Job ID = 1294887 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:40:39 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 ) 2019-06-03T01:40:39 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 : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:41 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669303 (3.91%) aligned 0 times 11145592 (65.05%) aligned exactly 1 time 5318657 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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] 2378330 / 16464249 = 0.1445 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 10:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.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 10:56:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:56:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.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 10:56:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:56:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.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 10:56:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:56:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:56:49: 1000000 INFO @ Mon, 03 Jun 2019 10:56:50: 1000000 INFO @ Mon, 03 Jun 2019 10:56:51: 1000000 INFO @ Mon, 03 Jun 2019 10:56:57: 2000000 INFO @ Mon, 03 Jun 2019 10:56:58: 2000000 INFO @ Mon, 03 Jun 2019 10:57:01: 2000000 INFO @ Mon, 03 Jun 2019 10:57:05: 3000000 INFO @ Mon, 03 Jun 2019 10:57:07: 3000000 INFO @ Mon, 03 Jun 2019 10:57:11: 3000000 INFO @ Mon, 03 Jun 2019 10:57:13: 4000000 INFO @ Mon, 03 Jun 2019 10:57:16: 4000000 INFO @ Mon, 03 Jun 2019 10:57:22: 4000000 INFO @ Mon, 03 Jun 2019 10:57:22: 5000000 INFO @ Mon, 03 Jun 2019 10:57:25: 5000000 INFO @ Mon, 03 Jun 2019 10:57:30: 6000000 INFO @ Mon, 03 Jun 2019 10:57:32: 5000000 INFO @ Mon, 03 Jun 2019 10:57:34: 6000000 INFO @ Mon, 03 Jun 2019 10:57:38: 7000000 INFO @ Mon, 03 Jun 2019 10:57:42: 6000000 INFO @ Mon, 03 Jun 2019 10:57:44: 7000000 INFO @ Mon, 03 Jun 2019 10:57:46: 8000000 INFO @ Mon, 03 Jun 2019 10:57:52: 7000000 INFO @ Mon, 03 Jun 2019 10:57:53: 8000000 INFO @ Mon, 03 Jun 2019 10:57:54: 9000000 INFO @ Mon, 03 Jun 2019 10:58:01: 10000000 INFO @ Mon, 03 Jun 2019 10:58:02: 9000000 INFO @ Mon, 03 Jun 2019 10:58:02: 8000000 INFO @ Mon, 03 Jun 2019 10:58:09: 11000000 INFO @ Mon, 03 Jun 2019 10:58:11: 10000000 INFO @ Mon, 03 Jun 2019 10:58:13: 9000000 INFO @ Mon, 03 Jun 2019 10:58:17: 12000000 INFO @ Mon, 03 Jun 2019 10:58:20: 11000000 INFO @ Mon, 03 Jun 2019 10:58:24: 10000000 INFO @ Mon, 03 Jun 2019 10:58:25: 13000000 INFO @ Mon, 03 Jun 2019 10:58:30: 12000000 INFO @ Mon, 03 Jun 2019 10:58:33: 14000000 INFO @ Mon, 03 Jun 2019 10:58:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:58:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:58:34: #1 total tags in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:58:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:58:34: #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 10:58:34: 11000000 INFO @ Mon, 03 Jun 2019 10:58:34: #1 tags after filtering in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:58:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:58:34: #1 finished! INFO @ Mon, 03 Jun 2019 10:58:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:58:36: #2 number of paired peaks: 350 WARNING @ Mon, 03 Jun 2019 10:58:36: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 03 Jun 2019 10:58:36: start model_add_line... INFO @ Mon, 03 Jun 2019 10:58:36: start X-correlation... INFO @ Mon, 03 Jun 2019 10:58:36: end of X-cor INFO @ Mon, 03 Jun 2019 10:58:36: #2 finished! INFO @ Mon, 03 Jun 2019 10:58:36: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:58:36: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10_model.r WARNING @ Mon, 03 Jun 2019 10:58:36: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:58:36: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:58:36: #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 10:58:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:58:39: 13000000 INFO @ Mon, 03 Jun 2019 10:58:45: 12000000 INFO @ Mon, 03 Jun 2019 10:58:49: 14000000 INFO @ Mon, 03 Jun 2019 10:58:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:58:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:58:50: #1 total tags in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:58:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:58:50: #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 10:58:50: #1 tags after filtering in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:58:50: #1 finished! INFO @ Mon, 03 Jun 2019 10:58:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:58:51: #2 number of paired peaks: 350 WARNING @ Mon, 03 Jun 2019 10:58:51: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 03 Jun 2019 10:58:51: start model_add_line... INFO @ Mon, 03 Jun 2019 10:58:51: start X-correlation... INFO @ Mon, 03 Jun 2019 10:58:51: end of X-cor INFO @ Mon, 03 Jun 2019 10:58:51: #2 finished! INFO @ Mon, 03 Jun 2019 10:58:51: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:58:51: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05_model.r WARNING @ Mon, 03 Jun 2019 10:58:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:58:51: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:58:51: #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 10:58:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:58:56: 13000000 INFO @ Mon, 03 Jun 2019 10:59:07: 14000000 INFO @ Mon, 03 Jun 2019 10:59:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:59:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:59:08: #1 total tags in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:59:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:59:08: #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 10:59:08: #1 tags after filtering in treatment: 14085919 INFO @ Mon, 03 Jun 2019 10:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:59:08: #1 finished! INFO @ Mon, 03 Jun 2019 10:59:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:59:09: #2 number of paired peaks: 350 WARNING @ Mon, 03 Jun 2019 10:59:09: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 03 Jun 2019 10:59:09: start model_add_line... INFO @ Mon, 03 Jun 2019 10:59:09: start X-correlation... INFO @ Mon, 03 Jun 2019 10:59:09: end of X-cor INFO @ Mon, 03 Jun 2019 10:59:09: #2 finished! INFO @ Mon, 03 Jun 2019 10:59:09: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:59:09: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20_model.r WARNING @ Mon, 03 Jun 2019 10:59:09: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:59:09: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:59:09: #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 10:59:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:59:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.10_summits.bed INFO @ Mon, 03 Jun 2019 10:59:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1913 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:59:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.05_summits.bed INFO @ Mon, 03 Jun 2019 10:59:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2201 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287964/SRX287964.20_summits.bed INFO @ Mon, 03 Jun 2019 11:00:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1487 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。