Job ID = 1294367 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:55:14 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 ) 2019-06-02T21:55:14 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 : 22,425,200 reads read : 22,425,200 reads written : 22,425,200 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: 00:08:02 22425200 reads; of these: 22425200 (100.00%) were unpaired; of these: 3403799 (15.18%) aligned 0 times 14257046 (63.58%) aligned exactly 1 time 4764355 (21.25%) aligned >1 times 84.82% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 6659463 / 19021401 = 0.3501 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 07:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.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 07:16:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:16:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.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 07:16:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:16:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.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 07:16:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:16:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:16:46: 1000000 INFO @ Mon, 03 Jun 2019 07:16:46: 1000000 INFO @ Mon, 03 Jun 2019 07:16:47: 1000000 INFO @ Mon, 03 Jun 2019 07:16:55: 2000000 INFO @ Mon, 03 Jun 2019 07:16:55: 2000000 INFO @ Mon, 03 Jun 2019 07:16:57: 2000000 INFO @ Mon, 03 Jun 2019 07:17:03: 3000000 INFO @ Mon, 03 Jun 2019 07:17:03: 3000000 INFO @ Mon, 03 Jun 2019 07:17:07: 3000000 INFO @ Mon, 03 Jun 2019 07:17:11: 4000000 INFO @ Mon, 03 Jun 2019 07:17:11: 4000000 INFO @ Mon, 03 Jun 2019 07:17:16: 4000000 INFO @ Mon, 03 Jun 2019 07:17:19: 5000000 INFO @ Mon, 03 Jun 2019 07:17:20: 5000000 INFO @ Mon, 03 Jun 2019 07:17:26: 5000000 INFO @ Mon, 03 Jun 2019 07:17:28: 6000000 INFO @ Mon, 03 Jun 2019 07:17:28: 6000000 INFO @ Mon, 03 Jun 2019 07:17:35: 6000000 INFO @ Mon, 03 Jun 2019 07:17:36: 7000000 INFO @ Mon, 03 Jun 2019 07:17:36: 7000000 INFO @ Mon, 03 Jun 2019 07:17:45: 7000000 INFO @ Mon, 03 Jun 2019 07:17:45: 8000000 INFO @ Mon, 03 Jun 2019 07:17:46: 8000000 INFO @ Mon, 03 Jun 2019 07:17:53: 9000000 INFO @ Mon, 03 Jun 2019 07:17:54: 9000000 INFO @ Mon, 03 Jun 2019 07:17:54: 8000000 INFO @ Mon, 03 Jun 2019 07:18:02: 10000000 INFO @ Mon, 03 Jun 2019 07:18:02: 10000000 INFO @ Mon, 03 Jun 2019 07:18:04: 9000000 INFO @ Mon, 03 Jun 2019 07:18:11: 11000000 INFO @ Mon, 03 Jun 2019 07:18:11: 11000000 INFO @ Mon, 03 Jun 2019 07:18:14: 10000000 INFO @ Mon, 03 Jun 2019 07:18:19: 12000000 INFO @ Mon, 03 Jun 2019 07:18:20: 12000000 INFO @ Mon, 03 Jun 2019 07:18:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:18:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:18:23: #1 total tags in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:18:23: #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 07:18:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:18:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:18:23: #1 total tags in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:18:23: #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 07:18:23: #1 tags after filtering in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:18:23: #1 finished! INFO @ Mon, 03 Jun 2019 07:18:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:18:23: #1 tags after filtering in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:18:23: #1 finished! INFO @ Mon, 03 Jun 2019 07:18:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:18:24: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 07:18:24: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 07:18:24: start model_add_line... INFO @ Mon, 03 Jun 2019 07:18:24: start X-correlation... INFO @ Mon, 03 Jun 2019 07:18:24: end of X-cor INFO @ Mon, 03 Jun 2019 07:18:24: #2 finished! INFO @ Mon, 03 Jun 2019 07:18:24: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 07:18:24: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 07:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10_model.r WARNING @ Mon, 03 Jun 2019 07:18:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:18:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 07:18:24: #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 07:18:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:18:24: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 07:18:24: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 07:18:24: start model_add_line... INFO @ Mon, 03 Jun 2019 07:18:24: start X-correlation... INFO @ Mon, 03 Jun 2019 07:18:24: 11000000 INFO @ Mon, 03 Jun 2019 07:18:24: end of X-cor INFO @ Mon, 03 Jun 2019 07:18:24: #2 finished! INFO @ Mon, 03 Jun 2019 07:18:24: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 07:18:24: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 07:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20_model.r WARNING @ Mon, 03 Jun 2019 07:18:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:18:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 07:18:24: #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 07:18:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:18:34: 12000000 INFO @ Mon, 03 Jun 2019 07:18:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:18:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:18:37: #1 total tags in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:18:37: #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 07:18:37: #1 tags after filtering in treatment: 12361938 INFO @ Mon, 03 Jun 2019 07:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:18:37: #1 finished! INFO @ Mon, 03 Jun 2019 07:18:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:18:39: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 07:18:39: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 07:18:39: start model_add_line... INFO @ Mon, 03 Jun 2019 07:18:39: start X-correlation... INFO @ Mon, 03 Jun 2019 07:18:39: end of X-cor INFO @ Mon, 03 Jun 2019 07:18:39: #2 finished! INFO @ Mon, 03 Jun 2019 07:18:39: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 07:18:39: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 07:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05_model.r WARNING @ Mon, 03 Jun 2019 07:18:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:18:39: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 07:18:39: #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 07:18:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:18:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:18:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:19:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.10_summits.bed INFO @ Mon, 03 Jun 2019 07:19:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1365 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:19:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:19:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:19:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.20_summits.bed INFO @ Mon, 03 Jun 2019 07:19:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1009 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2663650/SRX2663650.05_summits.bed INFO @ Mon, 03 Jun 2019 07:19:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1797 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。