Job ID = 2640718 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:25:48 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 ) 2019-08-24T09:25:48 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 ) 2019-08-24T09:33:26 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 ) spots read : 24,774,867 reads read : 49,549,734 reads written : 24,774,867 reads 0-length : 24,774,867 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: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:21:04 24774867 reads; of these: 24774867 (100.00%) were unpaired; of these: 668957 (2.70%) aligned 0 times 18976444 (76.60%) aligned exactly 1 time 5129466 (20.70%) aligned >1 times 97.30% overall alignment rate Time searching: 00:21:11 Overall time: 00:21:11 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] 5651267 / 24105910 = 0.2344 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.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 19:01:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:01:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:02:06: 1000000 INFO @ Sat, 24 Aug 2019 19:02:14: 2000000 INFO @ Sat, 24 Aug 2019 19:02:21: 3000000 INFO @ Sat, 24 Aug 2019 19:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.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 19:02:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:02:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:02:29: 4000000 INFO @ Sat, 24 Aug 2019 19:02:36: 5000000 INFO @ Sat, 24 Aug 2019 19:02:37: 1000000 INFO @ Sat, 24 Aug 2019 19:02:44: 6000000 INFO @ Sat, 24 Aug 2019 19:02:47: 2000000 INFO @ Sat, 24 Aug 2019 19:02:52: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.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 19:02:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:02:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:02:57: 3000000 INFO @ Sat, 24 Aug 2019 19:02:59: 8000000 INFO @ Sat, 24 Aug 2019 19:03:06: 1000000 INFO @ Sat, 24 Aug 2019 19:03:07: 9000000 INFO @ Sat, 24 Aug 2019 19:03:08: 4000000 INFO @ Sat, 24 Aug 2019 19:03:15: 2000000 INFO @ Sat, 24 Aug 2019 19:03:15: 10000000 INFO @ Sat, 24 Aug 2019 19:03:18: 5000000 INFO @ Sat, 24 Aug 2019 19:03:23: 11000000 INFO @ Sat, 24 Aug 2019 19:03:23: 3000000 INFO @ Sat, 24 Aug 2019 19:03:28: 6000000 INFO @ Sat, 24 Aug 2019 19:03:31: 12000000 INFO @ Sat, 24 Aug 2019 19:03:32: 4000000 INFO @ Sat, 24 Aug 2019 19:03:38: 13000000 INFO @ Sat, 24 Aug 2019 19:03:39: 7000000 INFO @ Sat, 24 Aug 2019 19:03:41: 5000000 INFO @ Sat, 24 Aug 2019 19:03:47: 14000000 INFO @ Sat, 24 Aug 2019 19:03:49: 8000000 INFO @ Sat, 24 Aug 2019 19:03:50: 6000000 INFO @ Sat, 24 Aug 2019 19:03:55: 15000000 INFO @ Sat, 24 Aug 2019 19:03:58: 7000000 INFO @ Sat, 24 Aug 2019 19:03:59: 9000000 INFO @ Sat, 24 Aug 2019 19:04:03: 16000000 INFO @ Sat, 24 Aug 2019 19:04:07: 8000000 INFO @ Sat, 24 Aug 2019 19:04:10: 10000000 INFO @ Sat, 24 Aug 2019 19:04:11: 17000000 INFO @ Sat, 24 Aug 2019 19:04:16: 9000000 INFO @ Sat, 24 Aug 2019 19:04:19: 18000000 INFO @ Sat, 24 Aug 2019 19:04:20: 11000000 INFO @ Sat, 24 Aug 2019 19:04:22: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:04:22: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:04:22: #1 total tags in treatment: 18454643 INFO @ Sat, 24 Aug 2019 19:04:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:04:22: #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 19:04:23: #1 tags after filtering in treatment: 18454489 INFO @ Sat, 24 Aug 2019 19:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:04:23: #1 finished! INFO @ Sat, 24 Aug 2019 19:04:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:04:25: 10000000 INFO @ Sat, 24 Aug 2019 19:04:27: #2 number of paired peaks: 52106 INFO @ Sat, 24 Aug 2019 19:04:27: start model_add_line... INFO @ Sat, 24 Aug 2019 19:04:27: start X-correlation... INFO @ Sat, 24 Aug 2019 19:04:27: end of X-cor INFO @ Sat, 24 Aug 2019 19:04:27: #2 finished! INFO @ Sat, 24 Aug 2019 19:04:27: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:04:27: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 24 Aug 2019 19:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05_model.r INFO @ Sat, 24 Aug 2019 19:04:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:04:31: 12000000 INFO @ Sat, 24 Aug 2019 19:04:33: 11000000 INFO @ Sat, 24 Aug 2019 19:04:41: 13000000 INFO @ Sat, 24 Aug 2019 19:04:42: 12000000 INFO @ Sat, 24 Aug 2019 19:04:51: 13000000 INFO @ Sat, 24 Aug 2019 19:04:53: 14000000 INFO @ Sat, 24 Aug 2019 19:05:01: 14000000 INFO @ Sat, 24 Aug 2019 19:05:04: 15000000 INFO @ Sat, 24 Aug 2019 19:05:11: 15000000 INFO @ Sat, 24 Aug 2019 19:05:14: 16000000 INFO @ Sat, 24 Aug 2019 19:05:20: 16000000 INFO @ Sat, 24 Aug 2019 19:05:24: 17000000 INFO @ Sat, 24 Aug 2019 19:05:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:28: 17000000 INFO @ Sat, 24 Aug 2019 19:05:35: 18000000 INFO @ Sat, 24 Aug 2019 19:05:38: 18000000 INFO @ Sat, 24 Aug 2019 19:05:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:05:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:05:39: #1 total tags in treatment: 18454643 INFO @ Sat, 24 Aug 2019 19:05:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:39: #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 19:05:40: #1 tags after filtering in treatment: 18454489 INFO @ Sat, 24 Aug 2019 19:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:05:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:05:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:05:42: #1 total tags in treatment: 18454643 INFO @ Sat, 24 Aug 2019 19:05:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:42: #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 19:05:42: #1 tags after filtering in treatment: 18454489 INFO @ Sat, 24 Aug 2019 19:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:05:42: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:44: #2 number of paired peaks: 52106 INFO @ Sat, 24 Aug 2019 19:05:44: start model_add_line... INFO @ Sat, 24 Aug 2019 19:05:44: start X-correlation... INFO @ Sat, 24 Aug 2019 19:05:44: end of X-cor INFO @ Sat, 24 Aug 2019 19:05:44: #2 finished! INFO @ Sat, 24 Aug 2019 19:05:44: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:05:44: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 24 Aug 2019 19:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10_model.r INFO @ Sat, 24 Aug 2019 19:05:44: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:05:46: #2 number of paired peaks: 52106 INFO @ Sat, 24 Aug 2019 19:05:46: start model_add_line... INFO @ Sat, 24 Aug 2019 19:05:47: start X-correlation... INFO @ Sat, 24 Aug 2019 19:05:47: end of X-cor INFO @ Sat, 24 Aug 2019 19:05:47: #2 finished! INFO @ Sat, 24 Aug 2019 19:05:47: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:05:47: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 24 Aug 2019 19:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20_model.r INFO @ Sat, 24 Aug 2019 19:05:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.05_summits.bed INFO @ Sat, 24 Aug 2019 19:05:59: Done! pass1 - making usageList (87 chroms): 6 millis pass2 - checking and writing primary data (15688 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:06:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:06:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.10_summits.bed INFO @ Sat, 24 Aug 2019 19:07:16: Done! pass1 - making usageList (73 chroms): 3 millis pass2 - checking and writing primary data (11233 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375069/SRX5375069.20_summits.bed INFO @ Sat, 24 Aug 2019 19:07:19: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (6332 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。