Job ID = 2001704 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:14:48 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 23,730,215 reads read : 23,730,215 reads written : 23,730,215 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: 00:09:36 23730215 reads; of these: 23730215 (100.00%) were unpaired; of these: 463834 (1.95%) aligned 0 times 16281233 (68.61%) aligned exactly 1 time 6985148 (29.44%) aligned >1 times 98.05% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 750682 / 23266381 = 0.0323 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 09:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.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 09:36:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.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 09:36:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.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 09:36:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:13: 1000000 INFO @ Fri, 05 Jul 2019 09:36:13: 1000000 INFO @ Fri, 05 Jul 2019 09:36:14: 1000000 INFO @ Fri, 05 Jul 2019 09:36:20: 2000000 INFO @ Fri, 05 Jul 2019 09:36:20: 2000000 INFO @ Fri, 05 Jul 2019 09:36:21: 2000000 INFO @ Fri, 05 Jul 2019 09:36:27: 3000000 INFO @ Fri, 05 Jul 2019 09:36:27: 3000000 INFO @ Fri, 05 Jul 2019 09:36:28: 3000000 INFO @ Fri, 05 Jul 2019 09:36:33: 4000000 INFO @ Fri, 05 Jul 2019 09:36:34: 4000000 INFO @ Fri, 05 Jul 2019 09:36:35: 4000000 INFO @ Fri, 05 Jul 2019 09:36:40: 5000000 INFO @ Fri, 05 Jul 2019 09:36:41: 5000000 INFO @ Fri, 05 Jul 2019 09:36:42: 5000000 INFO @ Fri, 05 Jul 2019 09:36:46: 6000000 INFO @ Fri, 05 Jul 2019 09:36:48: 6000000 INFO @ Fri, 05 Jul 2019 09:36:49: 6000000 INFO @ Fri, 05 Jul 2019 09:36:52: 7000000 INFO @ Fri, 05 Jul 2019 09:36:55: 7000000 INFO @ Fri, 05 Jul 2019 09:36:55: 7000000 INFO @ Fri, 05 Jul 2019 09:36:58: 8000000 INFO @ Fri, 05 Jul 2019 09:37:02: 8000000 INFO @ Fri, 05 Jul 2019 09:37:02: 8000000 INFO @ Fri, 05 Jul 2019 09:37:05: 9000000 INFO @ Fri, 05 Jul 2019 09:37:09: 9000000 INFO @ Fri, 05 Jul 2019 09:37:10: 9000000 INFO @ Fri, 05 Jul 2019 09:37:11: 10000000 INFO @ Fri, 05 Jul 2019 09:37:16: 10000000 INFO @ Fri, 05 Jul 2019 09:37:17: 10000000 INFO @ Fri, 05 Jul 2019 09:37:17: 11000000 INFO @ Fri, 05 Jul 2019 09:37:23: 11000000 INFO @ Fri, 05 Jul 2019 09:37:24: 12000000 INFO @ Fri, 05 Jul 2019 09:37:24: 11000000 INFO @ Fri, 05 Jul 2019 09:37:30: 13000000 INFO @ Fri, 05 Jul 2019 09:37:30: 12000000 INFO @ Fri, 05 Jul 2019 09:37:31: 12000000 INFO @ Fri, 05 Jul 2019 09:37:36: 14000000 INFO @ Fri, 05 Jul 2019 09:37:37: 13000000 INFO @ Fri, 05 Jul 2019 09:37:38: 13000000 INFO @ Fri, 05 Jul 2019 09:37:42: 15000000 INFO @ Fri, 05 Jul 2019 09:37:44: 14000000 INFO @ Fri, 05 Jul 2019 09:37:45: 14000000 INFO @ Fri, 05 Jul 2019 09:37:49: 16000000 INFO @ Fri, 05 Jul 2019 09:37:51: 15000000 INFO @ Fri, 05 Jul 2019 09:37:51: 15000000 INFO @ Fri, 05 Jul 2019 09:37:55: 17000000 INFO @ Fri, 05 Jul 2019 09:37:57: 16000000 INFO @ Fri, 05 Jul 2019 09:37:58: 16000000 INFO @ Fri, 05 Jul 2019 09:38:01: 18000000 INFO @ Fri, 05 Jul 2019 09:38:04: 17000000 INFO @ Fri, 05 Jul 2019 09:38:05: 17000000 INFO @ Fri, 05 Jul 2019 09:38:07: 19000000 INFO @ Fri, 05 Jul 2019 09:38:11: 18000000 INFO @ Fri, 05 Jul 2019 09:38:12: 18000000 INFO @ Fri, 05 Jul 2019 09:38:14: 20000000 INFO @ Fri, 05 Jul 2019 09:38:18: 19000000 INFO @ Fri, 05 Jul 2019 09:38:19: 19000000 INFO @ Fri, 05 Jul 2019 09:38:20: 21000000 INFO @ Fri, 05 Jul 2019 09:38:25: 20000000 INFO @ Fri, 05 Jul 2019 09:38:26: 22000000 INFO @ Fri, 05 Jul 2019 09:38:27: 20000000 INFO @ Fri, 05 Jul 2019 09:38:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:38:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:38:30: #1 total tags in treatment: 22515699 INFO @ Fri, 05 Jul 2019 09:38:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:38:30: #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 09:38:30: #1 tags after filtering in treatment: 22515540 INFO @ Fri, 05 Jul 2019 09:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:38:30: #1 finished! INFO @ Fri, 05 Jul 2019 09:38:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:38:31: 21000000 INFO @ Fri, 05 Jul 2019 09:38:34: #2 number of paired peaks: 20976 INFO @ Fri, 05 Jul 2019 09:38:34: start model_add_line... INFO @ Fri, 05 Jul 2019 09:38:34: start X-correlation... INFO @ Fri, 05 Jul 2019 09:38:34: end of X-cor INFO @ Fri, 05 Jul 2019 09:38:34: #2 finished! INFO @ Fri, 05 Jul 2019 09:38:34: #2 predicted fragment length is 121 bps INFO @ Fri, 05 Jul 2019 09:38:34: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 05 Jul 2019 09:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20_model.r INFO @ Fri, 05 Jul 2019 09:38:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:38:35: 21000000 INFO @ Fri, 05 Jul 2019 09:38:38: 22000000 INFO @ Fri, 05 Jul 2019 09:38:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:38:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:38:42: #1 total tags in treatment: 22515699 INFO @ Fri, 05 Jul 2019 09:38:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:38:42: #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 09:38:42: 22000000 INFO @ Fri, 05 Jul 2019 09:38:43: #1 tags after filtering in treatment: 22515540 INFO @ Fri, 05 Jul 2019 09:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:38:43: #1 finished! INFO @ Fri, 05 Jul 2019 09:38:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:38:46: #2 number of paired peaks: 20976 INFO @ Fri, 05 Jul 2019 09:38:46: start model_add_line... INFO @ Fri, 05 Jul 2019 09:38:46: start X-correlation... INFO @ Fri, 05 Jul 2019 09:38:46: end of X-cor INFO @ Fri, 05 Jul 2019 09:38:46: #2 finished! INFO @ Fri, 05 Jul 2019 09:38:46: #2 predicted fragment length is 121 bps INFO @ Fri, 05 Jul 2019 09:38:46: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 05 Jul 2019 09:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10_model.r INFO @ Fri, 05 Jul 2019 09:38:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:38:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:38:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:38:46: #1 total tags in treatment: 22515699 INFO @ Fri, 05 Jul 2019 09:38:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:38:46: #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 09:38:47: #1 tags after filtering in treatment: 22515540 INFO @ Fri, 05 Jul 2019 09:38:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:38:47: #1 finished! INFO @ Fri, 05 Jul 2019 09:38:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:38:51: #2 number of paired peaks: 20976 INFO @ Fri, 05 Jul 2019 09:38:51: start model_add_line... INFO @ Fri, 05 Jul 2019 09:38:51: start X-correlation... INFO @ Fri, 05 Jul 2019 09:38:51: end of X-cor INFO @ Fri, 05 Jul 2019 09:38:51: #2 finished! INFO @ Fri, 05 Jul 2019 09:38:51: #2 predicted fragment length is 121 bps INFO @ Fri, 05 Jul 2019 09:38:51: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 05 Jul 2019 09:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05_model.r INFO @ Fri, 05 Jul 2019 09:38:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:39:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:39:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:40:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.20_summits.bed INFO @ Fri, 05 Jul 2019 09:40:20: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 114 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.10_summits.bed INFO @ Fri, 05 Jul 2019 09:40:33: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:40:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102014/ERX102014.05_summits.bed INFO @ Fri, 05 Jul 2019 09:40:37: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1794 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。