Job ID = 6508489 SRX = SRX287910 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:22:42 prefetch.2.10.7: 1) Downloading 'SRR870099'... 2020-06-26T14:22:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:24:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:24:42 prefetch.2.10.7: 1) 'SRR870099' was downloaded successfully Read 18691248 spots for SRR870099/SRR870099.sra Written 18691248 spots for SRR870099/SRR870099.sra 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: 00:05:59 18691248 reads; of these: 18691248 (100.00%) were unpaired; of these: 1198384 (6.41%) aligned 0 times 11734842 (62.78%) aligned exactly 1 time 5758022 (30.81%) aligned >1 times 93.59% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2904806 / 17492864 = 0.1661 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.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 @ Fri, 26 Jun 2020 23:36:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:36:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:36:42: 1000000 INFO @ Fri, 26 Jun 2020 23:36:48: 2000000 INFO @ Fri, 26 Jun 2020 23:36:53: 3000000 INFO @ Fri, 26 Jun 2020 23:36:59: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:37:05: 5000000 INFO @ Fri, 26 Jun 2020 23:37:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.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 @ Fri, 26 Jun 2020 23:37:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:37:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:37:11: 6000000 INFO @ Fri, 26 Jun 2020 23:37:12: 1000000 INFO @ Fri, 26 Jun 2020 23:37:18: 7000000 INFO @ Fri, 26 Jun 2020 23:37:18: 2000000 INFO @ Fri, 26 Jun 2020 23:37:24: 8000000 INFO @ Fri, 26 Jun 2020 23:37:25: 3000000 INFO @ Fri, 26 Jun 2020 23:37:30: 9000000 INFO @ Fri, 26 Jun 2020 23:37:31: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:37:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.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 @ Fri, 26 Jun 2020 23:37:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:37:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:37:37: 10000000 INFO @ Fri, 26 Jun 2020 23:37:38: 5000000 INFO @ Fri, 26 Jun 2020 23:37:42: 1000000 INFO @ Fri, 26 Jun 2020 23:37:44: 11000000 INFO @ Fri, 26 Jun 2020 23:37:45: 6000000 INFO @ Fri, 26 Jun 2020 23:37:49: 2000000 INFO @ Fri, 26 Jun 2020 23:37:51: 12000000 INFO @ Fri, 26 Jun 2020 23:37:52: 7000000 INFO @ Fri, 26 Jun 2020 23:37:56: 3000000 INFO @ Fri, 26 Jun 2020 23:37:57: 13000000 INFO @ Fri, 26 Jun 2020 23:37:59: 8000000 INFO @ Fri, 26 Jun 2020 23:38:03: 4000000 INFO @ Fri, 26 Jun 2020 23:38:04: 14000000 INFO @ Fri, 26 Jun 2020 23:38:06: 9000000 INFO @ Fri, 26 Jun 2020 23:38:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:38:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:38:08: #1 total tags in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:38:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:38:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:38:08: #1 tags after filtering in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:38:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:38:08: #1 finished! INFO @ Fri, 26 Jun 2020 23:38:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:38:10: 5000000 INFO @ Fri, 26 Jun 2020 23:38:10: #2 number of paired peaks: 669 WARNING @ Fri, 26 Jun 2020 23:38:10: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 26 Jun 2020 23:38:10: start model_add_line... INFO @ Fri, 26 Jun 2020 23:38:10: start X-correlation... INFO @ Fri, 26 Jun 2020 23:38:10: end of X-cor INFO @ Fri, 26 Jun 2020 23:38:10: #2 finished! INFO @ Fri, 26 Jun 2020 23:38:10: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 23:38:10: #2 alternative fragment length(s) may be 3,45,580 bps INFO @ Fri, 26 Jun 2020 23:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05_model.r WARNING @ Fri, 26 Jun 2020 23:38:10: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:38:10: #2 You may need to consider one of the other alternative d(s): 3,45,580 WARNING @ Fri, 26 Jun 2020 23:38:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:38:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:38:13: 10000000 INFO @ Fri, 26 Jun 2020 23:38:16: 6000000 INFO @ Fri, 26 Jun 2020 23:38:19: 11000000 INFO @ Fri, 26 Jun 2020 23:38:23: 7000000 INFO @ Fri, 26 Jun 2020 23:38:26: 12000000 INFO @ Fri, 26 Jun 2020 23:38:30: 8000000 INFO @ Fri, 26 Jun 2020 23:38:33: 13000000 INFO @ Fri, 26 Jun 2020 23:38:36: 9000000 INFO @ Fri, 26 Jun 2020 23:38:39: 14000000 INFO @ Fri, 26 Jun 2020 23:38:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:43: 10000000 INFO @ Fri, 26 Jun 2020 23:38:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:38:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:38:43: #1 total tags in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:38:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:38:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:38:44: #1 tags after filtering in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:38:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:38:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:38:45: #2 number of paired peaks: 669 WARNING @ Fri, 26 Jun 2020 23:38:45: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 26 Jun 2020 23:38:45: start model_add_line... INFO @ Fri, 26 Jun 2020 23:38:45: start X-correlation... INFO @ Fri, 26 Jun 2020 23:38:45: end of X-cor INFO @ Fri, 26 Jun 2020 23:38:45: #2 finished! INFO @ Fri, 26 Jun 2020 23:38:45: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 23:38:45: #2 alternative fragment length(s) may be 3,45,580 bps INFO @ Fri, 26 Jun 2020 23:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10_model.r WARNING @ Fri, 26 Jun 2020 23:38:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:38:45: #2 You may need to consider one of the other alternative d(s): 3,45,580 WARNING @ Fri, 26 Jun 2020 23:38:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:38:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:38:45: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:38:49: 11000000 INFO @ Fri, 26 Jun 2020 23:38:56: 12000000 INFO @ Fri, 26 Jun 2020 23:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.05_summits.bed INFO @ Fri, 26 Jun 2020 23:38:57: Done! pass1 - making usageList (679 chroms): 1 millis pass2 - checking and writing primary data (2423 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:39:02: 13000000 INFO @ Fri, 26 Jun 2020 23:39:08: 14000000 INFO @ Fri, 26 Jun 2020 23:39:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:39:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:39:12: #1 total tags in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:39:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:39:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:39:12: #1 tags after filtering in treatment: 14588058 INFO @ Fri, 26 Jun 2020 23:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:39:12: #1 finished! INFO @ Fri, 26 Jun 2020 23:39:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:39:13: #2 number of paired peaks: 669 WARNING @ Fri, 26 Jun 2020 23:39:13: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 26 Jun 2020 23:39:13: start model_add_line... INFO @ Fri, 26 Jun 2020 23:39:13: start X-correlation... INFO @ Fri, 26 Jun 2020 23:39:13: end of X-cor INFO @ Fri, 26 Jun 2020 23:39:13: #2 finished! INFO @ Fri, 26 Jun 2020 23:39:13: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 23:39:13: #2 alternative fragment length(s) may be 3,45,580 bps INFO @ Fri, 26 Jun 2020 23:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20_model.r WARNING @ Fri, 26 Jun 2020 23:39:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:39:13: #2 You may need to consider one of the other alternative d(s): 3,45,580 WARNING @ Fri, 26 Jun 2020 23:39:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:39:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:39:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:39:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:39:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.10_summits.bed INFO @ Fri, 26 Jun 2020 23:39:31: Done! pass1 - making usageList (555 chroms): 2 millis pass2 - checking and writing primary data (2001 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:39:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:40:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287910/SRX287910.20_summits.bed INFO @ Fri, 26 Jun 2020 23:40:00: Done! pass1 - making usageList (413 chroms): 1 millis pass2 - checking and writing primary data (1015 records, 4 fields): 15 millis CompletedMACS2peakCalling