Job ID = 2001553 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:40:53 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T19:45:04 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 ) 2019-07-04T19:45:04 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 : 35,412,920 reads read : 35,412,920 reads written : 35,412,920 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:03 35412920 reads; of these: 35412920 (100.00%) were unpaired; of these: 783887 (2.21%) aligned 0 times 26124880 (73.77%) aligned exactly 1 time 8504153 (24.01%) aligned >1 times 97.79% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 2423104 / 34629033 = 0.0700 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 05:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.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 05:20:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:20:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.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 05:20:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:20:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.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 05:20:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:20:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:20:35: 1000000 INFO @ Fri, 05 Jul 2019 05:20:35: 1000000 INFO @ Fri, 05 Jul 2019 05:20:36: 1000000 INFO @ Fri, 05 Jul 2019 05:20:45: 2000000 INFO @ Fri, 05 Jul 2019 05:20:45: 2000000 INFO @ Fri, 05 Jul 2019 05:20:45: 2000000 INFO @ Fri, 05 Jul 2019 05:20:54: 3000000 INFO @ Fri, 05 Jul 2019 05:20:55: 3000000 INFO @ Fri, 05 Jul 2019 05:20:55: 3000000 INFO @ Fri, 05 Jul 2019 05:21:05: 4000000 INFO @ Fri, 05 Jul 2019 05:21:06: 4000000 INFO @ Fri, 05 Jul 2019 05:21:06: 4000000 INFO @ Fri, 05 Jul 2019 05:21:16: 5000000 INFO @ Fri, 05 Jul 2019 05:21:17: 5000000 INFO @ Fri, 05 Jul 2019 05:21:17: 5000000 INFO @ Fri, 05 Jul 2019 05:21:28: 6000000 INFO @ Fri, 05 Jul 2019 05:21:28: 6000000 INFO @ Fri, 05 Jul 2019 05:21:28: 6000000 INFO @ Fri, 05 Jul 2019 05:21:37: 7000000 INFO @ Fri, 05 Jul 2019 05:21:38: 7000000 INFO @ Fri, 05 Jul 2019 05:21:39: 7000000 INFO @ Fri, 05 Jul 2019 05:21:47: 8000000 INFO @ Fri, 05 Jul 2019 05:21:47: 8000000 INFO @ Fri, 05 Jul 2019 05:21:48: 8000000 INFO @ Fri, 05 Jul 2019 05:21:58: 9000000 INFO @ Fri, 05 Jul 2019 05:21:58: 9000000 INFO @ Fri, 05 Jul 2019 05:21:59: 9000000 INFO @ Fri, 05 Jul 2019 05:22:09: 10000000 INFO @ Fri, 05 Jul 2019 05:22:10: 10000000 INFO @ Fri, 05 Jul 2019 05:22:10: 10000000 INFO @ Fri, 05 Jul 2019 05:22:20: 11000000 INFO @ Fri, 05 Jul 2019 05:22:21: 11000000 INFO @ Fri, 05 Jul 2019 05:22:21: 11000000 INFO @ Fri, 05 Jul 2019 05:22:31: 12000000 INFO @ Fri, 05 Jul 2019 05:22:32: 12000000 INFO @ Fri, 05 Jul 2019 05:22:32: 12000000 INFO @ Fri, 05 Jul 2019 05:22:42: 13000000 INFO @ Fri, 05 Jul 2019 05:22:43: 13000000 INFO @ Fri, 05 Jul 2019 05:22:43: 13000000 INFO @ Fri, 05 Jul 2019 05:22:53: 14000000 INFO @ Fri, 05 Jul 2019 05:22:54: 14000000 INFO @ Fri, 05 Jul 2019 05:22:54: 14000000 INFO @ Fri, 05 Jul 2019 05:23:04: 15000000 INFO @ Fri, 05 Jul 2019 05:23:04: 15000000 INFO @ Fri, 05 Jul 2019 05:23:05: 15000000 INFO @ Fri, 05 Jul 2019 05:23:15: 16000000 INFO @ Fri, 05 Jul 2019 05:23:15: 16000000 INFO @ Fri, 05 Jul 2019 05:23:16: 16000000 INFO @ Fri, 05 Jul 2019 05:23:26: 17000000 INFO @ Fri, 05 Jul 2019 05:23:27: 17000000 INFO @ Fri, 05 Jul 2019 05:23:28: 17000000 INFO @ Fri, 05 Jul 2019 05:23:37: 18000000 INFO @ Fri, 05 Jul 2019 05:23:37: 18000000 INFO @ Fri, 05 Jul 2019 05:23:39: 18000000 INFO @ Fri, 05 Jul 2019 05:23:46: 19000000 INFO @ Fri, 05 Jul 2019 05:23:46: 19000000 INFO @ Fri, 05 Jul 2019 05:23:48: 19000000 INFO @ Fri, 05 Jul 2019 05:23:56: 20000000 INFO @ Fri, 05 Jul 2019 05:23:56: 20000000 INFO @ Fri, 05 Jul 2019 05:23:58: 20000000 INFO @ Fri, 05 Jul 2019 05:24:06: 21000000 INFO @ Fri, 05 Jul 2019 05:24:06: 21000000 INFO @ Fri, 05 Jul 2019 05:24:07: 21000000 INFO @ Fri, 05 Jul 2019 05:24:15: 22000000 INFO @ Fri, 05 Jul 2019 05:24:15: 22000000 INFO @ Fri, 05 Jul 2019 05:24:16: 22000000 INFO @ Fri, 05 Jul 2019 05:24:25: 23000000 INFO @ Fri, 05 Jul 2019 05:24:26: 23000000 INFO @ Fri, 05 Jul 2019 05:24:26: 23000000 INFO @ Fri, 05 Jul 2019 05:24:35: 24000000 INFO @ Fri, 05 Jul 2019 05:24:35: 24000000 INFO @ Fri, 05 Jul 2019 05:24:36: 24000000 INFO @ Fri, 05 Jul 2019 05:24:45: 25000000 INFO @ Fri, 05 Jul 2019 05:24:45: 25000000 INFO @ Fri, 05 Jul 2019 05:24:46: 25000000 INFO @ Fri, 05 Jul 2019 05:24:55: 26000000 INFO @ Fri, 05 Jul 2019 05:24:55: 26000000 INFO @ Fri, 05 Jul 2019 05:24:56: 26000000 INFO @ Fri, 05 Jul 2019 05:25:05: 27000000 INFO @ Fri, 05 Jul 2019 05:25:05: 27000000 INFO @ Fri, 05 Jul 2019 05:25:05: 27000000 INFO @ Fri, 05 Jul 2019 05:25:14: 28000000 INFO @ Fri, 05 Jul 2019 05:25:15: 28000000 INFO @ Fri, 05 Jul 2019 05:25:15: 28000000 INFO @ Fri, 05 Jul 2019 05:25:23: 29000000 INFO @ Fri, 05 Jul 2019 05:25:25: 29000000 INFO @ Fri, 05 Jul 2019 05:25:25: 29000000 INFO @ Fri, 05 Jul 2019 05:25:33: 30000000 INFO @ Fri, 05 Jul 2019 05:25:33: 30000000 INFO @ Fri, 05 Jul 2019 05:25:34: 30000000 INFO @ Fri, 05 Jul 2019 05:25:43: 31000000 INFO @ Fri, 05 Jul 2019 05:25:43: 31000000 INFO @ Fri, 05 Jul 2019 05:25:44: 31000000 INFO @ Fri, 05 Jul 2019 05:25:52: 32000000 INFO @ Fri, 05 Jul 2019 05:25:53: 32000000 INFO @ Fri, 05 Jul 2019 05:25:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:25:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:25:54: #1 total tags in treatment: 32205929 INFO @ Fri, 05 Jul 2019 05:25:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:25:54: #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 05:25:54: 32000000 INFO @ Fri, 05 Jul 2019 05:25:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:25:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:25:55: #1 total tags in treatment: 32205929 INFO @ Fri, 05 Jul 2019 05:25:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:25:55: #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 05:25:55: #1 tags after filtering in treatment: 32205797 INFO @ Fri, 05 Jul 2019 05:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:25:55: #1 finished! INFO @ Fri, 05 Jul 2019 05:25:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:25:56: #1 tags after filtering in treatment: 32205797 INFO @ Fri, 05 Jul 2019 05:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:25:56: #1 finished! INFO @ Fri, 05 Jul 2019 05:25:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:25:56: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:25:56: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:25:56: #1 total tags in treatment: 32205929 INFO @ Fri, 05 Jul 2019 05:25:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:25:56: #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 05:25:57: #1 tags after filtering in treatment: 32205797 INFO @ Fri, 05 Jul 2019 05:25:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:25:57: #1 finished! INFO @ Fri, 05 Jul 2019 05:25:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:25:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:26:01: #2 number of paired peaks: 45303 INFO @ Fri, 05 Jul 2019 05:26:01: start model_add_line... INFO @ Fri, 05 Jul 2019 05:26:01: start X-correlation... INFO @ Fri, 05 Jul 2019 05:26:02: end of X-cor INFO @ Fri, 05 Jul 2019 05:26:02: #2 finished! INFO @ Fri, 05 Jul 2019 05:26:02: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:26:02: #2 alternative fragment length(s) may be 132,298,503 bps INFO @ Fri, 05 Jul 2019 05:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20_model.r INFO @ Fri, 05 Jul 2019 05:26:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:26:02: #2 number of paired peaks: 45303 INFO @ Fri, 05 Jul 2019 05:26:02: start model_add_line... INFO @ Fri, 05 Jul 2019 05:26:02: start X-correlation... INFO @ Fri, 05 Jul 2019 05:26:02: end of X-cor INFO @ Fri, 05 Jul 2019 05:26:02: #2 finished! INFO @ Fri, 05 Jul 2019 05:26:02: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:26:02: #2 alternative fragment length(s) may be 132,298,503 bps INFO @ Fri, 05 Jul 2019 05:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05_model.r INFO @ Fri, 05 Jul 2019 05:26:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:26:03: #2 number of paired peaks: 45303 INFO @ Fri, 05 Jul 2019 05:26:03: start model_add_line... INFO @ Fri, 05 Jul 2019 05:26:03: start X-correlation... INFO @ Fri, 05 Jul 2019 05:26:03: end of X-cor INFO @ Fri, 05 Jul 2019 05:26:03: #2 finished! INFO @ Fri, 05 Jul 2019 05:26:03: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:26:03: #2 alternative fragment length(s) may be 132,298,503 bps INFO @ Fri, 05 Jul 2019 05:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10_model.r INFO @ Fri, 05 Jul 2019 05:26:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:27:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:27:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:27:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.20_summits.bed INFO @ Fri, 05 Jul 2019 05:29:00: Done! INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.10_summits.bed INFO @ Fri, 05 Jul 2019 05:29:00: Done! pass1 - making usageList (27 chroms): 1 millis INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05_peaks.xls pass2 - checking and writing primary data (98 records, 4 fields): 27 millis CompletedMACS2peakCalling pass1 - making usageList (37 chroms): 1 millis INFO @ Fri, 05 Jul 2019 05:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05_peaks.narrowPeak pass2 - checking and writing primary data (534 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101896/ERX101896.05_summits.bed INFO @ Fri, 05 Jul 2019 05:29:01: Done! pass1 - making usageList (59 chroms): 3 millis pass2 - checking and writing primary data (2585 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。