Job ID = 4178535 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:44:11 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 17,835,831 reads read : 17,835,831 reads written : 17,835,831 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:20 17835831 reads; of these: 17835831 (100.00%) were unpaired; of these: 2503060 (14.03%) aligned 0 times 11496256 (64.46%) aligned exactly 1 time 3836515 (21.51%) aligned >1 times 85.97% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 3969984 / 15332771 = 0.2589 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.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 @ Thu, 05 Dec 2019 13:00:01: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:01: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:08: 1000000 INFO @ Thu, 05 Dec 2019 13:00:15: 2000000 INFO @ Thu, 05 Dec 2019 13:00:22: 3000000 INFO @ Thu, 05 Dec 2019 13:00:29: 4000000 INFO @ Thu, 05 Dec 2019 13:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.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 @ Thu, 05 Dec 2019 13:00:30: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:30: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:36: 5000000 INFO @ Thu, 05 Dec 2019 13:00:38: 1000000 INFO @ Thu, 05 Dec 2019 13:00:43: 6000000 INFO @ Thu, 05 Dec 2019 13:00:46: 2000000 INFO @ Thu, 05 Dec 2019 13:00:50: 7000000 INFO @ Thu, 05 Dec 2019 13:00:53: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:00:58: 8000000 INFO @ Thu, 05 Dec 2019 13:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.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 @ Thu, 05 Dec 2019 13:01:00: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:01:00: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:01:01: 4000000 INFO @ Thu, 05 Dec 2019 13:01:07: 9000000 INFO @ Thu, 05 Dec 2019 13:01:08: 1000000 INFO @ Thu, 05 Dec 2019 13:01:09: 5000000 INFO @ Thu, 05 Dec 2019 13:01:15: 2000000 INFO @ Thu, 05 Dec 2019 13:01:16: 10000000 INFO @ Thu, 05 Dec 2019 13:01:16: 6000000 INFO @ Thu, 05 Dec 2019 13:01:22: 3000000 INFO @ Thu, 05 Dec 2019 13:01:24: 7000000 INFO @ Thu, 05 Dec 2019 13:01:25: 11000000 INFO @ Thu, 05 Dec 2019 13:01:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:01:29: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:01:29: #1 total tags in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:01:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:01:29: #1 tags after filtering in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:01:29: #1 finished! INFO @ Thu, 05 Dec 2019 13:01:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:01:29: 4000000 INFO @ Thu, 05 Dec 2019 13:01:30: #2 number of paired peaks: 1793 INFO @ Thu, 05 Dec 2019 13:01:30: start model_add_line... INFO @ Thu, 05 Dec 2019 13:01:30: start X-correlation... INFO @ Thu, 05 Dec 2019 13:01:30: end of X-cor INFO @ Thu, 05 Dec 2019 13:01:30: #2 finished! INFO @ Thu, 05 Dec 2019 13:01:30: #2 predicted fragment length is 162 bps INFO @ Thu, 05 Dec 2019 13:01:30: #2 alternative fragment length(s) may be 0,162,175,178,221,267,271,588 bps INFO @ Thu, 05 Dec 2019 13:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05_model.r INFO @ Thu, 05 Dec 2019 13:01:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:01:31: 8000000 INFO @ Thu, 05 Dec 2019 13:01:36: 5000000 INFO @ Thu, 05 Dec 2019 13:01:39: 9000000 INFO @ Thu, 05 Dec 2019 13:01:43: 6000000 INFO @ Thu, 05 Dec 2019 13:01:46: 10000000 INFO @ Thu, 05 Dec 2019 13:01:50: 7000000 INFO @ Thu, 05 Dec 2019 13:01:54: 11000000 INFO @ Thu, 05 Dec 2019 13:01:57: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:01:57: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:01:57: #1 total tags in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:01:57: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:01:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:01:57: #1 tags after filtering in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:01:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:01:57: #1 finished! INFO @ Thu, 05 Dec 2019 13:01:57: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:01:57: 8000000 INFO @ Thu, 05 Dec 2019 13:01:58: #2 number of paired peaks: 1793 INFO @ Thu, 05 Dec 2019 13:01:58: start model_add_line... INFO @ Thu, 05 Dec 2019 13:01:58: start X-correlation... INFO @ Thu, 05 Dec 2019 13:01:58: end of X-cor INFO @ Thu, 05 Dec 2019 13:01:58: #2 finished! INFO @ Thu, 05 Dec 2019 13:01:58: #2 predicted fragment length is 162 bps INFO @ Thu, 05 Dec 2019 13:01:58: #2 alternative fragment length(s) may be 0,162,175,178,221,267,271,588 bps INFO @ Thu, 05 Dec 2019 13:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10_model.r INFO @ Thu, 05 Dec 2019 13:01:58: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:04: 9000000 INFO @ Thu, 05 Dec 2019 13:02:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:02:10: 10000000 INFO @ Thu, 05 Dec 2019 13:02:20: 11000000 INFO @ Thu, 05 Dec 2019 13:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.05_summits.bed INFO @ Thu, 05 Dec 2019 13:02:23: Done! INFO @ Thu, 05 Dec 2019 13:02:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:02:23: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:02:23: #1 total tags in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:02:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1943 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:02:23: #1 tags after filtering in treatment: 11362787 INFO @ Thu, 05 Dec 2019 13:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:02:23: #1 finished! INFO @ Thu, 05 Dec 2019 13:02:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:02:24: #2 number of paired peaks: 1793 INFO @ Thu, 05 Dec 2019 13:02:24: start model_add_line... INFO @ Thu, 05 Dec 2019 13:02:24: start X-correlation... INFO @ Thu, 05 Dec 2019 13:02:24: end of X-cor INFO @ Thu, 05 Dec 2019 13:02:24: #2 finished! INFO @ Thu, 05 Dec 2019 13:02:24: #2 predicted fragment length is 162 bps INFO @ Thu, 05 Dec 2019 13:02:24: #2 alternative fragment length(s) may be 0,162,175,178,221,267,271,588 bps INFO @ Thu, 05 Dec 2019 13:02:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20_model.r INFO @ Thu, 05 Dec 2019 13:02:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.10_summits.bed INFO @ Thu, 05 Dec 2019 13:02:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717051/SRX5717051.20_summits.bed INFO @ Thu, 05 Dec 2019 13:03:17: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (376 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。