Job ID = 2640727 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:39:48 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 : 15,795,966 reads read : 15,795,966 reads written : 15,795,966 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:50 15795966 reads; of these: 15795966 (100.00%) were unpaired; of these: 2038507 (12.91%) aligned 0 times 10158579 (64.31%) aligned exactly 1 time 3598880 (22.78%) aligned >1 times 87.09% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 467492 / 13757459 = 0.0340 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:51:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:51:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:59: 1000000 INFO @ Sat, 24 Aug 2019 18:52:06: 2000000 INFO @ Sat, 24 Aug 2019 18:52:13: 3000000 INFO @ Sat, 24 Aug 2019 18:52:19: 4000000 INFO @ Sat, 24 Aug 2019 18:52:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:52:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:52:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:52:26: 5000000 INFO @ Sat, 24 Aug 2019 18:52:30: 1000000 INFO @ Sat, 24 Aug 2019 18:52:32: 6000000 INFO @ Sat, 24 Aug 2019 18:52:37: 2000000 INFO @ Sat, 24 Aug 2019 18:52:39: 7000000 INFO @ Sat, 24 Aug 2019 18:52:45: 3000000 INFO @ Sat, 24 Aug 2019 18:52:46: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:52:52: 4000000 INFO @ Sat, 24 Aug 2019 18:52:52: 9000000 INFO @ Sat, 24 Aug 2019 18:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:52:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:52:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:52:59: 5000000 INFO @ Sat, 24 Aug 2019 18:52:59: 10000000 INFO @ Sat, 24 Aug 2019 18:53:00: 1000000 INFO @ Sat, 24 Aug 2019 18:53:06: 11000000 INFO @ Sat, 24 Aug 2019 18:53:06: 6000000 INFO @ Sat, 24 Aug 2019 18:53:08: 2000000 INFO @ Sat, 24 Aug 2019 18:53:12: 12000000 INFO @ Sat, 24 Aug 2019 18:53:14: 7000000 INFO @ Sat, 24 Aug 2019 18:53:15: 3000000 INFO @ Sat, 24 Aug 2019 18:53:19: 13000000 INFO @ Sat, 24 Aug 2019 18:53:21: 8000000 INFO @ Sat, 24 Aug 2019 18:53:21: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:53:21: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:53:21: #1 total tags in treatment: 13289967 INFO @ Sat, 24 Aug 2019 18:53:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:53:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:53:22: #1 tags after filtering in treatment: 13289792 INFO @ Sat, 24 Aug 2019 18:53:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:53:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:53:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:53:22: 4000000 INFO @ Sat, 24 Aug 2019 18:53:26: #2 number of paired peaks: 69220 INFO @ Sat, 24 Aug 2019 18:53:26: start model_add_line... INFO @ Sat, 24 Aug 2019 18:53:26: start X-correlation... INFO @ Sat, 24 Aug 2019 18:53:26: end of X-cor INFO @ Sat, 24 Aug 2019 18:53:26: #2 finished! INFO @ Sat, 24 Aug 2019 18:53:26: #2 predicted fragment length is 90 bps INFO @ Sat, 24 Aug 2019 18:53:26: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 24 Aug 2019 18:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05_model.r INFO @ Sat, 24 Aug 2019 18:53:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:53:28: 9000000 INFO @ Sat, 24 Aug 2019 18:53:29: 5000000 INFO @ Sat, 24 Aug 2019 18:53:35: 10000000 INFO @ Sat, 24 Aug 2019 18:53:37: 6000000 INFO @ Sat, 24 Aug 2019 18:53:43: 11000000 INFO @ Sat, 24 Aug 2019 18:53:44: 7000000 INFO @ Sat, 24 Aug 2019 18:53:50: 12000000 INFO @ Sat, 24 Aug 2019 18:53:51: 8000000 INFO @ Sat, 24 Aug 2019 18:53:58: 13000000 INFO @ Sat, 24 Aug 2019 18:53:59: 9000000 INFO @ Sat, 24 Aug 2019 18:54:00: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:54:00: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:54:00: #1 total tags in treatment: 13289967 INFO @ Sat, 24 Aug 2019 18:54:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:54:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:54:00: #1 tags after filtering in treatment: 13289792 INFO @ Sat, 24 Aug 2019 18:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:54:00: #1 finished! INFO @ Sat, 24 Aug 2019 18:54:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:54:04: #2 number of paired peaks: 69220 INFO @ Sat, 24 Aug 2019 18:54:04: start model_add_line... INFO @ Sat, 24 Aug 2019 18:54:04: start X-correlation... INFO @ Sat, 24 Aug 2019 18:54:04: end of X-cor INFO @ Sat, 24 Aug 2019 18:54:04: #2 finished! INFO @ Sat, 24 Aug 2019 18:54:04: #2 predicted fragment length is 90 bps INFO @ Sat, 24 Aug 2019 18:54:04: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 24 Aug 2019 18:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10_model.r INFO @ Sat, 24 Aug 2019 18:54:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:06: 10000000 INFO @ Sat, 24 Aug 2019 18:54:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:54:13: 11000000 INFO @ Sat, 24 Aug 2019 18:54:20: 12000000 INFO @ Sat, 24 Aug 2019 18:54:27: 13000000 INFO @ Sat, 24 Aug 2019 18:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:54:29: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:54:29: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:54:29: #1 total tags in treatment: 13289967 INFO @ Sat, 24 Aug 2019 18:54:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:54:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.05_summits.bed INFO @ Sat, 24 Aug 2019 18:54:29: Done! INFO @ Sat, 24 Aug 2019 18:54:30: #1 tags after filtering in treatment: 13289792 INFO @ Sat, 24 Aug 2019 18:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:54:30: #1 finished! INFO @ Sat, 24 Aug 2019 18:54:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:54:30: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (72 chroms): 6 millis pass2 - checking and writing primary data (12691 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:54:34: #2 number of paired peaks: 69220 INFO @ Sat, 24 Aug 2019 18:54:34: start model_add_line... INFO @ Sat, 24 Aug 2019 18:54:34: start X-correlation... INFO @ Sat, 24 Aug 2019 18:54:34: end of X-cor INFO @ Sat, 24 Aug 2019 18:54:34: #2 finished! INFO @ Sat, 24 Aug 2019 18:54:34: #2 predicted fragment length is 90 bps INFO @ Sat, 24 Aug 2019 18:54:34: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 24 Aug 2019 18:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20_model.r INFO @ Sat, 24 Aug 2019 18:54:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.10_summits.bed INFO @ Sat, 24 Aug 2019 18:55:08: Done! pass1 - making usageList (36 chroms): 3 millis pass2 - checking and writing primary data (3748 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:55:15: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555171/SRX555171.20_summits.bed INFO @ Sat, 24 Aug 2019 18:55:37: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (898 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。