Job ID = 1293166 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:18:56 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 ) 2019-06-02T13:18:56 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 ) 2019-06-02T13:18:56 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 ) 2019-06-02T13:18:56 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 : 31,280,312 reads read : 31,280,312 reads written : 31,280,312 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: 00:07:14 31280312 reads; of these: 31280312 (100.00%) were unpaired; of these: 3535247 (11.30%) aligned 0 times 23662389 (75.65%) aligned exactly 1 time 4082676 (13.05%) aligned >1 times 88.70% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 8951150 / 27745065 = 0.3226 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 @ Sun, 02 Jun 2019 22:35:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.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 @ Sun, 02 Jun 2019 22:35:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.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 @ Sun, 02 Jun 2019 22:35:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.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 @ Sun, 02 Jun 2019 22:35:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:27: 1000000 INFO @ Sun, 02 Jun 2019 22:35:28: 1000000 INFO @ Sun, 02 Jun 2019 22:35:30: 1000000 INFO @ Sun, 02 Jun 2019 22:35:35: 2000000 INFO @ Sun, 02 Jun 2019 22:35:36: 2000000 INFO @ Sun, 02 Jun 2019 22:35:40: 2000000 INFO @ Sun, 02 Jun 2019 22:35:43: 3000000 INFO @ Sun, 02 Jun 2019 22:35:44: 3000000 INFO @ Sun, 02 Jun 2019 22:35:50: 4000000 INFO @ Sun, 02 Jun 2019 22:35:51: 3000000 INFO @ Sun, 02 Jun 2019 22:35:52: 4000000 INFO @ Sun, 02 Jun 2019 22:35:58: 5000000 INFO @ Sun, 02 Jun 2019 22:36:01: 5000000 INFO @ Sun, 02 Jun 2019 22:36:01: 4000000 INFO @ Sun, 02 Jun 2019 22:36:05: 6000000 INFO @ Sun, 02 Jun 2019 22:36:09: 6000000 INFO @ Sun, 02 Jun 2019 22:36:11: 5000000 INFO @ Sun, 02 Jun 2019 22:36:12: 7000000 INFO @ Sun, 02 Jun 2019 22:36:16: 7000000 INFO @ Sun, 02 Jun 2019 22:36:20: 8000000 INFO @ Sun, 02 Jun 2019 22:36:20: 6000000 INFO @ Sun, 02 Jun 2019 22:36:24: 8000000 INFO @ Sun, 02 Jun 2019 22:36:28: 9000000 INFO @ Sun, 02 Jun 2019 22:36:29: 7000000 INFO @ Sun, 02 Jun 2019 22:36:32: 9000000 INFO @ Sun, 02 Jun 2019 22:36:36: 10000000 INFO @ Sun, 02 Jun 2019 22:36:38: 8000000 INFO @ Sun, 02 Jun 2019 22:36:41: 10000000 INFO @ Sun, 02 Jun 2019 22:36:44: 11000000 INFO @ Sun, 02 Jun 2019 22:36:48: 9000000 INFO @ Sun, 02 Jun 2019 22:36:49: 11000000 INFO @ Sun, 02 Jun 2019 22:36:51: 12000000 INFO @ Sun, 02 Jun 2019 22:36:57: 12000000 INFO @ Sun, 02 Jun 2019 22:36:58: 13000000 INFO @ Sun, 02 Jun 2019 22:36:58: 10000000 INFO @ Sun, 02 Jun 2019 22:37:05: 13000000 INFO @ Sun, 02 Jun 2019 22:37:06: 14000000 INFO @ Sun, 02 Jun 2019 22:37:09: 11000000 INFO @ Sun, 02 Jun 2019 22:37:13: 14000000 INFO @ Sun, 02 Jun 2019 22:37:13: 15000000 INFO @ Sun, 02 Jun 2019 22:37:19: 12000000 INFO @ Sun, 02 Jun 2019 22:37:21: 15000000 INFO @ Sun, 02 Jun 2019 22:37:22: 16000000 INFO @ Sun, 02 Jun 2019 22:37:29: 17000000 INFO @ Sun, 02 Jun 2019 22:37:29: 16000000 INFO @ Sun, 02 Jun 2019 22:37:29: 13000000 INFO @ Sun, 02 Jun 2019 22:37:36: 18000000 INFO @ Sun, 02 Jun 2019 22:37:37: 17000000 INFO @ Sun, 02 Jun 2019 22:37:39: 14000000 INFO @ Sun, 02 Jun 2019 22:37:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:37:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:37:42: #1 total tags in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:37:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:37:43: #1 tags after filtering in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:45: 18000000 INFO @ Sun, 02 Jun 2019 22:37:45: #2 number of paired peaks: 2317 INFO @ Sun, 02 Jun 2019 22:37:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:45: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:45: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:37:45: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05_model.r INFO @ Sun, 02 Jun 2019 22:37:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:49: 15000000 INFO @ Sun, 02 Jun 2019 22:37:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:37:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:37:51: #1 total tags in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:37:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:37:52: #1 tags after filtering in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:52: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:53: #2 number of paired peaks: 2317 INFO @ Sun, 02 Jun 2019 22:37:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:54: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:37:54: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:37:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10_model.r INFO @ Sun, 02 Jun 2019 22:37:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:59: 16000000 INFO @ Sun, 02 Jun 2019 22:38:08: 17000000 INFO @ Sun, 02 Jun 2019 22:38:18: 18000000 INFO @ Sun, 02 Jun 2019 22:38:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:38:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:38:26: #1 total tags in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:38:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:38:27: #1 tags after filtering in treatment: 18793915 INFO @ Sun, 02 Jun 2019 22:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:38:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:38:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:38:29: #2 number of paired peaks: 2317 INFO @ Sun, 02 Jun 2019 22:38:29: start model_add_line... INFO @ Sun, 02 Jun 2019 22:38:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:38:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:38:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:38:29: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:38:29: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20_model.r INFO @ Sun, 02 Jun 2019 22:38:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:38:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:38:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.05_summits.bed INFO @ Sun, 02 Jun 2019 22:39:00: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (7201 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.10_summits.bed INFO @ Sun, 02 Jun 2019 22:39:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5716 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:39:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402731/SRX5402731.20_summits.bed INFO @ Sun, 02 Jun 2019 22:39:45: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4634 records, 4 fields): 42 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。