Job ID = 2001571 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:13:51 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 : 25,629,614 reads read : 25,629,614 reads written : 25,629,614 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: 00:10:53 25629614 reads; of these: 25629614 (100.00%) were unpaired; of these: 534566 (2.09%) aligned 0 times 19359723 (75.54%) aligned exactly 1 time 5735325 (22.38%) aligned >1 times 97.91% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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] 1773149 / 25095048 = 0.0707 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 05:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.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 05:41:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:41:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.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 05:41:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:41:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.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 05:41:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:41:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:42:05: 1000000 INFO @ Fri, 05 Jul 2019 05:42:06: 1000000 INFO @ Fri, 05 Jul 2019 05:42:08: 1000000 INFO @ Fri, 05 Jul 2019 05:42:13: 2000000 INFO @ Fri, 05 Jul 2019 05:42:13: 2000000 INFO @ Fri, 05 Jul 2019 05:42:16: 2000000 INFO @ Fri, 05 Jul 2019 05:42:20: 3000000 INFO @ Fri, 05 Jul 2019 05:42:20: 3000000 INFO @ Fri, 05 Jul 2019 05:42:24: 3000000 INFO @ Fri, 05 Jul 2019 05:42:27: 4000000 INFO @ Fri, 05 Jul 2019 05:42:27: 4000000 INFO @ Fri, 05 Jul 2019 05:42:32: 4000000 INFO @ Fri, 05 Jul 2019 05:42:34: 5000000 INFO @ Fri, 05 Jul 2019 05:42:35: 5000000 INFO @ Fri, 05 Jul 2019 05:42:41: 5000000 INFO @ Fri, 05 Jul 2019 05:42:41: 6000000 INFO @ Fri, 05 Jul 2019 05:42:42: 6000000 INFO @ Fri, 05 Jul 2019 05:42:48: 7000000 INFO @ Fri, 05 Jul 2019 05:42:49: 6000000 INFO @ Fri, 05 Jul 2019 05:42:49: 7000000 INFO @ Fri, 05 Jul 2019 05:42:55: 8000000 INFO @ Fri, 05 Jul 2019 05:42:56: 8000000 INFO @ Fri, 05 Jul 2019 05:42:57: 7000000 INFO @ Fri, 05 Jul 2019 05:43:02: 9000000 INFO @ Fri, 05 Jul 2019 05:43:03: 9000000 INFO @ Fri, 05 Jul 2019 05:43:06: 8000000 INFO @ Fri, 05 Jul 2019 05:43:10: 10000000 INFO @ Fri, 05 Jul 2019 05:43:11: 10000000 INFO @ Fri, 05 Jul 2019 05:43:15: 9000000 INFO @ Fri, 05 Jul 2019 05:43:17: 11000000 INFO @ Fri, 05 Jul 2019 05:43:19: 11000000 INFO @ Fri, 05 Jul 2019 05:43:23: 10000000 INFO @ Fri, 05 Jul 2019 05:43:25: 12000000 INFO @ Fri, 05 Jul 2019 05:43:26: 12000000 INFO @ Fri, 05 Jul 2019 05:43:31: 11000000 INFO @ Fri, 05 Jul 2019 05:43:32: 13000000 INFO @ Fri, 05 Jul 2019 05:43:34: 13000000 INFO @ Fri, 05 Jul 2019 05:43:39: 14000000 INFO @ Fri, 05 Jul 2019 05:43:40: 12000000 INFO @ Fri, 05 Jul 2019 05:43:41: 14000000 INFO @ Fri, 05 Jul 2019 05:43:47: 15000000 INFO @ Fri, 05 Jul 2019 05:43:49: 13000000 INFO @ Fri, 05 Jul 2019 05:43:49: 15000000 INFO @ Fri, 05 Jul 2019 05:43:55: 16000000 INFO @ Fri, 05 Jul 2019 05:43:57: 16000000 INFO @ Fri, 05 Jul 2019 05:43:57: 14000000 INFO @ Fri, 05 Jul 2019 05:44:02: 17000000 INFO @ Fri, 05 Jul 2019 05:44:05: 17000000 INFO @ Fri, 05 Jul 2019 05:44:06: 15000000 INFO @ Fri, 05 Jul 2019 05:44:11: 18000000 INFO @ Fri, 05 Jul 2019 05:44:13: 18000000 INFO @ Fri, 05 Jul 2019 05:44:14: 16000000 INFO @ Fri, 05 Jul 2019 05:44:19: 19000000 INFO @ Fri, 05 Jul 2019 05:44:20: 19000000 INFO @ Fri, 05 Jul 2019 05:44:23: 17000000 INFO @ Fri, 05 Jul 2019 05:44:26: 20000000 INFO @ Fri, 05 Jul 2019 05:44:28: 20000000 INFO @ Fri, 05 Jul 2019 05:44:31: 18000000 INFO @ Fri, 05 Jul 2019 05:44:34: 21000000 INFO @ Fri, 05 Jul 2019 05:44:35: 21000000 INFO @ Fri, 05 Jul 2019 05:44:40: 19000000 INFO @ Fri, 05 Jul 2019 05:44:41: 22000000 INFO @ Fri, 05 Jul 2019 05:44:43: 22000000 INFO @ Fri, 05 Jul 2019 05:44:48: 20000000 INFO @ Fri, 05 Jul 2019 05:44:49: 23000000 INFO @ Fri, 05 Jul 2019 05:44:51: 23000000 INFO @ Fri, 05 Jul 2019 05:44:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:44:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:44:52: #1 total tags in treatment: 23321899 INFO @ Fri, 05 Jul 2019 05:44:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:44:52: #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 05:44:53: #1 tags after filtering in treatment: 23321734 INFO @ Fri, 05 Jul 2019 05:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:44:53: #1 finished! INFO @ Fri, 05 Jul 2019 05:44:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:44:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:44:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:44:53: #1 total tags in treatment: 23321899 INFO @ Fri, 05 Jul 2019 05:44:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:44:53: #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 05:44:54: #1 tags after filtering in treatment: 23321734 INFO @ Fri, 05 Jul 2019 05:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:44:54: #1 finished! INFO @ Fri, 05 Jul 2019 05:44:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:44:55: 21000000 INFO @ Fri, 05 Jul 2019 05:44:58: #2 number of paired peaks: 71866 INFO @ Fri, 05 Jul 2019 05:44:58: start model_add_line... INFO @ Fri, 05 Jul 2019 05:44:59: start X-correlation... INFO @ Fri, 05 Jul 2019 05:44:59: end of X-cor INFO @ Fri, 05 Jul 2019 05:44:59: #2 finished! INFO @ Fri, 05 Jul 2019 05:44:59: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 05:44:59: #2 alternative fragment length(s) may be 139,306,516 bps INFO @ Fri, 05 Jul 2019 05:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10_model.r INFO @ Fri, 05 Jul 2019 05:44:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:00: #2 number of paired peaks: 71866 INFO @ Fri, 05 Jul 2019 05:45:00: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:00: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:00: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:00: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:00: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 05:45:00: #2 alternative fragment length(s) may be 139,306,516 bps INFO @ Fri, 05 Jul 2019 05:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05_model.r INFO @ Fri, 05 Jul 2019 05:45:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:03: 22000000 INFO @ Fri, 05 Jul 2019 05:45:11: 23000000 INFO @ Fri, 05 Jul 2019 05:45:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:45:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:45:14: #1 total tags in treatment: 23321899 INFO @ Fri, 05 Jul 2019 05:45:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:14: #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 05:45:15: #1 tags after filtering in treatment: 23321734 INFO @ Fri, 05 Jul 2019 05:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:15: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:20: #2 number of paired peaks: 71866 INFO @ Fri, 05 Jul 2019 05:45:20: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:21: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:21: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:21: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:21: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 05:45:21: #2 alternative fragment length(s) may be 139,306,516 bps INFO @ Fri, 05 Jul 2019 05:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20_model.r INFO @ Fri, 05 Jul 2019 05:45:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:46:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:46:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:46:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.05_summits.bed INFO @ Fri, 05 Jul 2019 05:47:08: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (3964 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.10_summits.bed INFO @ Fri, 05 Jul 2019 05:47:09: Done! pass1 - making usageList (42 chroms): 10 millis pass2 - checking and writing primary data (799 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101914/ERX101914.20_summits.bed INFO @ Fri, 05 Jul 2019 05:47:35: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。