Job ID = 10609057 sra ファイルのダウンロード中... Completed: 250779K bytes transferred in 26 seconds (76287K 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... 2018-05-03T22:03:35 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 ) 2018-05-03T22:04:21 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 ) 2018-05-03T22:04:21 fastq-dump.2.9.0 err: timeout exhausted while reading file within network system module - Failed to KClientHttpRequestHEAD('https://sra-download.ncbi.nlm.nih.gov/traces/refseq/BX284605.4' (130.14.250.25)) from '172.20.0.24' 2018-05-03T22:04:21 fastq-dump.2.9.0 err: timeout exhausted while reading file within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/refseq/BX284605.4' Read 23824880 spots for /home/okishinya/chipatlas/results/ce10/SRX2202784/SRR4319290.sra Written 23824880 spots for /home/okishinya/chipatlas/results/ce10/SRX2202784/SRR4319290.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: 00:06:09 23824880 reads; of these: 23824880 (100.00%) were unpaired; of these: 2615039 (10.98%) aligned 0 times 12335425 (51.78%) aligned exactly 1 time 8874416 (37.25%) aligned >1 times 89.02% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 8966267 / 21209841 = 0.4227 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 07:14:58: # Command line: callpeak -t SRX2202784.bam -f BAM -g ce -n SRX2202784.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202784.05 # format = BAM # ChIP-seq file = ['SRX2202784.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 07:14:58: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:58: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:58: # Command line: callpeak -t SRX2202784.bam -f BAM -g ce -n SRX2202784.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202784.10 # format = BAM # ChIP-seq file = ['SRX2202784.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 07:14:58: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:58: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:58: # Command line: callpeak -t SRX2202784.bam -f BAM -g ce -n SRX2202784.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202784.20 # format = BAM # ChIP-seq file = ['SRX2202784.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 07:14:58: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:58: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:04: 1000000 INFO @ Fri, 04 May 2018 07:15:04: 1000000 INFO @ Fri, 04 May 2018 07:15:04: 1000000 INFO @ Fri, 04 May 2018 07:15:10: 2000000 INFO @ Fri, 04 May 2018 07:15:10: 2000000 INFO @ Fri, 04 May 2018 07:15:10: 2000000 INFO @ Fri, 04 May 2018 07:15:15: 3000000 INFO @ Fri, 04 May 2018 07:15:16: 3000000 INFO @ Fri, 04 May 2018 07:15:16: 3000000 INFO @ Fri, 04 May 2018 07:15:21: 4000000 INFO @ Fri, 04 May 2018 07:15:22: 4000000 INFO @ Fri, 04 May 2018 07:15:22: 4000000 INFO @ Fri, 04 May 2018 07:15:27: 5000000 INFO @ Fri, 04 May 2018 07:15:28: 5000000 INFO @ Fri, 04 May 2018 07:15:29: 5000000 INFO @ Fri, 04 May 2018 07:15:33: 6000000 INFO @ Fri, 04 May 2018 07:15:35: 6000000 INFO @ Fri, 04 May 2018 07:15:35: 6000000 INFO @ Fri, 04 May 2018 07:15:39: 7000000 INFO @ Fri, 04 May 2018 07:15:41: 7000000 INFO @ Fri, 04 May 2018 07:15:41: 7000000 INFO @ Fri, 04 May 2018 07:15:45: 8000000 INFO @ Fri, 04 May 2018 07:15:47: 8000000 INFO @ Fri, 04 May 2018 07:15:47: 8000000 INFO @ Fri, 04 May 2018 07:15:51: 9000000 INFO @ Fri, 04 May 2018 07:15:53: 9000000 INFO @ Fri, 04 May 2018 07:15:54: 9000000 INFO @ Fri, 04 May 2018 07:15:57: 10000000 INFO @ Fri, 04 May 2018 07:16:00: 10000000 INFO @ Fri, 04 May 2018 07:16:00: 10000000 INFO @ Fri, 04 May 2018 07:16:03: 11000000 INFO @ Fri, 04 May 2018 07:16:06: 11000000 INFO @ Fri, 04 May 2018 07:16:06: 11000000 INFO @ Fri, 04 May 2018 07:16:09: 12000000 INFO @ Fri, 04 May 2018 07:16:10: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:16:10: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:16:10: #1 total tags in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:10: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:10: #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 07:16:11: #1 tags after filtering in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:11: #1 finished! INFO @ Fri, 04 May 2018 07:16:11: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:12: 12000000 INFO @ Fri, 04 May 2018 07:16:12: #2 number of paired peaks: 4309 INFO @ Fri, 04 May 2018 07:16:12: start model_add_line... INFO @ Fri, 04 May 2018 07:16:12: start X-correlation... INFO @ Fri, 04 May 2018 07:16:12: end of X-cor INFO @ Fri, 04 May 2018 07:16:12: #2 finished! INFO @ Fri, 04 May 2018 07:16:12: #2 predicted fragment length is 140 bps INFO @ Fri, 04 May 2018 07:16:12: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 04 May 2018 07:16:12: #2.2 Generate R script for model : SRX2202784.05_model.r INFO @ Fri, 04 May 2018 07:16:12: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:13: 12000000 INFO @ Fri, 04 May 2018 07:16:14: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:16:14: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:16:14: #1 total tags in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:14: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:14: #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 07:16:14: #1 tags after filtering in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:14: #1 finished! INFO @ Fri, 04 May 2018 07:16:14: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:14: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:16:14: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:16:14: #1 total tags in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:14: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:14: #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 07:16:15: #1 tags after filtering in treatment: 12243574 INFO @ Fri, 04 May 2018 07:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:15: #1 finished! INFO @ Fri, 04 May 2018 07:16:15: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:15: #2 number of paired peaks: 4309 INFO @ Fri, 04 May 2018 07:16:15: start model_add_line... INFO @ Fri, 04 May 2018 07:16:16: start X-correlation... INFO @ Fri, 04 May 2018 07:16:16: end of X-cor INFO @ Fri, 04 May 2018 07:16:16: #2 finished! INFO @ Fri, 04 May 2018 07:16:16: #2 predicted fragment length is 140 bps INFO @ Fri, 04 May 2018 07:16:16: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 04 May 2018 07:16:16: #2.2 Generate R script for model : SRX2202784.10_model.r INFO @ Fri, 04 May 2018 07:16:16: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:16: #2 number of paired peaks: 4309 INFO @ Fri, 04 May 2018 07:16:16: start model_add_line... INFO @ Fri, 04 May 2018 07:16:16: start X-correlation... INFO @ Fri, 04 May 2018 07:16:16: end of X-cor INFO @ Fri, 04 May 2018 07:16:16: #2 finished! INFO @ Fri, 04 May 2018 07:16:16: #2 predicted fragment length is 140 bps INFO @ Fri, 04 May 2018 07:16:16: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 04 May 2018 07:16:16: #2.2 Generate R script for model : SRX2202784.20_model.r INFO @ Fri, 04 May 2018 07:16:16: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:56: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:59: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:06: #4 Write output xls file... SRX2202784.05_peaks.xls INFO @ Fri, 04 May 2018 07:17:06: #4 Write peak in narrowPeak format file... SRX2202784.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:06: #4 Write summits bed file... SRX2202784.05_summits.bed INFO @ Fri, 04 May 2018 07:17:07: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (13009 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:11: #4 Write output xls file... SRX2202784.10_peaks.xls INFO @ Fri, 04 May 2018 07:17:11: #4 Write peak in narrowPeak format file... SRX2202784.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:11: #4 Write summits bed file... SRX2202784.10_summits.bed INFO @ Fri, 04 May 2018 07:17:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9441 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:17:14: #4 Write output xls file... SRX2202784.20_peaks.xls INFO @ Fri, 04 May 2018 07:17:14: #4 Write peak in narrowPeak format file... SRX2202784.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:17:14: #4 Write summits bed file... SRX2202784.20_summits.bed INFO @ Fri, 04 May 2018 07:17:14: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5707 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。