Job ID = 1294560 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:55:16 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 ) 2019-06-02T23:56:07 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 ) 2019-06-02T23:58:00 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 ) 2019-06-03T00:01:18 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 : 21,266,404 reads read : 21,266,404 reads written : 21,266,404 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: 00:09:34 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1402732 (6.60%) aligned 0 times 13365792 (62.85%) aligned exactly 1 time 6497880 (30.55%) aligned >1 times 93.40% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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] 3846161 / 19863672 = 0.1936 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 09:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.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 09:20:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:20:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.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 09:20:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:20:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.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 09:20:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:20:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:20:39: 1000000 INFO @ Mon, 03 Jun 2019 09:20:40: 1000000 INFO @ Mon, 03 Jun 2019 09:20:41: 1000000 INFO @ Mon, 03 Jun 2019 09:20:46: 2000000 INFO @ Mon, 03 Jun 2019 09:20:47: 2000000 INFO @ Mon, 03 Jun 2019 09:20:49: 2000000 INFO @ Mon, 03 Jun 2019 09:20:53: 3000000 INFO @ Mon, 03 Jun 2019 09:20:55: 3000000 INFO @ Mon, 03 Jun 2019 09:20:57: 3000000 INFO @ Mon, 03 Jun 2019 09:21:00: 4000000 INFO @ Mon, 03 Jun 2019 09:21:03: 4000000 INFO @ Mon, 03 Jun 2019 09:21:05: 4000000 INFO @ Mon, 03 Jun 2019 09:21:07: 5000000 INFO @ Mon, 03 Jun 2019 09:21:10: 5000000 INFO @ Mon, 03 Jun 2019 09:21:14: 5000000 INFO @ Mon, 03 Jun 2019 09:21:14: 6000000 INFO @ Mon, 03 Jun 2019 09:21:18: 6000000 INFO @ Mon, 03 Jun 2019 09:21:21: 7000000 INFO @ Mon, 03 Jun 2019 09:21:21: 6000000 INFO @ Mon, 03 Jun 2019 09:21:25: 7000000 INFO @ Mon, 03 Jun 2019 09:21:28: 8000000 INFO @ Mon, 03 Jun 2019 09:21:29: 7000000 INFO @ Mon, 03 Jun 2019 09:21:32: 8000000 INFO @ Mon, 03 Jun 2019 09:21:34: 9000000 INFO @ Mon, 03 Jun 2019 09:21:38: 8000000 INFO @ Mon, 03 Jun 2019 09:21:39: 9000000 INFO @ Mon, 03 Jun 2019 09:21:41: 10000000 INFO @ Mon, 03 Jun 2019 09:21:46: 9000000 INFO @ Mon, 03 Jun 2019 09:21:47: 10000000 INFO @ Mon, 03 Jun 2019 09:21:48: 11000000 INFO @ Mon, 03 Jun 2019 09:21:54: 11000000 INFO @ Mon, 03 Jun 2019 09:21:54: 10000000 INFO @ Mon, 03 Jun 2019 09:21:55: 12000000 INFO @ Mon, 03 Jun 2019 09:22:01: 12000000 INFO @ Mon, 03 Jun 2019 09:22:02: 13000000 INFO @ Mon, 03 Jun 2019 09:22:02: 11000000 INFO @ Mon, 03 Jun 2019 09:22:08: 13000000 INFO @ Mon, 03 Jun 2019 09:22:08: 14000000 INFO @ Mon, 03 Jun 2019 09:22:10: 12000000 INFO @ Mon, 03 Jun 2019 09:22:15: 15000000 INFO @ Mon, 03 Jun 2019 09:22:16: 14000000 INFO @ Mon, 03 Jun 2019 09:22:18: 13000000 INFO @ Mon, 03 Jun 2019 09:22:22: 16000000 INFO @ Mon, 03 Jun 2019 09:22:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:22:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:22:23: #1 total tags in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:22:23: #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 09:22:23: #1 tags after filtering in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:22:23: #1 finished! INFO @ Mon, 03 Jun 2019 09:22:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:22:23: 15000000 INFO @ Mon, 03 Jun 2019 09:22:24: #2 number of paired peaks: 223 WARNING @ Mon, 03 Jun 2019 09:22:24: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Mon, 03 Jun 2019 09:22:24: start model_add_line... INFO @ Mon, 03 Jun 2019 09:22:24: start X-correlation... INFO @ Mon, 03 Jun 2019 09:22:25: end of X-cor INFO @ Mon, 03 Jun 2019 09:22:25: #2 finished! INFO @ Mon, 03 Jun 2019 09:22:25: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:22:25: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20_model.r WARNING @ Mon, 03 Jun 2019 09:22:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:22:25: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:22:25: #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 09:22:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:22:27: 14000000 INFO @ Mon, 03 Jun 2019 09:22:31: 16000000 INFO @ Mon, 03 Jun 2019 09:22:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:22:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:22:31: #1 total tags in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:22:31: #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 09:22:32: #1 tags after filtering in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:22:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:22:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:22:33: #2 number of paired peaks: 223 WARNING @ Mon, 03 Jun 2019 09:22:33: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Mon, 03 Jun 2019 09:22:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:22:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:22:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:22:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:22:33: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:22:33: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10_model.r WARNING @ Mon, 03 Jun 2019 09:22:33: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:22:33: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:22:33: #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 09:22:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:22:36: 15000000 INFO @ Mon, 03 Jun 2019 09:22:44: 16000000 INFO @ Mon, 03 Jun 2019 09:22:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:22:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:22:44: #1 total tags in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:22:44: #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 09:22:44: #1 tags after filtering in treatment: 16017511 INFO @ Mon, 03 Jun 2019 09:22:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:22:44: #1 finished! INFO @ Mon, 03 Jun 2019 09:22:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:22:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:22:46: #2 number of paired peaks: 223 WARNING @ Mon, 03 Jun 2019 09:22:46: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Mon, 03 Jun 2019 09:22:46: start model_add_line... INFO @ Mon, 03 Jun 2019 09:22:46: start X-correlation... INFO @ Mon, 03 Jun 2019 09:22:46: end of X-cor INFO @ Mon, 03 Jun 2019 09:22:46: #2 finished! INFO @ Mon, 03 Jun 2019 09:22:46: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:22:46: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05_model.r WARNING @ Mon, 03 Jun 2019 09:22:46: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:22:46: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:22:46: #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 09:22:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.20_summits.bed INFO @ Mon, 03 Jun 2019 09:23:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:23:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.10_summits.bed INFO @ Mon, 03 Jun 2019 09:23:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1743 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287741/SRX287741.05_summits.bed INFO @ Mon, 03 Jun 2019 09:23:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2060 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。