Job ID = 1294514 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:33:21 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 ) 2019-06-02T23:34:37 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 ) 2019-06-02T23:38:41 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 : 9,174,577 reads read : 9,174,577 reads written : 9,174,577 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: 00:04:26 9174577 reads; of these: 9174577 (100.00%) were unpaired; of these: 277684 (3.03%) aligned 0 times 6500415 (70.85%) aligned exactly 1 time 2396478 (26.12%) aligned >1 times 96.97% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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_rmdupse_core] 1068766 / 8896893 = 0.1201 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 08:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.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 08:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.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 08:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.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 08:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:48:13: 1000000 INFO @ Mon, 03 Jun 2019 08:48:13: 1000000 INFO @ Mon, 03 Jun 2019 08:48:13: 1000000 INFO @ Mon, 03 Jun 2019 08:48:23: 2000000 INFO @ Mon, 03 Jun 2019 08:48:23: 2000000 INFO @ Mon, 03 Jun 2019 08:48:23: 2000000 INFO @ Mon, 03 Jun 2019 08:48:33: 3000000 INFO @ Mon, 03 Jun 2019 08:48:33: 3000000 INFO @ Mon, 03 Jun 2019 08:48:33: 3000000 INFO @ Mon, 03 Jun 2019 08:48:42: 4000000 INFO @ Mon, 03 Jun 2019 08:48:43: 4000000 INFO @ Mon, 03 Jun 2019 08:48:43: 4000000 INFO @ Mon, 03 Jun 2019 08:48:52: 5000000 INFO @ Mon, 03 Jun 2019 08:48:53: 5000000 INFO @ Mon, 03 Jun 2019 08:48:53: 5000000 INFO @ Mon, 03 Jun 2019 08:49:01: 6000000 INFO @ Mon, 03 Jun 2019 08:49:02: 6000000 INFO @ Mon, 03 Jun 2019 08:49:02: 6000000 INFO @ Mon, 03 Jun 2019 08:49:11: 7000000 INFO @ Mon, 03 Jun 2019 08:49:12: 7000000 INFO @ Mon, 03 Jun 2019 08:49:12: 7000000 INFO @ Mon, 03 Jun 2019 08:49:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:49:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:49:19: #1 total tags in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:49:19: #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 08:49:19: #1 tags after filtering in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:49:19: #1 finished! INFO @ Mon, 03 Jun 2019 08:49:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:49:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:49:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:49:20: #1 total tags in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:49:20: #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 08:49:20: #1 tags after filtering in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:49:20: #1 finished! INFO @ Mon, 03 Jun 2019 08:49:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:49:20: #2 number of paired peaks: 2680 INFO @ Mon, 03 Jun 2019 08:49:20: start model_add_line... INFO @ Mon, 03 Jun 2019 08:49:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:49:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:49:20: #1 total tags in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:49:20: #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 08:49:20: start X-correlation... INFO @ Mon, 03 Jun 2019 08:49:20: end of X-cor INFO @ Mon, 03 Jun 2019 08:49:20: #2 finished! INFO @ Mon, 03 Jun 2019 08:49:20: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 08:49:20: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 08:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20_model.r WARNING @ Mon, 03 Jun 2019 08:49:20: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:49:20: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 08:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:49:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:49:20: #1 tags after filtering in treatment: 7828127 INFO @ Mon, 03 Jun 2019 08:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:49:20: #1 finished! INFO @ Mon, 03 Jun 2019 08:49:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:49:21: #2 number of paired peaks: 2680 INFO @ Mon, 03 Jun 2019 08:49:21: start model_add_line... INFO @ Mon, 03 Jun 2019 08:49:21: start X-correlation... INFO @ Mon, 03 Jun 2019 08:49:21: end of X-cor INFO @ Mon, 03 Jun 2019 08:49:21: #2 finished! INFO @ Mon, 03 Jun 2019 08:49:21: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 08:49:21: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 08:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05_model.r WARNING @ Mon, 03 Jun 2019 08:49:21: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:49:21: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 08:49:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:49:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:49:21: #2 number of paired peaks: 2680 INFO @ Mon, 03 Jun 2019 08:49:21: start model_add_line... INFO @ Mon, 03 Jun 2019 08:49:22: start X-correlation... INFO @ Mon, 03 Jun 2019 08:49:22: end of X-cor INFO @ Mon, 03 Jun 2019 08:49:22: #2 finished! INFO @ Mon, 03 Jun 2019 08:49:22: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 08:49:22: #2 alternative fragment length(s) may be 67 bps INFO @ Mon, 03 Jun 2019 08:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10_model.r WARNING @ Mon, 03 Jun 2019 08:49:22: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:49:22: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Mon, 03 Jun 2019 08:49:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:49:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.20_summits.bed INFO @ Mon, 03 Jun 2019 08:49:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.05_summits.bed INFO @ Mon, 03 Jun 2019 08:49:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4455 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287712/SRX287712.10_summits.bed INFO @ Mon, 03 Jun 2019 08:49:56: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1660 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。