Job ID = 10609054 sra ファイルのダウンロード中... Completed: 218587K bytes transferred in 25 seconds (69779K 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... 2018-05-03T22:03:24 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 ) 2018-05-03T22:04:15 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 22115537 spots for /home/okishinya/chipatlas/results/ce10/SRX2202781/SRR4319287.sra Written 22115537 spots for /home/okishinya/chipatlas/results/ce10/SRX2202781/SRR4319287.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:45 22115537 reads; of these: 22115537 (100.00%) were unpaired; of these: 1315820 (5.95%) aligned 0 times 16389699 (74.11%) aligned exactly 1 time 4410018 (19.94%) aligned >1 times 94.05% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4273626 / 20799717 = 0.2055 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 07:13:49: # Command line: callpeak -t SRX2202781.bam -f BAM -g ce -n SRX2202781.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202781.05 # format = BAM # ChIP-seq file = ['SRX2202781.bam'] # control file = None # effective genome size = 9.00e+07 # 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 07:13:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:49: # Command line: callpeak -t SRX2202781.bam -f BAM -g ce -n SRX2202781.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202781.20 # format = BAM # ChIP-seq file = ['SRX2202781.bam'] # control file = None # effective genome size = 9.00e+07 # 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 07:13:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:49: # Command line: callpeak -t SRX2202781.bam -f BAM -g ce -n SRX2202781.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202781.10 # format = BAM # ChIP-seq file = ['SRX2202781.bam'] # control file = None # effective genome size = 9.00e+07 # 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 07:13:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:55: 1000000 INFO @ Fri, 04 May 2018 07:13:55: 1000000 INFO @ Fri, 04 May 2018 07:13:55: 1000000 INFO @ Fri, 04 May 2018 07:14:02: 2000000 INFO @ Fri, 04 May 2018 07:14:02: 2000000 INFO @ Fri, 04 May 2018 07:14:02: 2000000 INFO @ Fri, 04 May 2018 07:14:08: 3000000 INFO @ Fri, 04 May 2018 07:14:08: 3000000 INFO @ Fri, 04 May 2018 07:14:08: 3000000 INFO @ Fri, 04 May 2018 07:14:14: 4000000 INFO @ Fri, 04 May 2018 07:14:15: 4000000 INFO @ Fri, 04 May 2018 07:14:15: 4000000 INFO @ Fri, 04 May 2018 07:14:20: 5000000 INFO @ Fri, 04 May 2018 07:14:21: 5000000 INFO @ Fri, 04 May 2018 07:14:21: 5000000 INFO @ Fri, 04 May 2018 07:14:27: 6000000 INFO @ Fri, 04 May 2018 07:14:27: 6000000 INFO @ Fri, 04 May 2018 07:14:28: 6000000 INFO @ Fri, 04 May 2018 07:14:33: 7000000 INFO @ Fri, 04 May 2018 07:14:34: 7000000 INFO @ Fri, 04 May 2018 07:14:34: 7000000 INFO @ Fri, 04 May 2018 07:14:39: 8000000 INFO @ Fri, 04 May 2018 07:14:40: 8000000 INFO @ Fri, 04 May 2018 07:14:41: 8000000 INFO @ Fri, 04 May 2018 07:14:45: 9000000 INFO @ Fri, 04 May 2018 07:14:47: 9000000 INFO @ Fri, 04 May 2018 07:14:47: 9000000 INFO @ Fri, 04 May 2018 07:14:51: 10000000 INFO @ Fri, 04 May 2018 07:14:53: 10000000 INFO @ Fri, 04 May 2018 07:14:54: 10000000 INFO @ Fri, 04 May 2018 07:14:58: 11000000 INFO @ Fri, 04 May 2018 07:15:00: 11000000 INFO @ Fri, 04 May 2018 07:15:00: 11000000 INFO @ Fri, 04 May 2018 07:15:04: 12000000 INFO @ Fri, 04 May 2018 07:15:07: 12000000 INFO @ Fri, 04 May 2018 07:15:07: 12000000 INFO @ Fri, 04 May 2018 07:15:10: 13000000 INFO @ Fri, 04 May 2018 07:15:13: 13000000 INFO @ Fri, 04 May 2018 07:15:13: 13000000 INFO @ Fri, 04 May 2018 07:15:16: 14000000 INFO @ Fri, 04 May 2018 07:15:19: 14000000 INFO @ Fri, 04 May 2018 07:15:20: 14000000 INFO @ Fri, 04 May 2018 07:15:22: 15000000 INFO @ Fri, 04 May 2018 07:15:26: 15000000 INFO @ Fri, 04 May 2018 07:15:27: 15000000 INFO @ Fri, 04 May 2018 07:15:28: 16000000 INFO @ Fri, 04 May 2018 07:15:32: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:32: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:32: #1 total tags in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:32: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:32: #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 07:15:32: #1 tags after filtering in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:32: #1 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:32: 16000000 INFO @ Fri, 04 May 2018 07:15:33: 16000000 INFO @ Fri, 04 May 2018 07:15:33: #2 number of paired peaks: 914 WARNING @ Fri, 04 May 2018 07:15:33: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Fri, 04 May 2018 07:15:33: start model_add_line... INFO @ Fri, 04 May 2018 07:15:33: start X-correlation... INFO @ Fri, 04 May 2018 07:15:33: end of X-cor INFO @ Fri, 04 May 2018 07:15:33: #2 finished! INFO @ Fri, 04 May 2018 07:15:33: #2 predicted fragment length is 106 bps INFO @ Fri, 04 May 2018 07:15:33: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 May 2018 07:15:33: #2.2 Generate R script for model : SRX2202781.05_model.r INFO @ Fri, 04 May 2018 07:15:33: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:36: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:36: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:36: #1 total tags in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:36: #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 07:15:36: #1 tags after filtering in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:36: #1 finished! INFO @ Fri, 04 May 2018 07:15:36: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:37: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:37: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:37: #1 total tags in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:37: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:37: #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 07:15:37: #1 tags after filtering in treatment: 16526091 INFO @ Fri, 04 May 2018 07:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:37: #1 finished! INFO @ Fri, 04 May 2018 07:15:37: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:37: #2 number of paired peaks: 914 WARNING @ Fri, 04 May 2018 07:15:37: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Fri, 04 May 2018 07:15:37: start model_add_line... INFO @ Fri, 04 May 2018 07:15:38: start X-correlation... INFO @ Fri, 04 May 2018 07:15:38: end of X-cor INFO @ Fri, 04 May 2018 07:15:38: #2 finished! INFO @ Fri, 04 May 2018 07:15:38: #2 predicted fragment length is 106 bps INFO @ Fri, 04 May 2018 07:15:38: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 May 2018 07:15:38: #2.2 Generate R script for model : SRX2202781.10_model.r INFO @ Fri, 04 May 2018 07:15:38: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:38: #2 number of paired peaks: 914 WARNING @ Fri, 04 May 2018 07:15:38: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Fri, 04 May 2018 07:15:38: start model_add_line... INFO @ Fri, 04 May 2018 07:15:38: start X-correlation... INFO @ Fri, 04 May 2018 07:15:38: end of X-cor INFO @ Fri, 04 May 2018 07:15:38: #2 finished! INFO @ Fri, 04 May 2018 07:15:38: #2 predicted fragment length is 106 bps INFO @ Fri, 04 May 2018 07:15:38: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 May 2018 07:15:38: #2.2 Generate R script for model : SRX2202781.20_model.r INFO @ Fri, 04 May 2018 07:15:38: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:12: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:16: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:16: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:34: #4 Write output xls file... SRX2202781.05_peaks.xls INFO @ Fri, 04 May 2018 07:16:34: #4 Write peak in narrowPeak format file... SRX2202781.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:34: #4 Write summits bed file... SRX2202781.05_summits.bed INFO @ Fri, 04 May 2018 07:16:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8209 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:34: #4 Write output xls file... SRX2202781.10_peaks.xls INFO @ Fri, 04 May 2018 07:16:35: #4 Write peak in narrowPeak format file... SRX2202781.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:35: #4 Write summits bed file... SRX2202781.10_summits.bed INFO @ Fri, 04 May 2018 07:16:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4077 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:35: #4 Write output xls file... SRX2202781.20_peaks.xls INFO @ Fri, 04 May 2018 07:16:35: #4 Write peak in narrowPeak format file... SRX2202781.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:35: #4 Write summits bed file... SRX2202781.20_summits.bed INFO @ Fri, 04 May 2018 07:16:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1561 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。