Job ID = 1294513 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:34:37 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 ) 2019-06-02T23:34:37 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 ) 2019-06-02T23:39:34 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 ) 2019-06-02T23:39:34 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 ) 2019-06-02T23:41:18 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 : 24,549,420 reads read : 24,549,420 reads written : 24,549,420 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: 00:10:23 24549420 reads; of these: 24549420 (100.00%) were unpaired; of these: 1030414 (4.20%) aligned 0 times 17361853 (70.72%) aligned exactly 1 time 6157153 (25.08%) aligned >1 times 95.80% overall alignment rate Time searching: 00:10:23 Overall time: 00:10:23 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 12 files... [bam_rmdupse_core] 4642580 / 23519006 = 0.1974 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 09:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.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 09:04:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:04:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.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 09:04:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:04:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.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 09:04:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:04:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:04:37: 1000000 INFO @ Mon, 03 Jun 2019 09:04:38: 1000000 INFO @ Mon, 03 Jun 2019 09:04:38: 1000000 INFO @ Mon, 03 Jun 2019 09:04:46: 2000000 INFO @ Mon, 03 Jun 2019 09:04:47: 2000000 INFO @ Mon, 03 Jun 2019 09:04:48: 2000000 INFO @ Mon, 03 Jun 2019 09:04:55: 3000000 INFO @ Mon, 03 Jun 2019 09:04:56: 3000000 INFO @ Mon, 03 Jun 2019 09:04:57: 3000000 INFO @ Mon, 03 Jun 2019 09:05:03: 4000000 INFO @ Mon, 03 Jun 2019 09:05:05: 4000000 INFO @ Mon, 03 Jun 2019 09:05:06: 4000000 INFO @ Mon, 03 Jun 2019 09:05:12: 5000000 INFO @ Mon, 03 Jun 2019 09:05:14: 5000000 INFO @ Mon, 03 Jun 2019 09:05:15: 5000000 INFO @ Mon, 03 Jun 2019 09:05:21: 6000000 INFO @ Mon, 03 Jun 2019 09:05:23: 6000000 INFO @ Mon, 03 Jun 2019 09:05:24: 6000000 INFO @ Mon, 03 Jun 2019 09:05:29: 7000000 INFO @ Mon, 03 Jun 2019 09:05:32: 7000000 INFO @ Mon, 03 Jun 2019 09:05:32: 7000000 INFO @ Mon, 03 Jun 2019 09:05:38: 8000000 INFO @ Mon, 03 Jun 2019 09:05:40: 8000000 INFO @ Mon, 03 Jun 2019 09:05:41: 8000000 INFO @ Mon, 03 Jun 2019 09:05:46: 9000000 INFO @ Mon, 03 Jun 2019 09:05:48: 9000000 INFO @ Mon, 03 Jun 2019 09:05:50: 9000000 INFO @ Mon, 03 Jun 2019 09:05:55: 10000000 INFO @ Mon, 03 Jun 2019 09:05:56: 10000000 INFO @ Mon, 03 Jun 2019 09:05:59: 10000000 INFO @ Mon, 03 Jun 2019 09:06:03: 11000000 INFO @ Mon, 03 Jun 2019 09:06:04: 11000000 INFO @ Mon, 03 Jun 2019 09:06:08: 11000000 INFO @ Mon, 03 Jun 2019 09:06:11: 12000000 INFO @ Mon, 03 Jun 2019 09:06:12: 12000000 INFO @ Mon, 03 Jun 2019 09:06:17: 12000000 INFO @ Mon, 03 Jun 2019 09:06:19: 13000000 INFO @ Mon, 03 Jun 2019 09:06:20: 13000000 INFO @ Mon, 03 Jun 2019 09:06:26: 13000000 INFO @ Mon, 03 Jun 2019 09:06:27: 14000000 INFO @ Mon, 03 Jun 2019 09:06:29: 14000000 INFO @ Mon, 03 Jun 2019 09:06:34: 15000000 INFO @ Mon, 03 Jun 2019 09:06:35: 14000000 INFO @ Mon, 03 Jun 2019 09:06:37: 15000000 INFO @ Mon, 03 Jun 2019 09:06:42: 16000000 INFO @ Mon, 03 Jun 2019 09:06:44: 15000000 INFO @ Mon, 03 Jun 2019 09:06:46: 16000000 INFO @ Mon, 03 Jun 2019 09:06:49: 17000000 INFO @ Mon, 03 Jun 2019 09:06:53: 16000000 INFO @ Mon, 03 Jun 2019 09:06:55: 17000000 INFO @ Mon, 03 Jun 2019 09:06:58: 18000000 INFO @ Mon, 03 Jun 2019 09:07:02: 17000000 INFO @ Mon, 03 Jun 2019 09:07:04: 18000000 INFO @ Mon, 03 Jun 2019 09:07:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:05: #1 total tags in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:05: #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 09:07:06: #1 tags after filtering in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:06: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:08: #2 number of paired peaks: 1629 INFO @ Mon, 03 Jun 2019 09:07:08: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:08: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:08: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:08: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:08: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 09:07:08: #2 alternative fragment length(s) may be 4,102 bps INFO @ Mon, 03 Jun 2019 09:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05_model.r INFO @ Mon, 03 Jun 2019 09:07:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:07:11: 18000000 INFO @ Mon, 03 Jun 2019 09:07:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:11: #1 total tags in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:11: #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 09:07:12: #1 tags after filtering in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:12: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:14: #2 number of paired peaks: 1629 INFO @ Mon, 03 Jun 2019 09:07:14: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:14: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:14: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:14: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:14: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 09:07:14: #2 alternative fragment length(s) may be 4,102 bps INFO @ Mon, 03 Jun 2019 09:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20_model.r INFO @ Mon, 03 Jun 2019 09:07:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:07:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:18: #1 total tags in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:18: #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 09:07:19: #1 tags after filtering in treatment: 18876426 INFO @ Mon, 03 Jun 2019 09:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:19: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:21: #2 number of paired peaks: 1629 INFO @ Mon, 03 Jun 2019 09:07:21: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:21: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:21: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:21: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:21: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 09:07:21: #2 alternative fragment length(s) may be 4,102 bps INFO @ Mon, 03 Jun 2019 09:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10_model.r INFO @ Mon, 03 Jun 2019 09:07:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:08:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.05_summits.bed INFO @ Mon, 03 Jun 2019 09:08:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9319 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.20_summits.bed INFO @ Mon, 03 Jun 2019 09:08:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1737 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287711/SRX287711.10_summits.bed INFO @ Mon, 03 Jun 2019 09:08:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5106 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。