Job ID = 6627583 SRX = SRX8521416 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:04:47 prefetch.2.10.7: 1) Downloading 'SRR11978406'... 2020-07-14T03:04:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:54 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:55 prefetch.2.10.7: 'SRR11978406' is valid 2020-07-14T03:05:55 prefetch.2.10.7: 1) 'SRR11978406' was downloaded successfully 2020-07-14T03:05:55 prefetch.2.10.7: 'SRR11978406' has 0 unresolved dependencies Read 12727334 spots for SRR11978406/SRR11978406.sra Written 12727334 spots for SRR11978406/SRR11978406.sra 2020-07-14T03:06:50 prefetch.2.10.7: 1) Downloading 'SRR11978407'... 2020-07-14T03:06:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:04 prefetch.2.10.7: 'SRR11978407' is valid 2020-07-14T03:08:04 prefetch.2.10.7: 1) 'SRR11978407' was downloaded successfully 2020-07-14T03:08:04 prefetch.2.10.7: 'SRR11978407' has 0 unresolved dependencies Read 12409360 spots for SRR11978407/SRR11978407.sra Written 12409360 spots for SRR11978407/SRR11978407.sra 2020-07-14T03:09:05 prefetch.2.10.7: 1) Downloading 'SRR11978408'... 2020-07-14T03:09:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:12 prefetch.2.10.7: 'SRR11978408' is valid 2020-07-14T03:10:12 prefetch.2.10.7: 1) 'SRR11978408' was downloaded successfully 2020-07-14T03:10:12 prefetch.2.10.7: 'SRR11978408' has 0 unresolved dependencies Read 12505527 spots for SRR11978408/SRR11978408.sra Written 12505527 spots for SRR11978408/SRR11978408.sra 2020-07-14T03:11:07 prefetch.2.10.7: 1) Downloading 'SRR11978409'... 2020-07-14T03:11:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:12:55 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:12:56 prefetch.2.10.7: 'SRR11978409' is valid 2020-07-14T03:12:56 prefetch.2.10.7: 1) 'SRR11978409' was downloaded successfully 2020-07-14T03:12:56 prefetch.2.10.7: 'SRR11978409' has 0 unresolved dependencies Read 12482161 spots for SRR11978409/SRR11978409.sra Written 12482161 spots for SRR11978409/SRR11978409.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627772 ("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: 00:08:22 50124382 reads; of these: 50124382 (100.00%) were unpaired; of these: 41049019 (81.89%) aligned 0 times 6189399 (12.35%) aligned exactly 1 time 2885964 (5.76%) aligned >1 times 18.11% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 1801157 / 9075363 = 0.1985 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 12:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.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 12:25:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:25:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:25:24: 1000000 INFO @ Tue, 14 Jul 2020 12:25:33: 2000000 INFO @ Tue, 14 Jul 2020 12:25:41: 3000000 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 12:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.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 12:25:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:25:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:25:50: 4000000 INFO @ Tue, 14 Jul 2020 12:25:53: 1000000 INFO @ Tue, 14 Jul 2020 12:25:59: 5000000 INFO @ Tue, 14 Jul 2020 12:25:59: 2000000 INFO @ Tue, 14 Jul 2020 12:26:06: 3000000 INFO @ Tue, 14 Jul 2020 12:26:06: 6000000 INFO @ Tue, 14 Jul 2020 12:26:12: 4000000 INFO @ Tue, 14 Jul 2020 12:26:13: 7000000 INFO @ Tue, 14 Jul 2020 12:26:14: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:26:14: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:26:14: #1 total tags in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:26:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:26:14: #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 12:26:14: #1 tags after filtering in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:26:14: #1 finished! INFO @ Tue, 14 Jul 2020 12:26:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:26:15: #2 number of paired peaks: 219 WARNING @ Tue, 14 Jul 2020 12:26:15: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 14 Jul 2020 12:26:15: start model_add_line... INFO @ Tue, 14 Jul 2020 12:26:15: start X-correlation... INFO @ Tue, 14 Jul 2020 12:26:15: end of X-cor INFO @ Tue, 14 Jul 2020 12:26:15: #2 finished! INFO @ Tue, 14 Jul 2020 12:26:15: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:26:15: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05_model.r WARNING @ Tue, 14 Jul 2020 12:26:15: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:26:15: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:26:15: #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 12:26:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:26:15: #3 Pre-compute pvalue-qvalue table... 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 12:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.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 12:26:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:26:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:26:18: 5000000 INFO @ Tue, 14 Jul 2020 12:26:24: 1000000 INFO @ Tue, 14 Jul 2020 12:26:24: 6000000 INFO @ Tue, 14 Jul 2020 12:26:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:26:30: 7000000 INFO @ Tue, 14 Jul 2020 12:26:31: 2000000 INFO @ Tue, 14 Jul 2020 12:26:32: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:26:32: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:26:32: #1 total tags in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:26:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:26:32: #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 12:26:32: #1 tags after filtering in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:26:32: #1 finished! INFO @ Tue, 14 Jul 2020 12:26:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:26:33: #2 number of paired peaks: 219 WARNING @ Tue, 14 Jul 2020 12:26:33: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 14 Jul 2020 12:26:33: start model_add_line... INFO @ Tue, 14 Jul 2020 12:26:33: start X-correlation... INFO @ Tue, 14 Jul 2020 12:26:33: end of X-cor INFO @ Tue, 14 Jul 2020 12:26:33: #2 finished! INFO @ Tue, 14 Jul 2020 12:26:33: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:26:33: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10_model.r WARNING @ Tue, 14 Jul 2020 12:26:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:26:33: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:26:33: #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 12:26:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.05_summits.bed INFO @ Tue, 14 Jul 2020 12:26:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:26:38: 3000000 INFO @ Tue, 14 Jul 2020 12:26:45: 4000000 INFO @ Tue, 14 Jul 2020 12:26:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:26:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:26:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:26:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.10_summits.bed INFO @ Tue, 14 Jul 2020 12:26:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (874 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:26:58: 6000000 INFO @ Tue, 14 Jul 2020 12:27:05: 7000000 INFO @ Tue, 14 Jul 2020 12:27:07: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:27:07: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:27:07: #1 total tags in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:27:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:27:07: #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 12:27:07: #1 tags after filtering in treatment: 7274206 INFO @ Tue, 14 Jul 2020 12:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:07: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:08: #2 number of paired peaks: 219 WARNING @ Tue, 14 Jul 2020 12:27:08: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:08: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:08: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:08: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:08: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:08: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:27:08: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20_model.r WARNING @ Tue, 14 Jul 2020 12:27:08: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:08: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:27:08: #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 12:27:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:27:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521416/SRX8521416.20_summits.bed INFO @ Tue, 14 Jul 2020 12:27:30: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 1 millis CompletedMACS2peakCalling