Job ID = 2002154 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:38:47 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 : 12,579,396 reads read : 12,579,396 reads written : 12,579,396 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: 00:02:52 12579396 reads; of these: 12579396 (100.00%) were unpaired; of these: 315837 (2.51%) aligned 0 times 10818701 (86.00%) aligned exactly 1 time 1444858 (11.49%) aligned >1 times 97.49% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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_rmdupse_core] 3898011 / 12263559 = 0.3179 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 10:45:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.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 10:45:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:45:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:45:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.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 10:45:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:45:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:45:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.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 10:45:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:45:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:46:03: 1000000 INFO @ Fri, 05 Jul 2019 10:46:04: 1000000 INFO @ Fri, 05 Jul 2019 10:46:05: 1000000 INFO @ Fri, 05 Jul 2019 10:46:10: 2000000 INFO @ Fri, 05 Jul 2019 10:46:11: 2000000 INFO @ Fri, 05 Jul 2019 10:46:12: 2000000 INFO @ Fri, 05 Jul 2019 10:46:17: 3000000 INFO @ Fri, 05 Jul 2019 10:46:18: 3000000 INFO @ Fri, 05 Jul 2019 10:46:19: 3000000 INFO @ Fri, 05 Jul 2019 10:46:24: 4000000 INFO @ Fri, 05 Jul 2019 10:46:26: 4000000 INFO @ Fri, 05 Jul 2019 10:46:27: 4000000 INFO @ Fri, 05 Jul 2019 10:46:30: 5000000 INFO @ Fri, 05 Jul 2019 10:46:34: 5000000 INFO @ Fri, 05 Jul 2019 10:46:36: 5000000 INFO @ Fri, 05 Jul 2019 10:46:37: 6000000 INFO @ Fri, 05 Jul 2019 10:46:41: 6000000 INFO @ Fri, 05 Jul 2019 10:46:43: 7000000 INFO @ Fri, 05 Jul 2019 10:46:44: 6000000 INFO @ Fri, 05 Jul 2019 10:46:48: 7000000 INFO @ Fri, 05 Jul 2019 10:46:49: 8000000 INFO @ Fri, 05 Jul 2019 10:46:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:46:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:46:52: #1 total tags in treatment: 8365548 INFO @ Fri, 05 Jul 2019 10:46:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:46:52: #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 10:46:52: #1 tags after filtering in treatment: 8365238 INFO @ Fri, 05 Jul 2019 10:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:46:52: #1 finished! INFO @ Fri, 05 Jul 2019 10:46:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:46:53: 7000000 INFO @ Fri, 05 Jul 2019 10:46:55: #2 number of paired peaks: 34158 INFO @ Fri, 05 Jul 2019 10:46:55: start model_add_line... INFO @ Fri, 05 Jul 2019 10:46:55: start X-correlation... INFO @ Fri, 05 Jul 2019 10:46:55: end of X-cor INFO @ Fri, 05 Jul 2019 10:46:55: #2 finished! INFO @ Fri, 05 Jul 2019 10:46:55: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:46:55: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 05 Jul 2019 10:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10_model.r INFO @ Fri, 05 Jul 2019 10:46:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:46:55: 8000000 INFO @ Fri, 05 Jul 2019 10:46:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:46:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:46:57: #1 total tags in treatment: 8365548 INFO @ Fri, 05 Jul 2019 10:46:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:46:57: #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 10:46:58: #1 tags after filtering in treatment: 8365238 INFO @ Fri, 05 Jul 2019 10:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:46:58: #1 finished! INFO @ Fri, 05 Jul 2019 10:46:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:47:00: #2 number of paired peaks: 34158 INFO @ Fri, 05 Jul 2019 10:47:00: start model_add_line... INFO @ Fri, 05 Jul 2019 10:47:00: start X-correlation... INFO @ Fri, 05 Jul 2019 10:47:00: end of X-cor INFO @ Fri, 05 Jul 2019 10:47:00: #2 finished! INFO @ Fri, 05 Jul 2019 10:47:00: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:47:00: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 05 Jul 2019 10:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20_model.r INFO @ Fri, 05 Jul 2019 10:47:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:47:02: 8000000 INFO @ Fri, 05 Jul 2019 10:47:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:47:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:47:05: #1 total tags in treatment: 8365548 INFO @ Fri, 05 Jul 2019 10:47:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:47:05: #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 10:47:05: #1 tags after filtering in treatment: 8365238 INFO @ Fri, 05 Jul 2019 10:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:47:05: #1 finished! INFO @ Fri, 05 Jul 2019 10:47:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:47:07: #2 number of paired peaks: 34158 INFO @ Fri, 05 Jul 2019 10:47:07: start model_add_line... INFO @ Fri, 05 Jul 2019 10:47:08: start X-correlation... INFO @ Fri, 05 Jul 2019 10:47:08: end of X-cor INFO @ Fri, 05 Jul 2019 10:47:08: #2 finished! INFO @ Fri, 05 Jul 2019 10:47:08: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:47:08: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 05 Jul 2019 10:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05_model.r INFO @ Fri, 05 Jul 2019 10:47:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:47:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.10_summits.bed INFO @ Fri, 05 Jul 2019 10:47:35: Done! pass1 - making usageList (91 chroms): 8 millis pass2 - checking and writing primary data (25642 records, 4 fields): 37 millis INFO @ Fri, 05 Jul 2019 10:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.20_summits.bed INFO @ Fri, 05 Jul 2019 10:47:40: Done! pass1 - making usageList (59 chroms): 7 millis pass2 - checking and writing primary data (14960 records, 4 fields): 25 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102047/ERX102047.05_summits.bed INFO @ Fri, 05 Jul 2019 10:47:49: Done! pass1 - making usageList (108 chroms): 7 millis pass2 - checking and writing primary data (33150 records, 4 fields): 51 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。