Job ID = 1294271 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:04:01 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 : 25,604,892 reads read : 25,604,892 reads written : 25,604,892 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: 00:05:10 25604892 reads; of these: 25604892 (100.00%) were unpaired; of these: 2287678 (8.93%) aligned 0 times 20831288 (81.36%) aligned exactly 1 time 2485926 (9.71%) aligned >1 times 91.07% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 9774099 / 23317214 = 0.4192 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 06:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.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 06:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.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 06:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.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 06:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:24:08: 1000000 INFO @ Mon, 03 Jun 2019 06:24:10: 1000000 INFO @ Mon, 03 Jun 2019 06:24:10: 1000000 INFO @ Mon, 03 Jun 2019 06:24:16: 2000000 INFO @ Mon, 03 Jun 2019 06:24:19: 2000000 INFO @ Mon, 03 Jun 2019 06:24:20: 2000000 INFO @ Mon, 03 Jun 2019 06:24:23: 3000000 INFO @ Mon, 03 Jun 2019 06:24:28: 3000000 INFO @ Mon, 03 Jun 2019 06:24:29: 3000000 INFO @ Mon, 03 Jun 2019 06:24:31: 4000000 INFO @ Mon, 03 Jun 2019 06:24:36: 4000000 INFO @ Mon, 03 Jun 2019 06:24:38: 5000000 INFO @ Mon, 03 Jun 2019 06:24:39: 4000000 INFO @ Mon, 03 Jun 2019 06:24:45: 5000000 INFO @ Mon, 03 Jun 2019 06:24:46: 6000000 INFO @ Mon, 03 Jun 2019 06:24:48: 5000000 INFO @ Mon, 03 Jun 2019 06:24:53: 7000000 INFO @ Mon, 03 Jun 2019 06:24:54: 6000000 INFO @ Mon, 03 Jun 2019 06:24:58: 6000000 INFO @ Mon, 03 Jun 2019 06:25:01: 8000000 INFO @ Mon, 03 Jun 2019 06:25:03: 7000000 INFO @ Mon, 03 Jun 2019 06:25:07: 7000000 INFO @ Mon, 03 Jun 2019 06:25:08: 9000000 INFO @ Mon, 03 Jun 2019 06:25:11: 8000000 INFO @ Mon, 03 Jun 2019 06:25:15: 10000000 INFO @ Mon, 03 Jun 2019 06:25:16: 8000000 INFO @ Mon, 03 Jun 2019 06:25:20: 9000000 INFO @ Mon, 03 Jun 2019 06:25:23: 11000000 INFO @ Mon, 03 Jun 2019 06:25:26: 9000000 INFO @ Mon, 03 Jun 2019 06:25:29: 10000000 INFO @ Mon, 03 Jun 2019 06:25:30: 12000000 INFO @ Mon, 03 Jun 2019 06:25:35: 10000000 INFO @ Mon, 03 Jun 2019 06:25:37: 11000000 INFO @ Mon, 03 Jun 2019 06:25:37: 13000000 INFO @ Mon, 03 Jun 2019 06:25:42: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:25:42: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:25:42: #1 total tags in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:25:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:25:42: #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 06:25:42: #1 tags after filtering in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:25:42: #1 finished! INFO @ Mon, 03 Jun 2019 06:25:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:25:44: #2 number of paired peaks: 5838 INFO @ Mon, 03 Jun 2019 06:25:44: start model_add_line... INFO @ Mon, 03 Jun 2019 06:25:44: start X-correlation... INFO @ Mon, 03 Jun 2019 06:25:44: end of X-cor INFO @ Mon, 03 Jun 2019 06:25:44: #2 finished! INFO @ Mon, 03 Jun 2019 06:25:44: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 06:25:44: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 06:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05_model.r INFO @ Mon, 03 Jun 2019 06:25:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:25:44: 11000000 INFO @ Mon, 03 Jun 2019 06:25:46: 12000000 INFO @ Mon, 03 Jun 2019 06:25:53: 12000000 INFO @ Mon, 03 Jun 2019 06:25:54: 13000000 INFO @ Mon, 03 Jun 2019 06:25:59: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:25:59: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:25:59: #1 total tags in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:25:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:25:59: #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 06:25:59: #1 tags after filtering in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:25:59: #1 finished! INFO @ Mon, 03 Jun 2019 06:25:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:26:01: #2 number of paired peaks: 5838 INFO @ Mon, 03 Jun 2019 06:26:01: start model_add_line... INFO @ Mon, 03 Jun 2019 06:26:02: start X-correlation... INFO @ Mon, 03 Jun 2019 06:26:02: end of X-cor INFO @ Mon, 03 Jun 2019 06:26:02: #2 finished! INFO @ Mon, 03 Jun 2019 06:26:02: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 06:26:02: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 06:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10_model.r INFO @ Mon, 03 Jun 2019 06:26:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:26:02: 13000000 INFO @ Mon, 03 Jun 2019 06:26:07: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:26:07: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:26:07: #1 total tags in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:26:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:26:07: #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 06:26:07: #1 tags after filtering in treatment: 13543115 INFO @ Mon, 03 Jun 2019 06:26:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:26:07: #1 finished! INFO @ Mon, 03 Jun 2019 06:26:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:26:09: #2 number of paired peaks: 5838 INFO @ Mon, 03 Jun 2019 06:26:09: start model_add_line... INFO @ Mon, 03 Jun 2019 06:26:09: start X-correlation... INFO @ Mon, 03 Jun 2019 06:26:09: end of X-cor INFO @ Mon, 03 Jun 2019 06:26:09: #2 finished! INFO @ Mon, 03 Jun 2019 06:26:09: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 06:26:09: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 06:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20_model.r INFO @ Mon, 03 Jun 2019 06:26:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:26:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:26:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.05_summits.bed INFO @ Mon, 03 Jun 2019 06:26:46: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11444 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:26:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.10_summits.bed INFO @ Mon, 03 Jun 2019 06:27:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7550 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220297/SRX220297.20_summits.bed INFO @ Mon, 03 Jun 2019 06:27:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4794 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。