Job ID = 12265400 SRX = SRX5010728 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:13 18496695 reads; of these: 18496695 (100.00%) were unpaired; of these: 751626 (4.06%) aligned 0 times 14360143 (77.64%) aligned exactly 1 time 3384926 (18.30%) aligned >1 times 95.94% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 9534806 / 17745069 = 0.5373 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 06:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.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 06:58:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:27: 1000000 INFO @ Sat, 03 Apr 2021 06:58:34: 2000000 INFO @ Sat, 03 Apr 2021 06:58:42: 3000000 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 06:58:49: 4000000 INFO @ Sat, 03 Apr 2021 06:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.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 06:58:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:58: 5000000 INFO @ Sat, 03 Apr 2021 06:58:58: 1000000 INFO @ Sat, 03 Apr 2021 06:59:05: 6000000 INFO @ Sat, 03 Apr 2021 06:59:06: 2000000 INFO @ Sat, 03 Apr 2021 06:59:14: 3000000 INFO @ Sat, 03 Apr 2021 06:59:15: 7000000 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 06:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.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 06:59:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:21: 4000000 INFO @ Sat, 03 Apr 2021 06:59:22: 8000000 INFO @ Sat, 03 Apr 2021 06:59:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:24: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:24: #1 total tags in treatment: 8210263 INFO @ Sat, 03 Apr 2021 06:59:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:24: #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 06:59:25: #1 tags after filtering in treatment: 8210163 INFO @ Sat, 03 Apr 2021 06:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:59:25: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:26: #2 number of paired peaks: 664 WARNING @ Sat, 03 Apr 2021 06:59:26: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:26: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:26: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:26: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:26: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:26: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:59:26: #2 alternative fragment length(s) may be 4,56,549 bps INFO @ Sat, 03 Apr 2021 06:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05_model.r WARNING @ Sat, 03 Apr 2021 06:59:26: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:26: #2 You may need to consider one of the other alternative d(s): 4,56,549 WARNING @ Sat, 03 Apr 2021 06:59:26: #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 06:59:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:27: 1000000 INFO @ Sat, 03 Apr 2021 06:59:30: 5000000 INFO @ Sat, 03 Apr 2021 06:59:36: 2000000 INFO @ Sat, 03 Apr 2021 06:59:38: 6000000 INFO @ Sat, 03 Apr 2021 06:59:44: 3000000 INFO @ Sat, 03 Apr 2021 06:59:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:59:47: 7000000 INFO @ Sat, 03 Apr 2021 06:59:52: 4000000 INFO @ Sat, 03 Apr 2021 06:59:55: 8000000 INFO @ Sat, 03 Apr 2021 06:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.05_summits.bed INFO @ Sat, 03 Apr 2021 06:59:55: Done! pass1 - making usageList (392 chroms): 2 millis pass2 - checking and writing primary data (4530 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:59:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:57: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:57: #1 total tags in treatment: 8210263 INFO @ Sat, 03 Apr 2021 06:59:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:57: #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 06:59:57: #1 tags after filtering in treatment: 8210163 INFO @ Sat, 03 Apr 2021 06:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:59:57: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:58: #2 number of paired peaks: 664 WARNING @ Sat, 03 Apr 2021 06:59:58: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:58: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:58: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:58: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:58: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:59:58: #2 alternative fragment length(s) may be 4,56,549 bps INFO @ Sat, 03 Apr 2021 06:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10_model.r WARNING @ Sat, 03 Apr 2021 06:59:58: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:58: #2 You may need to consider one of the other alternative d(s): 4,56,549 WARNING @ Sat, 03 Apr 2021 06:59:58: #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 06:59:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:00: 5000000 INFO @ Sat, 03 Apr 2021 07:00:08: 6000000 INFO @ Sat, 03 Apr 2021 07:00:16: 7000000 INFO @ Sat, 03 Apr 2021 07:00:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:24: 8000000 INFO @ Sat, 03 Apr 2021 07:00:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:26: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:26: #1 total tags in treatment: 8210263 INFO @ Sat, 03 Apr 2021 07:00:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:26: #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 07:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.10_summits.bed INFO @ Sat, 03 Apr 2021 07:00:26: Done! INFO @ Sat, 03 Apr 2021 07:00:26: #1 tags after filtering in treatment: 8210163 INFO @ Sat, 03 Apr 2021 07:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:00:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:26: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (210 chroms): 11 millis pass2 - checking and writing primary data (1469 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:00:27: #2 number of paired peaks: 664 WARNING @ Sat, 03 Apr 2021 07:00:27: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:27: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:00:27: #2 alternative fragment length(s) may be 4,56,549 bps INFO @ Sat, 03 Apr 2021 07:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20_model.r WARNING @ Sat, 03 Apr 2021 07:00:27: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:27: #2 You may need to consider one of the other alternative d(s): 4,56,549 WARNING @ Sat, 03 Apr 2021 07:00:27: #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 07:00:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010728/SRX5010728.20_summits.bed INFO @ Sat, 03 Apr 2021 07:00:54: Done! pass1 - making usageList (98 chroms): 10 millis pass2 - checking and writing primary data (300 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。