Job ID = 14171677 SRX = SRX9986116 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:05:24 21397495 reads; of these: 21397495 (100.00%) were unpaired; of these: 1784494 (8.34%) aligned 0 times 14314090 (66.90%) aligned exactly 1 time 5298911 (24.76%) aligned >1 times 91.66% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 4166183 / 19613001 = 0.2124 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 12:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.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 12:34:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:17: 1000000 INFO @ Sat, 11 Dec 2021 12:34:23: 2000000 INFO @ Sat, 11 Dec 2021 12:34:28: 3000000 INFO @ Sat, 11 Dec 2021 12:34:34: 4000000 INFO @ Sat, 11 Dec 2021 12:34:39: 5000000 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 12:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.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 12:34:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:46: 6000000 INFO @ Sat, 11 Dec 2021 12:34:48: 1000000 INFO @ Sat, 11 Dec 2021 12:34:52: 7000000 INFO @ Sat, 11 Dec 2021 12:34:54: 2000000 INFO @ Sat, 11 Dec 2021 12:34:58: 8000000 INFO @ Sat, 11 Dec 2021 12:35:00: 3000000 INFO @ Sat, 11 Dec 2021 12:35:04: 9000000 INFO @ Sat, 11 Dec 2021 12:35:06: 4000000 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 12:35:10: 10000000 INFO @ Sat, 11 Dec 2021 12:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.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 12:35:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:35:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:35:12: 5000000 INFO @ Sat, 11 Dec 2021 12:35:17: 11000000 INFO @ Sat, 11 Dec 2021 12:35:19: 1000000 INFO @ Sat, 11 Dec 2021 12:35:19: 6000000 INFO @ Sat, 11 Dec 2021 12:35:24: 12000000 INFO @ Sat, 11 Dec 2021 12:35:26: 2000000 INFO @ Sat, 11 Dec 2021 12:35:26: 7000000 INFO @ Sat, 11 Dec 2021 12:35:31: 13000000 INFO @ Sat, 11 Dec 2021 12:35:32: 3000000 INFO @ Sat, 11 Dec 2021 12:35:33: 8000000 INFO @ Sat, 11 Dec 2021 12:35:38: 14000000 INFO @ Sat, 11 Dec 2021 12:35:39: 4000000 INFO @ Sat, 11 Dec 2021 12:35:40: 9000000 INFO @ Sat, 11 Dec 2021 12:35:44: 15000000 INFO @ Sat, 11 Dec 2021 12:35:46: 5000000 INFO @ Sat, 11 Dec 2021 12:35:46: 10000000 INFO @ Sat, 11 Dec 2021 12:35:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:35:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:35:48: #1 total tags in treatment: 15446818 INFO @ Sat, 11 Dec 2021 12:35:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:48: #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 12:35:48: #1 tags after filtering in treatment: 15446752 INFO @ Sat, 11 Dec 2021 12:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:35:48: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:49: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 12:35:49: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 12:35:49: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:49: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:49: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:49: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:49: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 12:35:49: #2 alternative fragment length(s) may be 1,48,516,550 bps INFO @ Sat, 11 Dec 2021 12:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05_model.r WARNING @ Sat, 11 Dec 2021 12:35:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:49: #2 You may need to consider one of the other alternative d(s): 1,48,516,550 WARNING @ Sat, 11 Dec 2021 12:35:49: #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 12:35:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:52: 6000000 INFO @ Sat, 11 Dec 2021 12:35:53: 11000000 INFO @ Sat, 11 Dec 2021 12:35:58: 7000000 INFO @ Sat, 11 Dec 2021 12:35:59: 12000000 INFO @ Sat, 11 Dec 2021 12:36:05: 8000000 INFO @ Sat, 11 Dec 2021 12:36:06: 13000000 INFO @ Sat, 11 Dec 2021 12:36:11: 9000000 INFO @ Sat, 11 Dec 2021 12:36:12: 14000000 INFO @ Sat, 11 Dec 2021 12:36:17: 10000000 INFO @ Sat, 11 Dec 2021 12:36:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:18: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:36:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:36:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:36:21: #1 total tags in treatment: 15446818 INFO @ Sat, 11 Dec 2021 12:36:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:36:21: #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 12:36:22: #1 tags after filtering in treatment: 15446752 INFO @ Sat, 11 Dec 2021 12:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:36:22: #1 finished! INFO @ Sat, 11 Dec 2021 12:36:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:36:23: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 12:36:23: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 12:36:23: start model_add_line... INFO @ Sat, 11 Dec 2021 12:36:23: start X-correlation... INFO @ Sat, 11 Dec 2021 12:36:23: end of X-cor INFO @ Sat, 11 Dec 2021 12:36:23: #2 finished! INFO @ Sat, 11 Dec 2021 12:36:23: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 12:36:23: #2 alternative fragment length(s) may be 1,48,516,550 bps INFO @ Sat, 11 Dec 2021 12:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10_model.r WARNING @ Sat, 11 Dec 2021 12:36:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:36:23: #2 You may need to consider one of the other alternative d(s): 1,48,516,550 WARNING @ Sat, 11 Dec 2021 12:36:23: #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 12:36:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:36:23: 11000000 INFO @ Sat, 11 Dec 2021 12:36:29: 12000000 INFO @ Sat, 11 Dec 2021 12:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.05_summits.bed INFO @ Sat, 11 Dec 2021 12:36:31: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:36:35: 13000000 INFO @ Sat, 11 Dec 2021 12:36:41: 14000000 INFO @ Sat, 11 Dec 2021 12:36:46: 15000000 INFO @ Sat, 11 Dec 2021 12:36:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:36:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:36:49: #1 total tags in treatment: 15446818 INFO @ Sat, 11 Dec 2021 12:36:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:36:49: #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 12:36:49: #1 tags after filtering in treatment: 15446752 INFO @ Sat, 11 Dec 2021 12:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:36:49: #1 finished! INFO @ Sat, 11 Dec 2021 12:36:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:36:50: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 12:36:50: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 12:36:50: start model_add_line... INFO @ Sat, 11 Dec 2021 12:36:50: start X-correlation... INFO @ Sat, 11 Dec 2021 12:36:50: end of X-cor INFO @ Sat, 11 Dec 2021 12:36:50: #2 finished! INFO @ Sat, 11 Dec 2021 12:36:50: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 12:36:50: #2 alternative fragment length(s) may be 1,48,516,550 bps INFO @ Sat, 11 Dec 2021 12:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20_model.r WARNING @ Sat, 11 Dec 2021 12:36:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:36:50: #2 You may need to consider one of the other alternative d(s): 1,48,516,550 WARNING @ Sat, 11 Dec 2021 12:36:50: #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 12:36:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:36:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.10_summits.bed INFO @ Sat, 11 Dec 2021 12:37:04: Done! pass1 - making usageList (231 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:37:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:37:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986116/SRX9986116.20_summits.bed INFO @ Sat, 11 Dec 2021 12:37:32: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 3 millis CompletedMACS2peakCalling