Job ID = 2001602 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:53:35 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 : 23,167,786 reads read : 23,167,786 reads written : 23,167,786 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: 00:00:00 Multiseed full-index search: 00:08:14 23167786 reads; of these: 23167786 (100.00%) were unpaired; of these: 474394 (2.05%) aligned 0 times 17225097 (74.35%) aligned exactly 1 time 5468295 (23.60%) aligned >1 times 97.95% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 1450978 / 22693392 = 0.0639 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 06:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.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 06:16:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:16:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.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 06:16:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:16:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.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 06:16:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:16:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:16:43: 1000000 INFO @ Fri, 05 Jul 2019 06:16:43: 1000000 INFO @ Fri, 05 Jul 2019 06:16:44: 1000000 INFO @ Fri, 05 Jul 2019 06:16:49: 2000000 INFO @ Fri, 05 Jul 2019 06:16:50: 2000000 INFO @ Fri, 05 Jul 2019 06:16:51: 2000000 INFO @ Fri, 05 Jul 2019 06:16:56: 3000000 INFO @ Fri, 05 Jul 2019 06:16:56: 3000000 INFO @ Fri, 05 Jul 2019 06:16:57: 3000000 INFO @ Fri, 05 Jul 2019 06:17:02: 4000000 INFO @ Fri, 05 Jul 2019 06:17:02: 4000000 INFO @ Fri, 05 Jul 2019 06:17:03: 4000000 INFO @ Fri, 05 Jul 2019 06:17:08: 5000000 INFO @ Fri, 05 Jul 2019 06:17:09: 5000000 INFO @ Fri, 05 Jul 2019 06:17:10: 5000000 INFO @ Fri, 05 Jul 2019 06:17:14: 6000000 INFO @ Fri, 05 Jul 2019 06:17:16: 6000000 INFO @ Fri, 05 Jul 2019 06:17:16: 6000000 INFO @ Fri, 05 Jul 2019 06:17:20: 7000000 INFO @ Fri, 05 Jul 2019 06:17:22: 7000000 INFO @ Fri, 05 Jul 2019 06:17:23: 7000000 INFO @ Fri, 05 Jul 2019 06:17:26: 8000000 INFO @ Fri, 05 Jul 2019 06:17:29: 8000000 INFO @ Fri, 05 Jul 2019 06:17:29: 8000000 INFO @ Fri, 05 Jul 2019 06:17:32: 9000000 INFO @ Fri, 05 Jul 2019 06:17:36: 9000000 INFO @ Fri, 05 Jul 2019 06:17:36: 9000000 INFO @ Fri, 05 Jul 2019 06:17:38: 10000000 INFO @ Fri, 05 Jul 2019 06:17:42: 10000000 INFO @ Fri, 05 Jul 2019 06:17:43: 10000000 INFO @ Fri, 05 Jul 2019 06:17:44: 11000000 INFO @ Fri, 05 Jul 2019 06:17:49: 11000000 INFO @ Fri, 05 Jul 2019 06:17:49: 11000000 INFO @ Fri, 05 Jul 2019 06:17:50: 12000000 INFO @ Fri, 05 Jul 2019 06:17:55: 12000000 INFO @ Fri, 05 Jul 2019 06:17:56: 12000000 INFO @ Fri, 05 Jul 2019 06:17:56: 13000000 INFO @ Fri, 05 Jul 2019 06:18:02: 13000000 INFO @ Fri, 05 Jul 2019 06:18:02: 14000000 INFO @ Fri, 05 Jul 2019 06:18:03: 13000000 INFO @ Fri, 05 Jul 2019 06:18:08: 14000000 INFO @ Fri, 05 Jul 2019 06:18:08: 15000000 INFO @ Fri, 05 Jul 2019 06:18:09: 14000000 INFO @ Fri, 05 Jul 2019 06:18:14: 15000000 INFO @ Fri, 05 Jul 2019 06:18:15: 16000000 INFO @ Fri, 05 Jul 2019 06:18:16: 15000000 INFO @ Fri, 05 Jul 2019 06:18:21: 17000000 INFO @ Fri, 05 Jul 2019 06:18:21: 16000000 INFO @ Fri, 05 Jul 2019 06:18:23: 16000000 INFO @ Fri, 05 Jul 2019 06:18:27: 18000000 INFO @ Fri, 05 Jul 2019 06:18:27: 17000000 INFO @ Fri, 05 Jul 2019 06:18:29: 17000000 INFO @ Fri, 05 Jul 2019 06:18:33: 19000000 INFO @ Fri, 05 Jul 2019 06:18:33: 18000000 INFO @ Fri, 05 Jul 2019 06:18:36: 18000000 INFO @ Fri, 05 Jul 2019 06:18:39: 20000000 INFO @ Fri, 05 Jul 2019 06:18:40: 19000000 INFO @ Fri, 05 Jul 2019 06:18:42: 19000000 INFO @ Fri, 05 Jul 2019 06:18:45: 21000000 INFO @ Fri, 05 Jul 2019 06:18:46: 20000000 INFO @ Fri, 05 Jul 2019 06:18:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:18:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:18:47: #1 total tags in treatment: 21242414 INFO @ Fri, 05 Jul 2019 06:18:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:18:47: #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 06:18:47: #1 tags after filtering in treatment: 21242245 INFO @ Fri, 05 Jul 2019 06:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:18:47: #1 finished! INFO @ Fri, 05 Jul 2019 06:18:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:18:49: 20000000 INFO @ Fri, 05 Jul 2019 06:18:52: #2 number of paired peaks: 63786 INFO @ Fri, 05 Jul 2019 06:18:52: start model_add_line... INFO @ Fri, 05 Jul 2019 06:18:52: start X-correlation... INFO @ Fri, 05 Jul 2019 06:18:52: end of X-cor INFO @ Fri, 05 Jul 2019 06:18:52: #2 finished! INFO @ Fri, 05 Jul 2019 06:18:52: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 06:18:52: #2 alternative fragment length(s) may be 4,137,503 bps INFO @ Fri, 05 Jul 2019 06:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10_model.r INFO @ Fri, 05 Jul 2019 06:18:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:18:53: 21000000 INFO @ Fri, 05 Jul 2019 06:18:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:18:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:18:55: #1 total tags in treatment: 21242414 INFO @ Fri, 05 Jul 2019 06:18:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:18:55: #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 06:18:55: #1 tags after filtering in treatment: 21242245 INFO @ Fri, 05 Jul 2019 06:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:18:55: #1 finished! INFO @ Fri, 05 Jul 2019 06:18:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:18:55: 21000000 INFO @ Fri, 05 Jul 2019 06:18:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:18:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:18:57: #1 total tags in treatment: 21242414 INFO @ Fri, 05 Jul 2019 06:18:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:18:57: #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 06:18:58: #1 tags after filtering in treatment: 21242245 INFO @ Fri, 05 Jul 2019 06:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:18:58: #1 finished! INFO @ Fri, 05 Jul 2019 06:18:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:19:00: #2 number of paired peaks: 63786 INFO @ Fri, 05 Jul 2019 06:19:00: start model_add_line... INFO @ Fri, 05 Jul 2019 06:19:00: start X-correlation... INFO @ Fri, 05 Jul 2019 06:19:00: end of X-cor INFO @ Fri, 05 Jul 2019 06:19:00: #2 finished! INFO @ Fri, 05 Jul 2019 06:19:00: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 06:19:00: #2 alternative fragment length(s) may be 4,137,503 bps INFO @ Fri, 05 Jul 2019 06:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20_model.r INFO @ Fri, 05 Jul 2019 06:19:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:19:03: #2 number of paired peaks: 63786 INFO @ Fri, 05 Jul 2019 06:19:03: start model_add_line... INFO @ Fri, 05 Jul 2019 06:19:03: start X-correlation... INFO @ Fri, 05 Jul 2019 06:19:03: end of X-cor INFO @ Fri, 05 Jul 2019 06:19:03: #2 finished! INFO @ Fri, 05 Jul 2019 06:19:03: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 06:19:03: #2 alternative fragment length(s) may be 4,137,503 bps INFO @ Fri, 05 Jul 2019 06:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05_model.r INFO @ Fri, 05 Jul 2019 06:19:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:19:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:20:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:20:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.10_summits.bed INFO @ Fri, 05 Jul 2019 06:20:33: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1132 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.20_summits.bed INFO @ Fri, 05 Jul 2019 06:20:42: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101929/ERX101929.05_summits.bed INFO @ Fri, 05 Jul 2019 06:20:45: Done! pass1 - making usageList (65 chroms): 4 millis pass2 - checking and writing primary data (4814 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。