Job ID = 12265466 SRX = SRX5010747 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: 00:09:40 43253549 reads; of these: 43253549 (100.00%) were unpaired; of these: 1358779 (3.14%) aligned 0 times 36062701 (83.38%) aligned exactly 1 time 5832069 (13.48%) aligned >1 times 96.86% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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 20 files... [bam_rmdupse_core] 29614860 / 41894770 = 0.7069 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.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, 03 Apr 2021 07:25:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:25:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:25:17: 1000000 INFO @ Sat, 03 Apr 2021 07:25:23: 2000000 INFO @ Sat, 03 Apr 2021 07:25:29: 3000000 INFO @ Sat, 03 Apr 2021 07:25:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.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, 03 Apr 2021 07:25:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:25:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:25:41: 5000000 INFO @ Sat, 03 Apr 2021 07:25:48: 6000000 INFO @ Sat, 03 Apr 2021 07:25:48: 1000000 INFO @ Sat, 03 Apr 2021 07:25:54: 7000000 INFO @ Sat, 03 Apr 2021 07:25:54: 2000000 INFO @ Sat, 03 Apr 2021 07:26:00: 8000000 INFO @ Sat, 03 Apr 2021 07:26:01: 3000000 INFO @ Sat, 03 Apr 2021 07:26:06: 9000000 INFO @ Sat, 03 Apr 2021 07:26:08: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:26:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.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, 03 Apr 2021 07:26:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:26:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:26:14: 10000000 INFO @ Sat, 03 Apr 2021 07:26:15: 5000000 INFO @ Sat, 03 Apr 2021 07:26:18: 1000000 INFO @ Sat, 03 Apr 2021 07:26:20: 11000000 INFO @ Sat, 03 Apr 2021 07:26:22: 6000000 INFO @ Sat, 03 Apr 2021 07:26:25: 2000000 INFO @ Sat, 03 Apr 2021 07:26:27: 12000000 INFO @ Sat, 03 Apr 2021 07:26:29: 7000000 INFO @ Sat, 03 Apr 2021 07:26:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:26:29: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:26:29: #1 total tags in treatment: 12279910 INFO @ Sat, 03 Apr 2021 07:26:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:26:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:26:30: #1 tags after filtering in treatment: 12279831 INFO @ Sat, 03 Apr 2021 07:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:26:30: #1 finished! INFO @ Sat, 03 Apr 2021 07:26:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:26:31: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 07:26:31: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 07:26:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:26:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:26:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:26:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:26:31: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 07:26:31: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Apr 2021 07:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05_model.r WARNING @ Sat, 03 Apr 2021 07:26:31: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:26:31: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Apr 2021 07:26:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:26:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:26:32: 3000000 INFO @ Sat, 03 Apr 2021 07:26:35: 8000000 INFO @ Sat, 03 Apr 2021 07:26:38: 4000000 INFO @ Sat, 03 Apr 2021 07:26:42: 9000000 INFO @ Sat, 03 Apr 2021 07:26:45: 5000000 INFO @ Sat, 03 Apr 2021 07:26:50: 10000000 INFO @ Sat, 03 Apr 2021 07:26:52: 6000000 INFO @ Sat, 03 Apr 2021 07:26:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:26:56: 11000000 INFO @ Sat, 03 Apr 2021 07:26:58: 7000000 INFO @ Sat, 03 Apr 2021 07:27:03: 12000000 INFO @ Sat, 03 Apr 2021 07:27:04: 8000000 INFO @ Sat, 03 Apr 2021 07:27:05: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:27:05: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:27:05: #1 total tags in treatment: 12279910 INFO @ Sat, 03 Apr 2021 07:27:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:27:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:27:06: #1 tags after filtering in treatment: 12279831 INFO @ Sat, 03 Apr 2021 07:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:27:06: #1 finished! INFO @ Sat, 03 Apr 2021 07:27:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:27:06: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 07:27:06: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 07:27:06: start model_add_line... INFO @ Sat, 03 Apr 2021 07:27:07: start X-correlation... INFO @ Sat, 03 Apr 2021 07:27:07: end of X-cor INFO @ Sat, 03 Apr 2021 07:27:07: #2 finished! INFO @ Sat, 03 Apr 2021 07:27:07: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 07:27:07: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Apr 2021 07:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10_model.r WARNING @ Sat, 03 Apr 2021 07:27:07: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:27:07: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Apr 2021 07:27:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:27:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.05_summits.bed INFO @ Sat, 03 Apr 2021 07:27:08: Done! pass1 - making usageList (472 chroms): 3 millis pass2 - checking and writing primary data (10948 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:27:11: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:27:18: 10000000 INFO @ Sat, 03 Apr 2021 07:27:24: 11000000 INFO @ Sat, 03 Apr 2021 07:27:31: 12000000 INFO @ Sat, 03 Apr 2021 07:27:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:27:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:27:33: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:27:33: #1 total tags in treatment: 12279910 INFO @ Sat, 03 Apr 2021 07:27:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:27:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:27:34: #1 tags after filtering in treatment: 12279831 INFO @ Sat, 03 Apr 2021 07:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:27:34: #1 finished! INFO @ Sat, 03 Apr 2021 07:27:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:27:35: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 07:27:35: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 07:27:35: start model_add_line... INFO @ Sat, 03 Apr 2021 07:27:35: start X-correlation... INFO @ Sat, 03 Apr 2021 07:27:35: end of X-cor INFO @ Sat, 03 Apr 2021 07:27:35: #2 finished! INFO @ Sat, 03 Apr 2021 07:27:35: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 07:27:35: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Apr 2021 07:27:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20_model.r WARNING @ Sat, 03 Apr 2021 07:27:35: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:27:35: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Apr 2021 07:27:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:27:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:27:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.10_summits.bed INFO @ Sat, 03 Apr 2021 07:27:45: Done! pass1 - making usageList (300 chroms): 2 millis pass2 - checking and writing primary data (5012 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:27:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:28:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:28:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010747/SRX5010747.20_summits.bed INFO @ Sat, 03 Apr 2021 07:28:13: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (1282 records, 4 fields): 11 millis CompletedMACS2peakCalling