Job ID = 2001144 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:38:16 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 : 28,174,015 reads read : 28,174,015 reads written : 28,174,015 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:07 28174015 reads; of these: 28174015 (100.00%) were unpaired; of these: 687331 (2.44%) aligned 0 times 24237625 (86.03%) aligned exactly 1 time 3249059 (11.53%) aligned >1 times 97.56% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 11340374 / 27486684 = 0.4126 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 04:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.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 04:05:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:05:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.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 04:05:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:05:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.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 04:05:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:05:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:05:48: 1000000 INFO @ Fri, 05 Jul 2019 04:05:50: 1000000 INFO @ Fri, 05 Jul 2019 04:05:51: 1000000 INFO @ Fri, 05 Jul 2019 04:05:54: 2000000 INFO @ Fri, 05 Jul 2019 04:05:57: 2000000 INFO @ Fri, 05 Jul 2019 04:05:59: 2000000 INFO @ Fri, 05 Jul 2019 04:06:01: 3000000 INFO @ Fri, 05 Jul 2019 04:06:04: 3000000 INFO @ Fri, 05 Jul 2019 04:06:07: 4000000 INFO @ Fri, 05 Jul 2019 04:06:08: 3000000 INFO @ Fri, 05 Jul 2019 04:06:12: 4000000 INFO @ Fri, 05 Jul 2019 04:06:14: 5000000 INFO @ Fri, 05 Jul 2019 04:06:17: 4000000 INFO @ Fri, 05 Jul 2019 04:06:19: 5000000 INFO @ Fri, 05 Jul 2019 04:06:21: 6000000 INFO @ Fri, 05 Jul 2019 04:06:25: 5000000 INFO @ Fri, 05 Jul 2019 04:06:26: 6000000 INFO @ Fri, 05 Jul 2019 04:06:27: 7000000 INFO @ Fri, 05 Jul 2019 04:06:33: 7000000 INFO @ Fri, 05 Jul 2019 04:06:33: 6000000 INFO @ Fri, 05 Jul 2019 04:06:34: 8000000 INFO @ Fri, 05 Jul 2019 04:06:40: 8000000 INFO @ Fri, 05 Jul 2019 04:06:40: 9000000 INFO @ Fri, 05 Jul 2019 04:06:42: 7000000 INFO @ Fri, 05 Jul 2019 04:06:47: 10000000 INFO @ Fri, 05 Jul 2019 04:06:47: 9000000 INFO @ Fri, 05 Jul 2019 04:06:50: 8000000 INFO @ Fri, 05 Jul 2019 04:06:53: 11000000 INFO @ Fri, 05 Jul 2019 04:06:55: 10000000 INFO @ Fri, 05 Jul 2019 04:06:59: 9000000 INFO @ Fri, 05 Jul 2019 04:07:00: 12000000 INFO @ Fri, 05 Jul 2019 04:07:02: 11000000 INFO @ Fri, 05 Jul 2019 04:07:07: 13000000 INFO @ Fri, 05 Jul 2019 04:07:07: 10000000 INFO @ Fri, 05 Jul 2019 04:07:09: 12000000 INFO @ Fri, 05 Jul 2019 04:07:13: 14000000 INFO @ Fri, 05 Jul 2019 04:07:16: 11000000 INFO @ Fri, 05 Jul 2019 04:07:16: 13000000 INFO @ Fri, 05 Jul 2019 04:07:20: 15000000 INFO @ Fri, 05 Jul 2019 04:07:23: 14000000 INFO @ Fri, 05 Jul 2019 04:07:24: 12000000 INFO @ Fri, 05 Jul 2019 04:07:27: 16000000 INFO @ Fri, 05 Jul 2019 04:07:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:07:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:07:28: #1 total tags in treatment: 16146310 INFO @ Fri, 05 Jul 2019 04:07:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:07:28: #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 04:07:28: #1 tags after filtering in treatment: 16146074 INFO @ Fri, 05 Jul 2019 04:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:07:28: #1 finished! INFO @ Fri, 05 Jul 2019 04:07:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:07:31: 15000000 INFO @ Fri, 05 Jul 2019 04:07:32: #2 number of paired peaks: 56189 INFO @ Fri, 05 Jul 2019 04:07:32: start model_add_line... INFO @ Fri, 05 Jul 2019 04:07:33: 13000000 INFO @ Fri, 05 Jul 2019 04:07:33: start X-correlation... INFO @ Fri, 05 Jul 2019 04:07:33: end of X-cor INFO @ Fri, 05 Jul 2019 04:07:33: #2 finished! INFO @ Fri, 05 Jul 2019 04:07:33: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:07:33: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10_model.r INFO @ Fri, 05 Jul 2019 04:07:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:07:38: 16000000 INFO @ Fri, 05 Jul 2019 04:07:39: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:07:39: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:07:39: #1 total tags in treatment: 16146310 INFO @ Fri, 05 Jul 2019 04:07:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:07:39: #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 04:07:39: #1 tags after filtering in treatment: 16146074 INFO @ Fri, 05 Jul 2019 04:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:07:39: #1 finished! INFO @ Fri, 05 Jul 2019 04:07:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:07:41: 14000000 INFO @ Fri, 05 Jul 2019 04:07:44: #2 number of paired peaks: 56189 INFO @ Fri, 05 Jul 2019 04:07:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:07:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:07:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:07:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:07:44: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:07:44: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20_model.r INFO @ Fri, 05 Jul 2019 04:07:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:07:49: 15000000 INFO @ Fri, 05 Jul 2019 04:07:58: 16000000 INFO @ Fri, 05 Jul 2019 04:07:59: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:07:59: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:07:59: #1 total tags in treatment: 16146310 INFO @ Fri, 05 Jul 2019 04:07:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:07:59: #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 04:07:59: #1 tags after filtering in treatment: 16146074 INFO @ Fri, 05 Jul 2019 04:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:07:59: #1 finished! INFO @ Fri, 05 Jul 2019 04:07:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:08:03: #2 number of paired peaks: 56189 INFO @ Fri, 05 Jul 2019 04:08:03: start model_add_line... INFO @ Fri, 05 Jul 2019 04:08:04: start X-correlation... INFO @ Fri, 05 Jul 2019 04:08:04: end of X-cor INFO @ Fri, 05 Jul 2019 04:08:04: #2 finished! INFO @ Fri, 05 Jul 2019 04:08:04: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:08:04: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05_model.r INFO @ Fri, 05 Jul 2019 04:08:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:08:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:08:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.10_summits.bed INFO @ Fri, 05 Jul 2019 04:08:49: Done! pass1 - making usageList (117 chroms): 14 millis pass2 - checking and writing primary data (35510 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:08:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.20_summits.bed INFO @ Fri, 05 Jul 2019 04:09:00: Done! pass1 - making usageList (85 chroms): 5 millis pass2 - checking and writing primary data (23329 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:09:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:09:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101834/ERX101834.05_summits.bed INFO @ Fri, 05 Jul 2019 04:09:21: Done! pass1 - making usageList (134 chroms): 11 millis pass2 - checking and writing primary data (45390 records, 4 fields): 61 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。