Job ID = 1293803 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:34:01 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 : 20,532,176 reads read : 20,532,176 reads written : 20,532,176 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:39 20532176 reads; of these: 20532176 (100.00%) were unpaired; of these: 1671786 (8.14%) aligned 0 times 16538253 (80.55%) aligned exactly 1 time 2322137 (11.31%) aligned >1 times 91.86% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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 8 files... [bam_rmdupse_core] 9768054 / 18860390 = 0.5179 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 @ Mon, 03 Jun 2019 02:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.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 @ Mon, 03 Jun 2019 02:46:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.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 @ Mon, 03 Jun 2019 02:46:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.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 @ Mon, 03 Jun 2019 02:46:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:13: 1000000 INFO @ Mon, 03 Jun 2019 02:46:13: 1000000 INFO @ Mon, 03 Jun 2019 02:46:13: 1000000 INFO @ Mon, 03 Jun 2019 02:46:22: 2000000 INFO @ Mon, 03 Jun 2019 02:46:22: 2000000 INFO @ Mon, 03 Jun 2019 02:46:22: 2000000 INFO @ Mon, 03 Jun 2019 02:46:31: 3000000 INFO @ Mon, 03 Jun 2019 02:46:31: 3000000 INFO @ Mon, 03 Jun 2019 02:46:31: 3000000 INFO @ Mon, 03 Jun 2019 02:46:40: 4000000 INFO @ Mon, 03 Jun 2019 02:46:40: 4000000 INFO @ Mon, 03 Jun 2019 02:46:40: 4000000 INFO @ Mon, 03 Jun 2019 02:46:49: 5000000 INFO @ Mon, 03 Jun 2019 02:46:49: 5000000 INFO @ Mon, 03 Jun 2019 02:46:49: 5000000 INFO @ Mon, 03 Jun 2019 02:46:57: 6000000 INFO @ Mon, 03 Jun 2019 02:46:58: 6000000 INFO @ Mon, 03 Jun 2019 02:46:58: 6000000 INFO @ Mon, 03 Jun 2019 02:47:06: 7000000 INFO @ Mon, 03 Jun 2019 02:47:06: 7000000 INFO @ Mon, 03 Jun 2019 02:47:06: 7000000 INFO @ Mon, 03 Jun 2019 02:47:14: 8000000 INFO @ Mon, 03 Jun 2019 02:47:15: 8000000 INFO @ Mon, 03 Jun 2019 02:47:15: 8000000 INFO @ Mon, 03 Jun 2019 02:47:23: 9000000 INFO @ Mon, 03 Jun 2019 02:47:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:47:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:47:24: #1 total tags in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:47:24: 9000000 INFO @ Mon, 03 Jun 2019 02:47:24: 9000000 INFO @ Mon, 03 Jun 2019 02:47:24: #1 tags after filtering in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:47:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:47:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:47:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:47:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:47:25: #1 total tags in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:47:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:47:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:47:25: #1 total tags in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:47:25: #1 tags after filtering in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:47:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:47:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:47:25: #1 tags after filtering in treatment: 9092336 INFO @ Mon, 03 Jun 2019 02:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:47:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:47:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:47:25: #2 number of paired peaks: 3537 INFO @ Mon, 03 Jun 2019 02:47:25: start model_add_line... INFO @ Mon, 03 Jun 2019 02:47:25: start X-correlation... INFO @ Mon, 03 Jun 2019 02:47:25: end of X-cor INFO @ Mon, 03 Jun 2019 02:47:25: #2 finished! INFO @ Mon, 03 Jun 2019 02:47:25: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 02:47:25: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 02:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05_model.r INFO @ Mon, 03 Jun 2019 02:47:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:47:26: #2 number of paired peaks: 3537 INFO @ Mon, 03 Jun 2019 02:47:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:47:26: #2 number of paired peaks: 3537 INFO @ Mon, 03 Jun 2019 02:47:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:47:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:47:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:47:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:47:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:47:26: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 02:47:26: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 02:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20_model.r INFO @ Mon, 03 Jun 2019 02:47:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:47:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:47:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:47:26: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 02:47:26: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 02:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10_model.r INFO @ Mon, 03 Jun 2019 02:47:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:47:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:47:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:47:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.20_summits.bed INFO @ Mon, 03 Jun 2019 02:48:14: Done! INFO @ Mon, 03 Jun 2019 02:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.10_summits.bed pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3264 records, 4 fields): 11 millis INFO @ Mon, 03 Jun 2019 02:48:15: Done! CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4493 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134704/SRX1134704.05_summits.bed INFO @ Mon, 03 Jun 2019 02:48:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5933 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。