Job ID = 2001596 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:33:23 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 : 14,172,254 reads read : 14,172,254 reads written : 14,172,254 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: 00:06:59 14172254 reads; of these: 14172254 (100.00%) were unpaired; of these: 301020 (2.12%) aligned 0 times 9516340 (67.15%) aligned exactly 1 time 4354894 (30.73%) aligned >1 times 97.88% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 364458 / 13871234 = 0.0263 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 05:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.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 05:47:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:47:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.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 05:47:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:47:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.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 05:47:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:47:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:47:45: 1000000 INFO @ Fri, 05 Jul 2019 05:47:45: 1000000 INFO @ Fri, 05 Jul 2019 05:47:45: 1000000 INFO @ Fri, 05 Jul 2019 05:47:53: 2000000 INFO @ Fri, 05 Jul 2019 05:47:53: 2000000 INFO @ Fri, 05 Jul 2019 05:47:53: 2000000 INFO @ Fri, 05 Jul 2019 05:48:00: 3000000 INFO @ Fri, 05 Jul 2019 05:48:01: 3000000 INFO @ Fri, 05 Jul 2019 05:48:01: 3000000 INFO @ Fri, 05 Jul 2019 05:48:07: 4000000 INFO @ Fri, 05 Jul 2019 05:48:08: 4000000 INFO @ Fri, 05 Jul 2019 05:48:09: 4000000 INFO @ Fri, 05 Jul 2019 05:48:15: 5000000 INFO @ Fri, 05 Jul 2019 05:48:16: 5000000 INFO @ Fri, 05 Jul 2019 05:48:16: 5000000 INFO @ Fri, 05 Jul 2019 05:48:22: 6000000 INFO @ Fri, 05 Jul 2019 05:48:24: 6000000 INFO @ Fri, 05 Jul 2019 05:48:24: 6000000 INFO @ Fri, 05 Jul 2019 05:48:30: 7000000 INFO @ Fri, 05 Jul 2019 05:48:31: 7000000 INFO @ Fri, 05 Jul 2019 05:48:32: 7000000 INFO @ Fri, 05 Jul 2019 05:48:38: 8000000 INFO @ Fri, 05 Jul 2019 05:48:39: 8000000 INFO @ Fri, 05 Jul 2019 05:48:39: 8000000 INFO @ Fri, 05 Jul 2019 05:48:45: 9000000 INFO @ Fri, 05 Jul 2019 05:48:46: 9000000 INFO @ Fri, 05 Jul 2019 05:48:47: 9000000 INFO @ Fri, 05 Jul 2019 05:48:53: 10000000 INFO @ Fri, 05 Jul 2019 05:48:54: 10000000 INFO @ Fri, 05 Jul 2019 05:48:55: 10000000 INFO @ Fri, 05 Jul 2019 05:49:00: 11000000 INFO @ Fri, 05 Jul 2019 05:49:02: 11000000 INFO @ Fri, 05 Jul 2019 05:49:03: 11000000 INFO @ Fri, 05 Jul 2019 05:49:07: 12000000 INFO @ Fri, 05 Jul 2019 05:49:10: 12000000 INFO @ Fri, 05 Jul 2019 05:49:11: 12000000 INFO @ Fri, 05 Jul 2019 05:49:14: 13000000 INFO @ Fri, 05 Jul 2019 05:49:18: 13000000 INFO @ Fri, 05 Jul 2019 05:49:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:49:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:49:18: #1 total tags in treatment: 13506776 INFO @ Fri, 05 Jul 2019 05:49:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:49:18: #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 05:49:18: #1 tags after filtering in treatment: 13506616 INFO @ Fri, 05 Jul 2019 05:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:49:18: #1 finished! INFO @ Fri, 05 Jul 2019 05:49:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:49:20: 13000000 INFO @ Fri, 05 Jul 2019 05:49:20: #2 number of paired peaks: 10275 INFO @ Fri, 05 Jul 2019 05:49:20: start model_add_line... INFO @ Fri, 05 Jul 2019 05:49:21: start X-correlation... INFO @ Fri, 05 Jul 2019 05:49:21: end of X-cor INFO @ Fri, 05 Jul 2019 05:49:21: #2 finished! INFO @ Fri, 05 Jul 2019 05:49:21: #2 predicted fragment length is 94 bps INFO @ Fri, 05 Jul 2019 05:49:21: #2 alternative fragment length(s) may be 94 bps INFO @ Fri, 05 Jul 2019 05:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10_model.r INFO @ Fri, 05 Jul 2019 05:49:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:49:22: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:49:22: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:49:22: #1 total tags in treatment: 13506776 INFO @ Fri, 05 Jul 2019 05:49:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:49:22: #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 05:49:22: #1 tags after filtering in treatment: 13506616 INFO @ Fri, 05 Jul 2019 05:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:49:22: #1 finished! INFO @ Fri, 05 Jul 2019 05:49:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:49:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:49:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:49:24: #1 total tags in treatment: 13506776 INFO @ Fri, 05 Jul 2019 05:49:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:49:24: #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 05:49:24: #1 tags after filtering in treatment: 13506616 INFO @ Fri, 05 Jul 2019 05:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:49:24: #1 finished! INFO @ Fri, 05 Jul 2019 05:49:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:49:24: #2 number of paired peaks: 10275 INFO @ Fri, 05 Jul 2019 05:49:24: start model_add_line... INFO @ Fri, 05 Jul 2019 05:49:24: start X-correlation... INFO @ Fri, 05 Jul 2019 05:49:24: end of X-cor INFO @ Fri, 05 Jul 2019 05:49:24: #2 finished! INFO @ Fri, 05 Jul 2019 05:49:24: #2 predicted fragment length is 94 bps INFO @ Fri, 05 Jul 2019 05:49:24: #2 alternative fragment length(s) may be 94 bps INFO @ Fri, 05 Jul 2019 05:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05_model.r INFO @ Fri, 05 Jul 2019 05:49:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:49:26: #2 number of paired peaks: 10275 INFO @ Fri, 05 Jul 2019 05:49:26: start model_add_line... INFO @ Fri, 05 Jul 2019 05:49:26: start X-correlation... INFO @ Fri, 05 Jul 2019 05:49:26: end of X-cor INFO @ Fri, 05 Jul 2019 05:49:26: #2 finished! INFO @ Fri, 05 Jul 2019 05:49:26: #2 predicted fragment length is 94 bps INFO @ Fri, 05 Jul 2019 05:49:26: #2 alternative fragment length(s) may be 94 bps INFO @ Fri, 05 Jul 2019 05:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20_model.r INFO @ Fri, 05 Jul 2019 05:49:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:50:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:50:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:50:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.10_summits.bed INFO @ Fri, 05 Jul 2019 05:50:24: Done! pass1 - making usageList (28 chroms): 3 millis pass2 - checking and writing primary data (402 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.05_summits.bed INFO @ Fri, 05 Jul 2019 05:50:28: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1476 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101924/ERX101924.20_summits.bed INFO @ Fri, 05 Jul 2019 05:50:30: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。