Job ID = 2640531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:34:47 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 ) 2019-08-24T08:34:47 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 ) 2019-08-24T08:34:47 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 ) 2019-08-24T08:34:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-08-24T08:34:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-08-24T08:35:31 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 ) 2019-08-24T08:35:32 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 : 23,700,058 reads read : 47,400,116 reads written : 23,700,058 reads 0-length : 23,700,058 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:36 23700058 reads; of these: 23700058 (100.00%) were unpaired; of these: 569160 (2.40%) aligned 0 times 18897075 (79.73%) aligned exactly 1 time 4233823 (17.86%) aligned >1 times 97.60% overall alignment rate Time searching: 00:15:38 Overall time: 00:15:38 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] 3268940 / 23130898 = 0.1413 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.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 18:01:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:09: 1000000 INFO @ Sat, 24 Aug 2019 18:01:17: 2000000 INFO @ Sat, 24 Aug 2019 18:01:25: 3000000 INFO @ Sat, 24 Aug 2019 18:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.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 18:01:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:33: 4000000 INFO @ Sat, 24 Aug 2019 18:01:41: 1000000 INFO @ Sat, 24 Aug 2019 18:01:41: 5000000 INFO @ Sat, 24 Aug 2019 18:01:50: 6000000 INFO @ Sat, 24 Aug 2019 18:01:51: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:01:59: 7000000 INFO @ Sat, 24 Aug 2019 18:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.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 18:02:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:02:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:02:01: 3000000 INFO @ Sat, 24 Aug 2019 18:02:08: 8000000 INFO @ Sat, 24 Aug 2019 18:02:08: 1000000 INFO @ Sat, 24 Aug 2019 18:02:12: 4000000 INFO @ Sat, 24 Aug 2019 18:02:17: 2000000 INFO @ Sat, 24 Aug 2019 18:02:17: 9000000 INFO @ Sat, 24 Aug 2019 18:02:22: 5000000 INFO @ Sat, 24 Aug 2019 18:02:25: 3000000 INFO @ Sat, 24 Aug 2019 18:02:25: 10000000 INFO @ Sat, 24 Aug 2019 18:02:32: 4000000 INFO @ Sat, 24 Aug 2019 18:02:33: 6000000 INFO @ Sat, 24 Aug 2019 18:02:34: 11000000 INFO @ Sat, 24 Aug 2019 18:02:40: 5000000 INFO @ Sat, 24 Aug 2019 18:02:43: 12000000 INFO @ Sat, 24 Aug 2019 18:02:43: 7000000 INFO @ Sat, 24 Aug 2019 18:02:49: 6000000 INFO @ Sat, 24 Aug 2019 18:02:51: 13000000 INFO @ Sat, 24 Aug 2019 18:02:55: 8000000 INFO @ Sat, 24 Aug 2019 18:02:57: 7000000 INFO @ Sat, 24 Aug 2019 18:03:00: 14000000 INFO @ Sat, 24 Aug 2019 18:03:05: 8000000 INFO @ Sat, 24 Aug 2019 18:03:05: 9000000 INFO @ Sat, 24 Aug 2019 18:03:09: 15000000 INFO @ Sat, 24 Aug 2019 18:03:13: 9000000 INFO @ Sat, 24 Aug 2019 18:03:16: 10000000 INFO @ Sat, 24 Aug 2019 18:03:18: 16000000 INFO @ Sat, 24 Aug 2019 18:03:21: 10000000 INFO @ Sat, 24 Aug 2019 18:03:26: 11000000 INFO @ Sat, 24 Aug 2019 18:03:27: 17000000 INFO @ Sat, 24 Aug 2019 18:03:29: 11000000 INFO @ Sat, 24 Aug 2019 18:03:36: 18000000 INFO @ Sat, 24 Aug 2019 18:03:36: 12000000 INFO @ Sat, 24 Aug 2019 18:03:37: 12000000 INFO @ Sat, 24 Aug 2019 18:03:44: 13000000 INFO @ Sat, 24 Aug 2019 18:03:45: 19000000 INFO @ Sat, 24 Aug 2019 18:03:47: 13000000 INFO @ Sat, 24 Aug 2019 18:03:52: 14000000 INFO @ Sat, 24 Aug 2019 18:03:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:03:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:03:53: #1 total tags in treatment: 19861958 INFO @ Sat, 24 Aug 2019 18:03:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:03:53: #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 18:03:54: #1 tags after filtering in treatment: 19861758 INFO @ Sat, 24 Aug 2019 18:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:03:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:03:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:03:57: 14000000 INFO @ Sat, 24 Aug 2019 18:03:59: #2 number of paired peaks: 66318 INFO @ Sat, 24 Aug 2019 18:03:59: start model_add_line... INFO @ Sat, 24 Aug 2019 18:03:59: start X-correlation... INFO @ Sat, 24 Aug 2019 18:03:59: end of X-cor INFO @ Sat, 24 Aug 2019 18:03:59: #2 finished! INFO @ Sat, 24 Aug 2019 18:03:59: #2 predicted fragment length is 154 bps INFO @ Sat, 24 Aug 2019 18:03:59: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 24 Aug 2019 18:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05_model.r INFO @ Sat, 24 Aug 2019 18:03:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:00: 15000000 INFO @ Sat, 24 Aug 2019 18:04:07: 15000000 INFO @ Sat, 24 Aug 2019 18:04:08: 16000000 INFO @ Sat, 24 Aug 2019 18:04:15: 17000000 INFO @ Sat, 24 Aug 2019 18:04:18: 16000000 INFO @ Sat, 24 Aug 2019 18:04:23: 18000000 INFO @ Sat, 24 Aug 2019 18:04:28: 17000000 INFO @ Sat, 24 Aug 2019 18:04:31: 19000000 INFO @ Sat, 24 Aug 2019 18:04:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:04:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:04:39: #1 total tags in treatment: 19861958 INFO @ Sat, 24 Aug 2019 18:04:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:39: #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 18:04:39: 18000000 INFO @ Sat, 24 Aug 2019 18:04:39: #1 tags after filtering in treatment: 19861758 INFO @ Sat, 24 Aug 2019 18:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:39: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:44: #2 number of paired peaks: 66318 INFO @ Sat, 24 Aug 2019 18:04:44: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:45: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:45: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:45: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:45: #2 predicted fragment length is 154 bps INFO @ Sat, 24 Aug 2019 18:04:45: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 24 Aug 2019 18:04:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20_model.r INFO @ Sat, 24 Aug 2019 18:04:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:49: 19000000 INFO @ Sat, 24 Aug 2019 18:04:58: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:04:58: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:04:58: #1 total tags in treatment: 19861958 INFO @ Sat, 24 Aug 2019 18:04:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:58: #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 18:04:59: #1 tags after filtering in treatment: 19861758 INFO @ Sat, 24 Aug 2019 18:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:59: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:05:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:05:04: #2 number of paired peaks: 66318 INFO @ Sat, 24 Aug 2019 18:05:04: start model_add_line... INFO @ Sat, 24 Aug 2019 18:05:04: start X-correlation... INFO @ Sat, 24 Aug 2019 18:05:04: end of X-cor INFO @ Sat, 24 Aug 2019 18:05:04: #2 finished! INFO @ Sat, 24 Aug 2019 18:05:04: #2 predicted fragment length is 154 bps INFO @ Sat, 24 Aug 2019 18:05:04: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 24 Aug 2019 18:05:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10_model.r INFO @ Sat, 24 Aug 2019 18:05:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:05:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.05_summits.bed INFO @ Sat, 24 Aug 2019 18:05:37: Done! pass1 - making usageList (127 chroms): 15 millis pass2 - checking and writing primary data (39493 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:05:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.20_summits.bed INFO @ Sat, 24 Aug 2019 18:06:21: Done! pass1 - making usageList (81 chroms): 4 millis pass2 - checking and writing primary data (15757 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375007/SRX5375007.10_summits.bed INFO @ Sat, 24 Aug 2019 18:06:41: Done! pass1 - making usageList (102 chroms): 10 millis pass2 - checking and writing primary data (27627 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。