Job ID = 6627158 SRX = SRX8156262 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: 00:05:02 19338448 reads; of these: 19338448 (100.00%) were unpaired; of these: 2264913 (11.71%) aligned 0 times 13380894 (69.19%) aligned exactly 1 time 3692641 (19.09%) aligned >1 times 88.29% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 3582168 / 17073535 = 0.2098 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 10:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.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 10:31:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:31:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:31:24: 1000000 INFO @ Tue, 14 Jul 2020 10:31:29: 2000000 INFO @ Tue, 14 Jul 2020 10:31:34: 3000000 INFO @ Tue, 14 Jul 2020 10:31:39: 4000000 INFO @ Tue, 14 Jul 2020 10:31:45: 5000000 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 10:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.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 10:31:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:31:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:31:50: 6000000 INFO @ Tue, 14 Jul 2020 10:31:54: 1000000 INFO @ Tue, 14 Jul 2020 10:31:55: 7000000 INFO @ Tue, 14 Jul 2020 10:32:00: 2000000 INFO @ Tue, 14 Jul 2020 10:32:01: 8000000 INFO @ Tue, 14 Jul 2020 10:32:06: 3000000 INFO @ Tue, 14 Jul 2020 10:32:07: 9000000 INFO @ Tue, 14 Jul 2020 10:32:11: 4000000 INFO @ Tue, 14 Jul 2020 10:32:12: 10000000 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 10:32:17: 5000000 INFO @ Tue, 14 Jul 2020 10:32:18: 11000000 INFO @ Tue, 14 Jul 2020 10:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.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 10:32:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:32:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:32:23: 6000000 INFO @ Tue, 14 Jul 2020 10:32:24: 12000000 INFO @ Tue, 14 Jul 2020 10:32:25: 1000000 INFO @ Tue, 14 Jul 2020 10:32:28: 7000000 INFO @ Tue, 14 Jul 2020 10:32:29: 13000000 INFO @ Tue, 14 Jul 2020 10:32:31: 2000000 INFO @ Tue, 14 Jul 2020 10:32:32: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:32:32: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:32:32: #1 total tags in treatment: 13491367 INFO @ Tue, 14 Jul 2020 10:32:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:32:32: #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 10:32:33: #1 tags after filtering in treatment: 13491296 INFO @ Tue, 14 Jul 2020 10:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:32:33: #1 finished! INFO @ Tue, 14 Jul 2020 10:32:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:32:34: #2 number of paired peaks: 112 WARNING @ Tue, 14 Jul 2020 10:32:34: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 14 Jul 2020 10:32:34: start model_add_line... INFO @ Tue, 14 Jul 2020 10:32:34: start X-correlation... INFO @ Tue, 14 Jul 2020 10:32:34: end of X-cor INFO @ Tue, 14 Jul 2020 10:32:34: #2 finished! INFO @ Tue, 14 Jul 2020 10:32:34: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 10:32:34: #2 alternative fragment length(s) may be 40,57,77,102,150,194,473,504,532,556,594 bps INFO @ Tue, 14 Jul 2020 10:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05_model.r WARNING @ Tue, 14 Jul 2020 10:32:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:32:34: #2 You may need to consider one of the other alternative d(s): 40,57,77,102,150,194,473,504,532,556,594 WARNING @ Tue, 14 Jul 2020 10:32:34: #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 10:32:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:32:34: 8000000 INFO @ Tue, 14 Jul 2020 10:32:37: 3000000 INFO @ Tue, 14 Jul 2020 10:32:40: 9000000 INFO @ Tue, 14 Jul 2020 10:32:43: 4000000 INFO @ Tue, 14 Jul 2020 10:32:45: 10000000 INFO @ Tue, 14 Jul 2020 10:32:50: 5000000 INFO @ Tue, 14 Jul 2020 10:32:51: 11000000 INFO @ Tue, 14 Jul 2020 10:32:56: 6000000 INFO @ Tue, 14 Jul 2020 10:32:57: 12000000 INFO @ Tue, 14 Jul 2020 10:32:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:33:02: 7000000 INFO @ Tue, 14 Jul 2020 10:33:02: 13000000 INFO @ Tue, 14 Jul 2020 10:33:05: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:33:05: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:33:05: #1 total tags in treatment: 13491367 INFO @ Tue, 14 Jul 2020 10:33:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:33:05: #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 10:33:06: #1 tags after filtering in treatment: 13491296 INFO @ Tue, 14 Jul 2020 10:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:33:06: #1 finished! INFO @ Tue, 14 Jul 2020 10:33:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:33:07: #2 number of paired peaks: 112 WARNING @ Tue, 14 Jul 2020 10:33:07: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 14 Jul 2020 10:33:07: start model_add_line... INFO @ Tue, 14 Jul 2020 10:33:07: start X-correlation... INFO @ Tue, 14 Jul 2020 10:33:07: end of X-cor INFO @ Tue, 14 Jul 2020 10:33:07: #2 finished! INFO @ Tue, 14 Jul 2020 10:33:07: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 10:33:07: #2 alternative fragment length(s) may be 40,57,77,102,150,194,473,504,532,556,594 bps INFO @ Tue, 14 Jul 2020 10:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10_model.r WARNING @ Tue, 14 Jul 2020 10:33:07: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:33:07: #2 You may need to consider one of the other alternative d(s): 40,57,77,102,150,194,473,504,532,556,594 WARNING @ Tue, 14 Jul 2020 10:33:07: #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 10:33:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:33:08: 8000000 INFO @ Tue, 14 Jul 2020 10:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.05_summits.bed INFO @ Tue, 14 Jul 2020 10:33:12: Done! pass1 - making usageList (263 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:33:14: 9000000 INFO @ Tue, 14 Jul 2020 10:33:20: 10000000 INFO @ Tue, 14 Jul 2020 10:33:26: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:33:32: 12000000 INFO @ Tue, 14 Jul 2020 10:33:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:33:38: 13000000 INFO @ Tue, 14 Jul 2020 10:33:41: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:33:41: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:33:41: #1 total tags in treatment: 13491367 INFO @ Tue, 14 Jul 2020 10:33:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:33:41: #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 10:33:41: #1 tags after filtering in treatment: 13491296 INFO @ Tue, 14 Jul 2020 10:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:33:41: #1 finished! INFO @ Tue, 14 Jul 2020 10:33:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:33:42: #2 number of paired peaks: 112 WARNING @ Tue, 14 Jul 2020 10:33:42: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 14 Jul 2020 10:33:42: start model_add_line... INFO @ Tue, 14 Jul 2020 10:33:42: start X-correlation... INFO @ Tue, 14 Jul 2020 10:33:42: end of X-cor INFO @ Tue, 14 Jul 2020 10:33:42: #2 finished! INFO @ Tue, 14 Jul 2020 10:33:42: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 10:33:42: #2 alternative fragment length(s) may be 40,57,77,102,150,194,473,504,532,556,594 bps INFO @ Tue, 14 Jul 2020 10:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20_model.r WARNING @ Tue, 14 Jul 2020 10:33:42: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:33:42: #2 You may need to consider one of the other alternative d(s): 40,57,77,102,150,194,473,504,532,556,594 WARNING @ Tue, 14 Jul 2020 10:33:42: #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 10:33:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.10_summits.bed INFO @ Tue, 14 Jul 2020 10:33:45: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:34:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8156262/SRX8156262.20_summits.bed INFO @ Tue, 14 Jul 2020 10:34:20: Done! pass1 - making usageList (21 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling