Job ID = 1294111 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:54:06 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 ) 2019-06-02T19:54:12 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 : 7,336,300 reads read : 7,336,300 reads written : 7,336,300 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: 00:02:56 7336300 reads; of these: 7336300 (100.00%) were unpaired; of these: 210435 (2.87%) aligned 0 times 4840727 (65.98%) aligned exactly 1 time 2285138 (31.15%) aligned >1 times 97.13% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 745433 / 7125865 = 0.1046 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 04:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.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 04:59:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.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 04:59:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.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 04:59:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:31: 1000000 INFO @ Mon, 03 Jun 2019 04:59:33: 1000000 INFO @ Mon, 03 Jun 2019 04:59:34: 1000000 INFO @ Mon, 03 Jun 2019 04:59:38: 2000000 INFO @ Mon, 03 Jun 2019 04:59:42: 2000000 INFO @ Mon, 03 Jun 2019 04:59:42: 2000000 INFO @ Mon, 03 Jun 2019 04:59:45: 3000000 INFO @ Mon, 03 Jun 2019 04:59:50: 3000000 INFO @ Mon, 03 Jun 2019 04:59:51: 3000000 INFO @ Mon, 03 Jun 2019 04:59:51: 4000000 INFO @ Mon, 03 Jun 2019 04:59:58: 5000000 INFO @ Mon, 03 Jun 2019 04:59:59: 4000000 INFO @ Mon, 03 Jun 2019 05:00:00: 4000000 INFO @ Mon, 03 Jun 2019 05:00:05: 6000000 INFO @ Mon, 03 Jun 2019 05:00:07: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:07: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:07: #1 total tags in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:07: #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 05:00:07: #1 tags after filtering in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:07: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:08: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 05:00:08: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:08: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:08: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:08: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:08: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:08: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:00:08: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10_model.r WARNING @ Mon, 03 Jun 2019 05:00:08: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:08: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:00:08: #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 05:00:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:08: 5000000 INFO @ Mon, 03 Jun 2019 05:00:09: 5000000 INFO @ Mon, 03 Jun 2019 05:00:18: 6000000 INFO @ Mon, 03 Jun 2019 05:00:18: 6000000 INFO @ Mon, 03 Jun 2019 05:00:21: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:21: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:21: #1 total tags in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:21: #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 05:00:21: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:21: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:21: #1 total tags in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:21: #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 05:00:21: #1 tags after filtering in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:21: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:21: #1 tags after filtering in treatment: 6380432 INFO @ Mon, 03 Jun 2019 05:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:21: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:22: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 05:00:22: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:22: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 05:00:22: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:22: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:00:22: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05_model.r WARNING @ Mon, 03 Jun 2019 05:00:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:22: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:00:22: #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 05:00:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:22: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:00:22: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20_model.r WARNING @ Mon, 03 Jun 2019 05:00:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:22: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:00:22: #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 05:00:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.10_summits.bed INFO @ Mon, 03 Jun 2019 05:00:35: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (977 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.05_summits.bed INFO @ Mon, 03 Jun 2019 05:00:49: Done! INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187081/SRX187081.20_summits.bed INFO @ Mon, 03 Jun 2019 05:00:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1906 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。