Job ID = 1294492 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:25:44 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 ) 2019-06-02T23:25:44 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 : 12,249,643 reads read : 12,249,643 reads written : 12,249,643 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: 00:07:36 12249643 reads; of these: 12249643 (100.00%) were unpaired; of these: 497044 (4.06%) aligned 0 times 5354962 (43.72%) aligned exactly 1 time 6397637 (52.23%) aligned >1 times 95.94% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 2051560 / 11752599 = 0.1746 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 08:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.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 08:40:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.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 08:40:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.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 08:40:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:29: 1000000 INFO @ Mon, 03 Jun 2019 08:40:30: 1000000 INFO @ Mon, 03 Jun 2019 08:40:32: 1000000 INFO @ Mon, 03 Jun 2019 08:40:37: 2000000 INFO @ Mon, 03 Jun 2019 08:40:39: 2000000 INFO @ Mon, 03 Jun 2019 08:40:43: 2000000 INFO @ Mon, 03 Jun 2019 08:40:45: 3000000 INFO @ Mon, 03 Jun 2019 08:40:48: 3000000 INFO @ Mon, 03 Jun 2019 08:40:53: 4000000 INFO @ Mon, 03 Jun 2019 08:40:54: 3000000 INFO @ Mon, 03 Jun 2019 08:40:58: 4000000 INFO @ Mon, 03 Jun 2019 08:41:01: 5000000 INFO @ Mon, 03 Jun 2019 08:41:05: 4000000 INFO @ Mon, 03 Jun 2019 08:41:07: 5000000 INFO @ Mon, 03 Jun 2019 08:41:10: 6000000 INFO @ Mon, 03 Jun 2019 08:41:17: 5000000 INFO @ Mon, 03 Jun 2019 08:41:17: 6000000 INFO @ Mon, 03 Jun 2019 08:41:18: 7000000 INFO @ Mon, 03 Jun 2019 08:41:26: 8000000 INFO @ Mon, 03 Jun 2019 08:41:26: 7000000 INFO @ Mon, 03 Jun 2019 08:41:28: 6000000 INFO @ Mon, 03 Jun 2019 08:41:34: 9000000 INFO @ Mon, 03 Jun 2019 08:41:36: 8000000 INFO @ Mon, 03 Jun 2019 08:41:39: 7000000 INFO @ Mon, 03 Jun 2019 08:41:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:41:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:41:40: #1 total tags in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:41:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:41:40: #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 08:41:40: #1 tags after filtering in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:41:40: #1 finished! INFO @ Mon, 03 Jun 2019 08:41:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:41:41: #2 number of paired peaks: 727 WARNING @ Mon, 03 Jun 2019 08:41:41: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Mon, 03 Jun 2019 08:41:41: start model_add_line... INFO @ Mon, 03 Jun 2019 08:41:41: start X-correlation... INFO @ Mon, 03 Jun 2019 08:41:41: end of X-cor INFO @ Mon, 03 Jun 2019 08:41:41: #2 finished! INFO @ Mon, 03 Jun 2019 08:41:41: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:41:41: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20_model.r WARNING @ Mon, 03 Jun 2019 08:41:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:41:41: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:41:41: #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 08:41:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:41:45: 9000000 INFO @ Mon, 03 Jun 2019 08:41:51: 8000000 INFO @ Mon, 03 Jun 2019 08:41:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:41:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:41:52: #1 total tags in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:41:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:41:52: #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 08:41:52: #1 tags after filtering in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:41:52: #1 finished! INFO @ Mon, 03 Jun 2019 08:41:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:41:53: #2 number of paired peaks: 727 WARNING @ Mon, 03 Jun 2019 08:41:53: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Mon, 03 Jun 2019 08:41:53: start model_add_line... INFO @ Mon, 03 Jun 2019 08:41:53: start X-correlation... INFO @ Mon, 03 Jun 2019 08:41:53: end of X-cor INFO @ Mon, 03 Jun 2019 08:41:53: #2 finished! INFO @ Mon, 03 Jun 2019 08:41:53: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:41:53: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10_model.r WARNING @ Mon, 03 Jun 2019 08:41:53: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:41:53: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:41:53: #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 08:41:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:42:02: 9000000 INFO @ Mon, 03 Jun 2019 08:42:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:42:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:42:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:42:09: #1 total tags in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:42:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:42:09: #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 08:42:09: #1 tags after filtering in treatment: 9701039 INFO @ Mon, 03 Jun 2019 08:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:42:09: #1 finished! INFO @ Mon, 03 Jun 2019 08:42:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:42:10: #2 number of paired peaks: 727 WARNING @ Mon, 03 Jun 2019 08:42:10: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Mon, 03 Jun 2019 08:42:10: start model_add_line... INFO @ Mon, 03 Jun 2019 08:42:10: start X-correlation... INFO @ Mon, 03 Jun 2019 08:42:10: end of X-cor INFO @ Mon, 03 Jun 2019 08:42:10: #2 finished! INFO @ Mon, 03 Jun 2019 08:42:10: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:42:10: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:42:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05_model.r WARNING @ Mon, 03 Jun 2019 08:42:10: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:42:10: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:42:10: #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 08:42:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:42:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:42:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.20_summits.bed INFO @ Mon, 03 Jun 2019 08:42:22: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.10_summits.bed INFO @ Mon, 03 Jun 2019 08:42:34: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1604 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:42:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287691/SRX287691.05_summits.bed INFO @ Mon, 03 Jun 2019 08:42:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2758 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。