Job ID = 6627167 SRX = SRX8521303 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:25:16 prefetch.2.10.7: 1) Downloading 'SRR11978534'... 2020-07-14T01:25:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:26:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:26:29 prefetch.2.10.7: 'SRR11978534' is valid 2020-07-14T01:26:29 prefetch.2.10.7: 1) 'SRR11978534' was downloaded successfully 2020-07-14T01:26:29 prefetch.2.10.7: 'SRR11978534' has 0 unresolved dependencies Read 10110595 spots for SRR11978534/SRR11978534.sra Written 10110595 spots for SRR11978534/SRR11978534.sra 2020-07-14T01:27:18 prefetch.2.10.7: 1) Downloading 'SRR11978535'... 2020-07-14T01:27:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:28:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:28:52 prefetch.2.10.7: 'SRR11978535' is valid 2020-07-14T01:28:52 prefetch.2.10.7: 1) 'SRR11978535' was downloaded successfully 2020-07-14T01:28:52 prefetch.2.10.7: 'SRR11978535' has 0 unresolved dependencies Read 10001482 spots for SRR11978535/SRR11978535.sra Written 10001482 spots for SRR11978535/SRR11978535.sra 2020-07-14T01:29:39 prefetch.2.10.7: 1) Downloading 'SRR11978536'... 2020-07-14T01:29:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:35:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:35:32 prefetch.2.10.7: 'SRR11978536' is valid 2020-07-14T01:35:32 prefetch.2.10.7: 1) 'SRR11978536' was downloaded successfully 2020-07-14T01:35:32 prefetch.2.10.7: 'SRR11978536' has 0 unresolved dependencies Read 10256776 spots for SRR11978536/SRR11978536.sra Written 10256776 spots for SRR11978536/SRR11978536.sra 2020-07-14T01:36:20 prefetch.2.10.7: 1) Downloading 'SRR11978664'... 2020-07-14T01:36:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:39:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:39:03 prefetch.2.10.7: 'SRR11978664' is valid 2020-07-14T01:39:03 prefetch.2.10.7: 1) 'SRR11978664' was downloaded successfully 2020-07-14T01:39:03 prefetch.2.10.7: 'SRR11978664' has 0 unresolved dependencies Read 10106882 spots for SRR11978664/SRR11978664.sra Written 10106882 spots for SRR11978664/SRR11978664.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627438 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:00 40475735 reads; of these: 40475735 (100.00%) were unpaired; of these: 33136577 (81.87%) aligned 0 times 5369962 (13.27%) aligned exactly 1 time 1969196 (4.87%) aligned >1 times 18.13% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 1284333 / 7339158 = 0.1750 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 @ Tue, 14 Jul 2020 10:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 10:49:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:49:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:49:45: 1000000 INFO @ Tue, 14 Jul 2020 10:49:52: 2000000 INFO @ Tue, 14 Jul 2020 10:49:58: 3000000 INFO @ Tue, 14 Jul 2020 10:50:05: 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 @ Tue, 14 Jul 2020 10:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 10:50:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:50:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:50:12: 5000000 INFO @ Tue, 14 Jul 2020 10:50:15: 1000000 INFO @ Tue, 14 Jul 2020 10:50:19: 6000000 INFO @ Tue, 14 Jul 2020 10:50:19: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 10:50:19: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 10:50:19: #1 total tags in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:50:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:50:20: #1 tags after filtering in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:50:20: #1 finished! INFO @ Tue, 14 Jul 2020 10:50:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:50:20: #2 number of paired peaks: 294 WARNING @ Tue, 14 Jul 2020 10:50:20: 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 @ Tue, 14 Jul 2020 10:50:20: start model_add_line... INFO @ Tue, 14 Jul 2020 10:50:20: start X-correlation... INFO @ Tue, 14 Jul 2020 10:50:20: end of X-cor INFO @ Tue, 14 Jul 2020 10:50:20: #2 finished! INFO @ Tue, 14 Jul 2020 10:50:20: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:50:20: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05_model.r WARNING @ Tue, 14 Jul 2020 10:50:20: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:50:20: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:50:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:50:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:50:21: 2000000 INFO @ Tue, 14 Jul 2020 10:50:28: 3000000 INFO @ Tue, 14 Jul 2020 10:50:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:50:34: 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 @ Tue, 14 Jul 2020 10:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 10:50:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:50:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:50:41: 5000000 INFO @ Tue, 14 Jul 2020 10:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.05_summits.bed INFO @ Tue, 14 Jul 2020 10:50:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1870 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:50:45: 1000000 INFO @ Tue, 14 Jul 2020 10:50:47: 6000000 INFO @ Tue, 14 Jul 2020 10:50:48: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 10:50:48: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 10:50:48: #1 total tags in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:50:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:50:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:50:48: #1 tags after filtering in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:50:48: #1 finished! INFO @ Tue, 14 Jul 2020 10:50:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:50:48: #2 number of paired peaks: 294 WARNING @ Tue, 14 Jul 2020 10:50:48: 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 @ Tue, 14 Jul 2020 10:50:48: start model_add_line... INFO @ Tue, 14 Jul 2020 10:50:48: start X-correlation... INFO @ Tue, 14 Jul 2020 10:50:48: end of X-cor INFO @ Tue, 14 Jul 2020 10:50:48: #2 finished! INFO @ Tue, 14 Jul 2020 10:50:48: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:50:48: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10_model.r WARNING @ Tue, 14 Jul 2020 10:50:48: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:50:48: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:50:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:50:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:50:51: 2000000 INFO @ Tue, 14 Jul 2020 10:50:57: 3000000 INFO @ Tue, 14 Jul 2020 10:51:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:51:03: 4000000 INFO @ Tue, 14 Jul 2020 10:51:10: 5000000 INFO @ Tue, 14 Jul 2020 10:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.10_summits.bed INFO @ Tue, 14 Jul 2020 10:51:10: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (708 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:51:16: 6000000 INFO @ Tue, 14 Jul 2020 10:51:16: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 10:51:16: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 10:51:16: #1 total tags in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:51:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:51:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:51:16: #1 tags after filtering in treatment: 6054825 INFO @ Tue, 14 Jul 2020 10:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:51:16: #1 finished! INFO @ Tue, 14 Jul 2020 10:51:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:51:17: #2 number of paired peaks: 294 WARNING @ Tue, 14 Jul 2020 10:51:17: 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 @ Tue, 14 Jul 2020 10:51:17: start model_add_line... INFO @ Tue, 14 Jul 2020 10:51:17: start X-correlation... INFO @ Tue, 14 Jul 2020 10:51:17: end of X-cor INFO @ Tue, 14 Jul 2020 10:51:17: #2 finished! INFO @ Tue, 14 Jul 2020 10:51:17: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:51:17: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20_model.r WARNING @ Tue, 14 Jul 2020 10:51:17: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:51:17: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:51:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:51:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:51:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521303/SRX8521303.20_summits.bed INFO @ Tue, 14 Jul 2020 10:51:39: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling