Job ID = 2002130 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:57:27 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 : 20,102,418 reads read : 20,102,418 reads written : 20,102,418 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: 00:07:25 20102418 reads; of these: 20102418 (100.00%) were unpaired; of these: 474244 (2.36%) aligned 0 times 14768696 (73.47%) aligned exactly 1 time 4859478 (24.17%) aligned >1 times 97.64% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 1059238 / 19628174 = 0.0540 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 10:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.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 10:15:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:15:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.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 10:15:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:15:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.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 10:15:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:15:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:15:36: 1000000 INFO @ Fri, 05 Jul 2019 10:15:38: 1000000 INFO @ Fri, 05 Jul 2019 10:15:40: 1000000 INFO @ Fri, 05 Jul 2019 10:15:43: 2000000 INFO @ Fri, 05 Jul 2019 10:15:46: 2000000 INFO @ Fri, 05 Jul 2019 10:15:49: 2000000 INFO @ Fri, 05 Jul 2019 10:15:49: 3000000 INFO @ Fri, 05 Jul 2019 10:15:54: 3000000 INFO @ Fri, 05 Jul 2019 10:15:56: 4000000 INFO @ Fri, 05 Jul 2019 10:15:57: 3000000 INFO @ Fri, 05 Jul 2019 10:16:02: 4000000 INFO @ Fri, 05 Jul 2019 10:16:02: 5000000 INFO @ Fri, 05 Jul 2019 10:16:05: 4000000 INFO @ Fri, 05 Jul 2019 10:16:09: 6000000 INFO @ Fri, 05 Jul 2019 10:16:09: 5000000 INFO @ Fri, 05 Jul 2019 10:16:14: 5000000 INFO @ Fri, 05 Jul 2019 10:16:16: 7000000 INFO @ Fri, 05 Jul 2019 10:16:17: 6000000 INFO @ Fri, 05 Jul 2019 10:16:22: 6000000 INFO @ Fri, 05 Jul 2019 10:16:22: 8000000 INFO @ Fri, 05 Jul 2019 10:16:25: 7000000 INFO @ Fri, 05 Jul 2019 10:16:29: 9000000 INFO @ Fri, 05 Jul 2019 10:16:30: 7000000 INFO @ Fri, 05 Jul 2019 10:16:33: 8000000 INFO @ Fri, 05 Jul 2019 10:16:36: 10000000 INFO @ Fri, 05 Jul 2019 10:16:38: 8000000 INFO @ Fri, 05 Jul 2019 10:16:41: 9000000 INFO @ Fri, 05 Jul 2019 10:16:42: 11000000 INFO @ Fri, 05 Jul 2019 10:16:47: 9000000 INFO @ Fri, 05 Jul 2019 10:16:48: 10000000 INFO @ Fri, 05 Jul 2019 10:16:49: 12000000 INFO @ Fri, 05 Jul 2019 10:16:55: 10000000 INFO @ Fri, 05 Jul 2019 10:16:55: 13000000 INFO @ Fri, 05 Jul 2019 10:16:56: 11000000 INFO @ Fri, 05 Jul 2019 10:17:01: 14000000 INFO @ Fri, 05 Jul 2019 10:17:03: 11000000 INFO @ Fri, 05 Jul 2019 10:17:04: 12000000 INFO @ Fri, 05 Jul 2019 10:17:08: 15000000 INFO @ Fri, 05 Jul 2019 10:17:11: 12000000 INFO @ Fri, 05 Jul 2019 10:17:12: 13000000 INFO @ Fri, 05 Jul 2019 10:17:14: 16000000 INFO @ Fri, 05 Jul 2019 10:17:19: 13000000 INFO @ Fri, 05 Jul 2019 10:17:20: 14000000 INFO @ Fri, 05 Jul 2019 10:17:20: 17000000 INFO @ Fri, 05 Jul 2019 10:17:27: 18000000 INFO @ Fri, 05 Jul 2019 10:17:27: 14000000 INFO @ Fri, 05 Jul 2019 10:17:27: 15000000 INFO @ Fri, 05 Jul 2019 10:17:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:17:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:17:31: #1 total tags in treatment: 18568936 INFO @ Fri, 05 Jul 2019 10:17:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:17:31: #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 10:17:31: #1 tags after filtering in treatment: 18568753 INFO @ Fri, 05 Jul 2019 10:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:17:31: #1 finished! INFO @ Fri, 05 Jul 2019 10:17:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:17:35: 16000000 INFO @ Fri, 05 Jul 2019 10:17:36: 15000000 INFO @ Fri, 05 Jul 2019 10:17:36: #2 number of paired peaks: 60293 INFO @ Fri, 05 Jul 2019 10:17:36: start model_add_line... INFO @ Fri, 05 Jul 2019 10:17:36: start X-correlation... INFO @ Fri, 05 Jul 2019 10:17:36: end of X-cor INFO @ Fri, 05 Jul 2019 10:17:36: #2 finished! INFO @ Fri, 05 Jul 2019 10:17:36: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:17:36: #2 alternative fragment length(s) may be 4,133,489 bps INFO @ Fri, 05 Jul 2019 10:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05_model.r INFO @ Fri, 05 Jul 2019 10:17:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:17:43: 17000000 INFO @ Fri, 05 Jul 2019 10:17:44: 16000000 INFO @ Fri, 05 Jul 2019 10:17:51: 18000000 INFO @ Fri, 05 Jul 2019 10:17:52: 17000000 INFO @ Fri, 05 Jul 2019 10:17:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:17:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:17:55: #1 total tags in treatment: 18568936 INFO @ Fri, 05 Jul 2019 10:17:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:17:55: #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 10:17:56: #1 tags after filtering in treatment: 18568753 INFO @ Fri, 05 Jul 2019 10:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:17:56: #1 finished! INFO @ Fri, 05 Jul 2019 10:17:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:18:00: 18000000 INFO @ Fri, 05 Jul 2019 10:18:00: #2 number of paired peaks: 60293 INFO @ Fri, 05 Jul 2019 10:18:00: start model_add_line... INFO @ Fri, 05 Jul 2019 10:18:00: start X-correlation... INFO @ Fri, 05 Jul 2019 10:18:00: end of X-cor INFO @ Fri, 05 Jul 2019 10:18:00: #2 finished! INFO @ Fri, 05 Jul 2019 10:18:00: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:18:00: #2 alternative fragment length(s) may be 4,133,489 bps INFO @ Fri, 05 Jul 2019 10:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10_model.r INFO @ Fri, 05 Jul 2019 10:18:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:18:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:18:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:18:05: #1 total tags in treatment: 18568936 INFO @ Fri, 05 Jul 2019 10:18:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:18:05: #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 10:18:05: #1 tags after filtering in treatment: 18568753 INFO @ Fri, 05 Jul 2019 10:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:18:05: #1 finished! INFO @ Fri, 05 Jul 2019 10:18:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:18:09: #2 number of paired peaks: 60293 INFO @ Fri, 05 Jul 2019 10:18:09: start model_add_line... INFO @ Fri, 05 Jul 2019 10:18:10: start X-correlation... INFO @ Fri, 05 Jul 2019 10:18:10: end of X-cor INFO @ Fri, 05 Jul 2019 10:18:10: #2 finished! INFO @ Fri, 05 Jul 2019 10:18:10: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:18:10: #2 alternative fragment length(s) may be 4,133,489 bps INFO @ Fri, 05 Jul 2019 10:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20_model.r INFO @ Fri, 05 Jul 2019 10:18:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:18:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.05_summits.bed INFO @ Fri, 05 Jul 2019 10:19:06: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (4181 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:19:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.10_summits.bed INFO @ Fri, 05 Jul 2019 10:19:30: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 384 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102032/ERX102032.20_summits.bed INFO @ Fri, 05 Jul 2019 10:19:40: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。