Job ID = 14171463 SRX = SRX9137154 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5618129 spots for SRR12655984/SRR12655984.sra Written 5618129 spots for SRR12655984/SRR12655984.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171947 ("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: 00:04:18 5618129 reads; of these: 5618129 (100.00%) were unpaired; of these: 915800 (16.30%) aligned 0 times 3810720 (67.83%) aligned exactly 1 time 891609 (15.87%) aligned >1 times 83.70% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 558975 / 4702329 = 0.1189 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.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 @ Sat, 11 Dec 2021 11:51:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:51:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:51:16: 1000000 INFO @ Sat, 11 Dec 2021 11:51:25: 2000000 INFO @ Sat, 11 Dec 2021 11:51:33: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.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 @ Sat, 11 Dec 2021 11:51:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:51:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:51:42: 4000000 INFO @ Sat, 11 Dec 2021 11:51:43: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:51:43: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:51:43: #1 total tags in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:51:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:51:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:51:43: #1 tags after filtering in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:51:43: #1 finished! INFO @ Sat, 11 Dec 2021 11:51:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:51:44: #2 number of paired peaks: 9937 INFO @ Sat, 11 Dec 2021 11:51:44: start model_add_line... INFO @ Sat, 11 Dec 2021 11:51:44: start X-correlation... INFO @ Sat, 11 Dec 2021 11:51:44: end of X-cor INFO @ Sat, 11 Dec 2021 11:51:44: #2 finished! INFO @ Sat, 11 Dec 2021 11:51:44: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 11:51:44: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 11:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05_model.r WARNING @ Sat, 11 Dec 2021 11:51:44: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:51:44: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 11:51:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:51:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:51:48: 1000000 INFO @ Sat, 11 Dec 2021 11:51:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:51:58: 2000000 INFO @ Sat, 11 Dec 2021 11:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:51:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.05_summits.bed INFO @ Sat, 11 Dec 2021 11:51:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7031 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:52:07: 3000000 INFO @ Sat, 11 Dec 2021 11:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.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 @ Sat, 11 Dec 2021 11:52:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:17: 4000000 INFO @ Sat, 11 Dec 2021 11:52:18: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:52:18: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:52:18: #1 total tags in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:52:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:52:18: #1 tags after filtering in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:52:18: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:18: 1000000 INFO @ Sat, 11 Dec 2021 11:52:19: #2 number of paired peaks: 9937 INFO @ Sat, 11 Dec 2021 11:52:19: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:19: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:19: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:19: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:19: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 11:52:19: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 11:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10_model.r WARNING @ Sat, 11 Dec 2021 11:52:19: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:19: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 11:52:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:52:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:27: 2000000 INFO @ Sat, 11 Dec 2021 11:52:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.10_summits.bed INFO @ Sat, 11 Dec 2021 11:52:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6525 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:52:36: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:52:46: 4000000 INFO @ Sat, 11 Dec 2021 11:52:47: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:52:47: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:52:47: #1 total tags in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:52:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:52:47: #1 tags after filtering in treatment: 4143354 INFO @ Sat, 11 Dec 2021 11:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:52:47: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:48: #2 number of paired peaks: 9937 INFO @ Sat, 11 Dec 2021 11:52:48: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:48: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:48: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:48: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:48: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 11:52:48: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 11:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20_model.r WARNING @ Sat, 11 Dec 2021 11:52:48: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:48: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 11:52:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:52:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137154/SRX9137154.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5654 records, 4 fields): 6 millis CompletedMACS2peakCalling