Job ID = 2001663 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T22:31:57 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 : 29,213,579 reads read : 29,213,579 reads written : 29,213,579 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:30 29213579 reads; of these: 29213579 (100.00%) were unpaired; of these: 636205 (2.18%) aligned 0 times 21812794 (74.67%) aligned exactly 1 time 6764580 (23.16%) aligned >1 times 97.82% overall alignment rate Time searching: 00:10:31 Overall time: 00:10:31 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] 1937989 / 28577374 = 0.0678 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 08:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.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 08:01:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.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 08:01:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.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 08:01:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:14: 1000000 INFO @ Fri, 05 Jul 2019 08:01:16: 1000000 INFO @ Fri, 05 Jul 2019 08:01:18: 1000000 INFO @ Fri, 05 Jul 2019 08:01:21: 2000000 INFO @ Fri, 05 Jul 2019 08:01:23: 2000000 INFO @ Fri, 05 Jul 2019 08:01:25: 2000000 INFO @ Fri, 05 Jul 2019 08:01:28: 3000000 INFO @ Fri, 05 Jul 2019 08:01:30: 3000000 INFO @ Fri, 05 Jul 2019 08:01:32: 3000000 INFO @ Fri, 05 Jul 2019 08:01:35: 4000000 INFO @ Fri, 05 Jul 2019 08:01:36: 4000000 INFO @ Fri, 05 Jul 2019 08:01:39: 4000000 INFO @ Fri, 05 Jul 2019 08:01:42: 5000000 INFO @ Fri, 05 Jul 2019 08:01:43: 5000000 INFO @ Fri, 05 Jul 2019 08:01:47: 5000000 INFO @ Fri, 05 Jul 2019 08:01:49: 6000000 INFO @ Fri, 05 Jul 2019 08:01:50: 6000000 INFO @ Fri, 05 Jul 2019 08:01:54: 6000000 INFO @ Fri, 05 Jul 2019 08:01:56: 7000000 INFO @ Fri, 05 Jul 2019 08:01:57: 7000000 INFO @ Fri, 05 Jul 2019 08:02:01: 7000000 INFO @ Fri, 05 Jul 2019 08:02:03: 8000000 INFO @ Fri, 05 Jul 2019 08:02:04: 8000000 INFO @ Fri, 05 Jul 2019 08:02:08: 8000000 INFO @ Fri, 05 Jul 2019 08:02:10: 9000000 INFO @ Fri, 05 Jul 2019 08:02:11: 9000000 INFO @ Fri, 05 Jul 2019 08:02:15: 9000000 INFO @ Fri, 05 Jul 2019 08:02:17: 10000000 INFO @ Fri, 05 Jul 2019 08:02:18: 10000000 INFO @ Fri, 05 Jul 2019 08:02:22: 10000000 INFO @ Fri, 05 Jul 2019 08:02:24: 11000000 INFO @ Fri, 05 Jul 2019 08:02:25: 11000000 INFO @ Fri, 05 Jul 2019 08:02:29: 11000000 INFO @ Fri, 05 Jul 2019 08:02:31: 12000000 INFO @ Fri, 05 Jul 2019 08:02:32: 12000000 INFO @ Fri, 05 Jul 2019 08:02:36: 12000000 INFO @ Fri, 05 Jul 2019 08:02:38: 13000000 INFO @ Fri, 05 Jul 2019 08:02:39: 13000000 INFO @ Fri, 05 Jul 2019 08:02:43: 13000000 INFO @ Fri, 05 Jul 2019 08:02:45: 14000000 INFO @ Fri, 05 Jul 2019 08:02:46: 14000000 INFO @ Fri, 05 Jul 2019 08:02:50: 14000000 INFO @ Fri, 05 Jul 2019 08:02:52: 15000000 INFO @ Fri, 05 Jul 2019 08:02:53: 15000000 INFO @ Fri, 05 Jul 2019 08:02:57: 15000000 INFO @ Fri, 05 Jul 2019 08:02:59: 16000000 INFO @ Fri, 05 Jul 2019 08:03:00: 16000000 INFO @ Fri, 05 Jul 2019 08:03:04: 16000000 INFO @ Fri, 05 Jul 2019 08:03:06: 17000000 INFO @ Fri, 05 Jul 2019 08:03:07: 17000000 INFO @ Fri, 05 Jul 2019 08:03:11: 17000000 INFO @ Fri, 05 Jul 2019 08:03:13: 18000000 INFO @ Fri, 05 Jul 2019 08:03:14: 18000000 INFO @ Fri, 05 Jul 2019 08:03:18: 18000000 INFO @ Fri, 05 Jul 2019 08:03:20: 19000000 INFO @ Fri, 05 Jul 2019 08:03:21: 19000000 INFO @ Fri, 05 Jul 2019 08:03:25: 19000000 INFO @ Fri, 05 Jul 2019 08:03:27: 20000000 INFO @ Fri, 05 Jul 2019 08:03:28: 20000000 INFO @ Fri, 05 Jul 2019 08:03:31: 20000000 INFO @ Fri, 05 Jul 2019 08:03:34: 21000000 INFO @ Fri, 05 Jul 2019 08:03:34: 21000000 INFO @ Fri, 05 Jul 2019 08:03:38: 21000000 INFO @ Fri, 05 Jul 2019 08:03:41: 22000000 INFO @ Fri, 05 Jul 2019 08:03:41: 22000000 INFO @ Fri, 05 Jul 2019 08:03:45: 22000000 INFO @ Fri, 05 Jul 2019 08:03:48: 23000000 INFO @ Fri, 05 Jul 2019 08:03:48: 23000000 INFO @ Fri, 05 Jul 2019 08:03:52: 23000000 INFO @ Fri, 05 Jul 2019 08:03:55: 24000000 INFO @ Fri, 05 Jul 2019 08:03:56: 24000000 INFO @ Fri, 05 Jul 2019 08:03:59: 24000000 INFO @ Fri, 05 Jul 2019 08:04:03: 25000000 INFO @ Fri, 05 Jul 2019 08:04:03: 25000000 INFO @ Fri, 05 Jul 2019 08:04:06: 25000000 INFO @ Fri, 05 Jul 2019 08:04:10: 26000000 INFO @ Fri, 05 Jul 2019 08:04:11: 26000000 INFO @ Fri, 05 Jul 2019 08:04:14: 26000000 INFO @ Fri, 05 Jul 2019 08:04:15: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:04:15: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:04:15: #1 total tags in treatment: 26639385 INFO @ Fri, 05 Jul 2019 08:04:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:04:15: #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 08:04:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:04:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:04:16: #1 total tags in treatment: 26639385 INFO @ Fri, 05 Jul 2019 08:04:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:04:16: #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 08:04:16: #1 tags after filtering in treatment: 26639222 INFO @ Fri, 05 Jul 2019 08:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:04:16: #1 finished! INFO @ Fri, 05 Jul 2019 08:04:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:04:16: #1 tags after filtering in treatment: 26639222 INFO @ Fri, 05 Jul 2019 08:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:04:16: #1 finished! INFO @ Fri, 05 Jul 2019 08:04:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:04:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:04:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:04:18: #1 total tags in treatment: 26639385 INFO @ Fri, 05 Jul 2019 08:04:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:04:18: #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 08:04:19: #1 tags after filtering in treatment: 26639222 INFO @ Fri, 05 Jul 2019 08:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:04:19: #1 finished! INFO @ Fri, 05 Jul 2019 08:04:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:04:21: #2 number of paired peaks: 57678 INFO @ Fri, 05 Jul 2019 08:04:21: start model_add_line... INFO @ Fri, 05 Jul 2019 08:04:21: #2 number of paired peaks: 57678 INFO @ Fri, 05 Jul 2019 08:04:21: start model_add_line... INFO @ Fri, 05 Jul 2019 08:04:22: start X-correlation... INFO @ Fri, 05 Jul 2019 08:04:22: end of X-cor INFO @ Fri, 05 Jul 2019 08:04:22: #2 finished! INFO @ Fri, 05 Jul 2019 08:04:22: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:04:22: #2 alternative fragment length(s) may be 1,133,290,502 bps INFO @ Fri, 05 Jul 2019 08:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10_model.r INFO @ Fri, 05 Jul 2019 08:04:22: start X-correlation... INFO @ Fri, 05 Jul 2019 08:04:22: end of X-cor INFO @ Fri, 05 Jul 2019 08:04:22: #2 finished! INFO @ Fri, 05 Jul 2019 08:04:22: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:04:22: #2 alternative fragment length(s) may be 1,133,290,502 bps INFO @ Fri, 05 Jul 2019 08:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05_model.r INFO @ Fri, 05 Jul 2019 08:04:24: #2 number of paired peaks: 57678 INFO @ Fri, 05 Jul 2019 08:04:24: start model_add_line... INFO @ Fri, 05 Jul 2019 08:04:25: start X-correlation... INFO @ Fri, 05 Jul 2019 08:04:25: end of X-cor INFO @ Fri, 05 Jul 2019 08:04:25: #2 finished! INFO @ Fri, 05 Jul 2019 08:04:25: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:04:25: #2 alternative fragment length(s) may be 1,133,290,502 bps INFO @ Fri, 05 Jul 2019 08:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20_model.r INFO @ Fri, 05 Jul 2019 08:04:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:04:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:04:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:05:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:05:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:05:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.20_summits.bed INFO @ Fri, 05 Jul 2019 08:06:35: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.10_summits.bed INFO @ Fri, 05 Jul 2019 08:06:37: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1190 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101978/ERX101978.05_summits.bed INFO @ Fri, 05 Jul 2019 08:06:39: Done! pass1 - making usageList (68 chroms): 4 millis pass2 - checking and writing primary data (5377 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。