Job ID = 10609091 sra ファイルのダウンロード中... Completed: 413121K bytes transferred in 50 seconds (66689K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... 2018-05-03T22:03:23 fastq-dump.2.9.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) Read 19846217 spots for /home/okishinya/chipatlas/results/dm3/SRX3011229/SRR5834706.sra Written 19846217 spots for /home/okishinya/chipatlas/results/dm3/SRX3011229/SRR5834706.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:30 19846217 reads; of these: 19846217 (100.00%) were unpaired; of these: 185030 (0.93%) aligned 0 times 19391589 (97.71%) aligned exactly 1 time 269598 (1.36%) aligned >1 times 99.07% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8346433 / 19661187 = 0.4245 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, 04 May 2018 07:11:22: # Command line: callpeak -t SRX3011229.bam -f BAM -g dm -n SRX3011229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011229.20 # format = BAM # ChIP-seq file = ['SRX3011229.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:22: # Command line: callpeak -t SRX3011229.bam -f BAM -g dm -n SRX3011229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011229.10 # format = BAM # ChIP-seq file = ['SRX3011229.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:22: # Command line: callpeak -t SRX3011229.bam -f BAM -g dm -n SRX3011229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011229.05 # format = BAM # ChIP-seq file = ['SRX3011229.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:29: 1000000 INFO @ Fri, 04 May 2018 07:11:29: 1000000 INFO @ Fri, 04 May 2018 07:11:29: 1000000 INFO @ Fri, 04 May 2018 07:11:35: 2000000 INFO @ Fri, 04 May 2018 07:11:35: 2000000 INFO @ Fri, 04 May 2018 07:11:35: 2000000 INFO @ Fri, 04 May 2018 07:11:42: 3000000 INFO @ Fri, 04 May 2018 07:11:42: 3000000 INFO @ Fri, 04 May 2018 07:11:42: 3000000 INFO @ Fri, 04 May 2018 07:11:48: 4000000 INFO @ Fri, 04 May 2018 07:11:48: 4000000 INFO @ Fri, 04 May 2018 07:11:48: 4000000 INFO @ Fri, 04 May 2018 07:11:55: 5000000 INFO @ Fri, 04 May 2018 07:11:55: 5000000 INFO @ Fri, 04 May 2018 07:11:55: 5000000 INFO @ Fri, 04 May 2018 07:12:01: 6000000 INFO @ Fri, 04 May 2018 07:12:01: 6000000 INFO @ Fri, 04 May 2018 07:12:02: 6000000 INFO @ Fri, 04 May 2018 07:12:08: 7000000 INFO @ Fri, 04 May 2018 07:12:08: 7000000 INFO @ Fri, 04 May 2018 07:12:08: 7000000 INFO @ Fri, 04 May 2018 07:12:14: 8000000 INFO @ Fri, 04 May 2018 07:12:14: 8000000 INFO @ Fri, 04 May 2018 07:12:15: 8000000 INFO @ Fri, 04 May 2018 07:12:21: 9000000 INFO @ Fri, 04 May 2018 07:12:21: 9000000 INFO @ Fri, 04 May 2018 07:12:21: 9000000 INFO @ Fri, 04 May 2018 07:12:27: 10000000 INFO @ Fri, 04 May 2018 07:12:27: 10000000 INFO @ Fri, 04 May 2018 07:12:28: 10000000 INFO @ Fri, 04 May 2018 07:12:34: 11000000 INFO @ Fri, 04 May 2018 07:12:34: 11000000 INFO @ Fri, 04 May 2018 07:12:34: 11000000 INFO @ Fri, 04 May 2018 07:12:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:12:36: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:12:36: #1 total tags in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:12:36: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:12:36: #1 total tags in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:36: #1 tags after filtering in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:36: #1 finished! INFO @ Fri, 04 May 2018 07:12:36: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:36: #1 tags after filtering in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:36: #1 finished! INFO @ Fri, 04 May 2018 07:12:36: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:37: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:12:37: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:12:37: #1 total tags in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:37: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:37: #1 tags after filtering in treatment: 11314754 INFO @ Fri, 04 May 2018 07:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:12:37: #1 finished! INFO @ Fri, 04 May 2018 07:12:37: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:37: #2 number of paired peaks: 8184 INFO @ Fri, 04 May 2018 07:12:37: start model_add_line... INFO @ Fri, 04 May 2018 07:12:38: #2 number of paired peaks: 8184 INFO @ Fri, 04 May 2018 07:12:38: start model_add_line... INFO @ Fri, 04 May 2018 07:12:38: start X-correlation... INFO @ Fri, 04 May 2018 07:12:38: end of X-cor INFO @ Fri, 04 May 2018 07:12:38: #2 finished! INFO @ Fri, 04 May 2018 07:12:38: #2 predicted fragment length is 208 bps INFO @ Fri, 04 May 2018 07:12:38: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 04 May 2018 07:12:38: #2.2 Generate R script for model : SRX3011229.05_model.r INFO @ Fri, 04 May 2018 07:12:38: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:38: start X-correlation... INFO @ Fri, 04 May 2018 07:12:38: end of X-cor INFO @ Fri, 04 May 2018 07:12:38: #2 finished! INFO @ Fri, 04 May 2018 07:12:38: #2 predicted fragment length is 208 bps INFO @ Fri, 04 May 2018 07:12:38: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 04 May 2018 07:12:38: #2.2 Generate R script for model : SRX3011229.10_model.r INFO @ Fri, 04 May 2018 07:12:38: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:38: #2 number of paired peaks: 8184 INFO @ Fri, 04 May 2018 07:12:38: start model_add_line... INFO @ Fri, 04 May 2018 07:12:39: start X-correlation... INFO @ Fri, 04 May 2018 07:12:39: end of X-cor INFO @ Fri, 04 May 2018 07:12:39: #2 finished! INFO @ Fri, 04 May 2018 07:12:39: #2 predicted fragment length is 208 bps INFO @ Fri, 04 May 2018 07:12:39: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 04 May 2018 07:12:39: #2.2 Generate R script for model : SRX3011229.20_model.r INFO @ Fri, 04 May 2018 07:12:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:21: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:21: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:21: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:37: #4 Write output xls file... SRX3011229.20_peaks.xls INFO @ Fri, 04 May 2018 07:13:37: #4 Write peak in narrowPeak format file... SRX3011229.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:37: #4 Write output xls file... SRX3011229.10_peaks.xls INFO @ Fri, 04 May 2018 07:13:37: #4 Write summits bed file... SRX3011229.20_summits.bed INFO @ Fri, 04 May 2018 07:13:37: Done! INFO @ Fri, 04 May 2018 07:13:37: #4 Write peak in narrowPeak format file... SRX3011229.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:37: #4 Write summits bed file... SRX3011229.10_summits.bed pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6152 records, 4 fields): 9 millis INFO @ Fri, 04 May 2018 07:13:37: Done! CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8092 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:13:38: #4 Write output xls file... SRX3011229.05_peaks.xls INFO @ Fri, 04 May 2018 07:13:38: #4 Write peak in narrowPeak format file... SRX3011229.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:38: #4 Write summits bed file... SRX3011229.05_summits.bed INFO @ Fri, 04 May 2018 07:13:38: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (10012 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。