 Aug 2019 17:40:48: 5000000 INFO @ Sat, 24 Aug 2019 17:40:52: 16000000 INFO @ Sat, 24 Aug 2019 17:40:53: 11000000 INFO @ Sat, 24 Aug 2019 17:40:56: 6000000 INFO @ Sat, 24 Aug 2019 17:40:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:40:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:40:59: #1 total tags in treatment: 16882615 INFO @ Sat, 24 Aug 2019 17:40:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:40:59: #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 17:40:59: #1 tags after filtering in treatment: 16882367 INFO @ Sat, 24 Aug 2019 17:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:40:59: #1 finished! INFO @ Sat, 24 Aug 2019 17:40:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:00: 12000000 INFO @ Sat, 24 Aug 2019 17:41:05: #2 number of paired peaks: 99749 INFO @ Sat, 24 Aug 2019 17:41:05: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:05: 7000000 INFO @ Sat, 24 Aug 2019 17:41:05: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:05: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:05: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:05: #2 predicted fragment length is 176 bps INFO @ Sat, 24 Aug 2019 17:41:05: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 24 Aug 2019 17:41:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05_model.r INFO @ Sat, 24 Aug 2019 17:41:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:07: 13000000 INFO @ Sat, 24 Aug 2019 17:41:13: 8000000 INFO @ Sat, 24 Aug 2019 17:41:14: 14000000 INFO @ Sat, 24 Aug 2019 17:41:22: 15000000 INFO @ Sat, 24 Aug 2019 17:41:22: 9000000 INFO @ Sat, 24 Aug 2019 17:41:29: 16000000 INFO @ Sat, 24 Aug 2019 17:41:30: 10000000 INFO @ Sat, 24 Aug 2019 17:41:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:41:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:41:36: #1 total tags in treatment: 16882615 INFO @ Sat, 24 Aug 2019 17:41:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:36: #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 17:41:36: #1 tags after filtering in treatment: 16882367 INFO @ Sat, 24 Aug 2019 17:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:36: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:39: 11000000 INFO @ Sat, 24 Aug 2019 17:41:42: #2 number of paired peaks: 99749 INFO @ Sat, 24 Aug 2019 17:41:42: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:42: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:42: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:42: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:42: #2 predicted fragment length is 176 bps INFO @ Sat, 24 Aug 2019 17:41:42: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 24 Aug 2019 17:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10_model.r INFO @ Sat, 24 Aug 2019 17:41:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:47: 12000000 INFO @ Sat, 24 Aug 2019 17:41:55: 13000000 INFO @ Sat, 24 Aug 2019 17:41:59: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:04: 14000000 INFO @ Sat, 24 Aug 2019 17:42:12: 15000000 INFO @ Sat, 24 Aug 2019 17:42:20: 16000000 INFO @ Sat, 24 Aug 2019 17:42:28: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:42:28: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:42:28: #1 total tags in treatment: 16882615 INFO @ Sat, 24 Aug 2019 17:42:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:42:28: #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 17:42:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:28: #1 tags after filtering in treatment: 16882367 INFO @ Sat, 24 Aug 2019 17:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:42:28: #1 finished! INFO @ Sat, 24 Aug 2019 17:42:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.05_summits.bed INFO @ Sat, 24 Aug 2019 17:42:29: Done! pass1 - making usageList (121 chroms): 13 millis pass2 - checking and writing primary data (44409 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:42:34: #2 number of paired peaks: 99749 INFO @ Sat, 24 Aug 2019 17:42:34: start model_add_line... INFO @ Sat, 24 Aug 2019 17:42:34: start X-correlation... INFO @ Sat, 24 Aug 2019 17:42:34: end of X-cor INFO @ Sat, 24 Aug 2019 17:42:34: #2 finished! INFO @ Sat, 24 Aug 2019 17:42:34: #2 predicted fragment length is 176 bps INFO @ Sat, 24 Aug 2019 17:42:34: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 24 Aug 2019 17:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20_model.r INFO @ Sat, 24 Aug 2019 17:42:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:42:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.10_summits.bed INFO @ Sat, 24 Aug 2019 17:43:07: Done! pass1 - making usageList (92 chroms): 9 millis pass2 - checking and writing primary data (26024 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:43:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374994/SRX5374994.20_summits.bed INFO @ Sat, 24 Aug 2019 17:43:55: Done! pass1 - making usageList (54 chroms): 5 millis pass2 - checking and writing primary data (9297 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。