Job ID = 6529607 SRX = SRX3404020 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: 00:06:23 26288689 reads; of these: 26288689 (100.00%) were unpaired; of these: 835350 (3.18%) aligned 0 times 18383051 (69.93%) aligned exactly 1 time 7070288 (26.89%) aligned >1 times 96.82% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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 12 files... [bam_rmdupse_core] 2750259 / 25453339 = 0.1081 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, 30 Jun 2020 02:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.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, 30 Jun 2020 02:49:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:59: 1000000 INFO @ Tue, 30 Jun 2020 02:50:05: 2000000 INFO @ Tue, 30 Jun 2020 02:50:11: 3000000 INFO @ Tue, 30 Jun 2020 02:50:17: 4000000 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, 30 Jun 2020 02:50:23: 5000000 INFO @ Tue, 30 Jun 2020 02:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.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, 30 Jun 2020 02:50:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:29: 6000000 INFO @ Tue, 30 Jun 2020 02:50:30: 1000000 INFO @ Tue, 30 Jun 2020 02:50:36: 7000000 INFO @ Tue, 30 Jun 2020 02:50:36: 2000000 INFO @ Tue, 30 Jun 2020 02:50:42: 8000000 INFO @ Tue, 30 Jun 2020 02:50:43: 3000000 INFO @ Tue, 30 Jun 2020 02:50:48: 9000000 INFO @ Tue, 30 Jun 2020 02:50:49: 4000000 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, 30 Jun 2020 02:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.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, 30 Jun 2020 02:50:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:55: 10000000 INFO @ Tue, 30 Jun 2020 02:50:56: 5000000 INFO @ Tue, 30 Jun 2020 02:50:59: 1000000 INFO @ Tue, 30 Jun 2020 02:51:01: 11000000 INFO @ Tue, 30 Jun 2020 02:51:02: 6000000 INFO @ Tue, 30 Jun 2020 02:51:06: 2000000 INFO @ Tue, 30 Jun 2020 02:51:08: 12000000 INFO @ Tue, 30 Jun 2020 02:51:09: 7000000 INFO @ Tue, 30 Jun 2020 02:51:12: 3000000 INFO @ Tue, 30 Jun 2020 02:51:15: 13000000 INFO @ Tue, 30 Jun 2020 02:51:16: 8000000 INFO @ Tue, 30 Jun 2020 02:51:18: 4000000 INFO @ Tue, 30 Jun 2020 02:51:21: 14000000 INFO @ Tue, 30 Jun 2020 02:51:23: 9000000 INFO @ Tue, 30 Jun 2020 02:51:25: 5000000 INFO @ Tue, 30 Jun 2020 02:51:28: 15000000 INFO @ Tue, 30 Jun 2020 02:51:30: 10000000 INFO @ Tue, 30 Jun 2020 02:51:31: 6000000 INFO @ Tue, 30 Jun 2020 02:51:35: 16000000 INFO @ Tue, 30 Jun 2020 02:51:36: 11000000 INFO @ Tue, 30 Jun 2020 02:51:37: 7000000 INFO @ Tue, 30 Jun 2020 02:51:41: 17000000 INFO @ Tue, 30 Jun 2020 02:51:42: 12000000 INFO @ Tue, 30 Jun 2020 02:51:44: 8000000 INFO @ Tue, 30 Jun 2020 02:51:48: 18000000 INFO @ Tue, 30 Jun 2020 02:51:48: 13000000 INFO @ Tue, 30 Jun 2020 02:51:50: 9000000 INFO @ Tue, 30 Jun 2020 02:51:54: 14000000 INFO @ Tue, 30 Jun 2020 02:51:55: 19000000 INFO @ Tue, 30 Jun 2020 02:51:57: 10000000 INFO @ Tue, 30 Jun 2020 02:52:00: 15000000 INFO @ Tue, 30 Jun 2020 02:52:01: 20000000 INFO @ Tue, 30 Jun 2020 02:52:03: 11000000 INFO @ Tue, 30 Jun 2020 02:52:06: 16000000 INFO @ Tue, 30 Jun 2020 02:52:07: 21000000 INFO @ Tue, 30 Jun 2020 02:52:09: 12000000 INFO @ Tue, 30 Jun 2020 02:52:12: 17000000 INFO @ Tue, 30 Jun 2020 02:52:14: 22000000 INFO @ Tue, 30 Jun 2020 02:52:15: 13000000 INFO @ Tue, 30 Jun 2020 02:52:18: 18000000 INFO @ Tue, 30 Jun 2020 02:52:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:52:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:52:19: #1 total tags in treatment: 22703080 INFO @ Tue, 30 Jun 2020 02:52:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:52:19: #1 tags after filtering in treatment: 22703034 INFO @ Tue, 30 Jun 2020 02:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:21: #2 number of paired peaks: 676 WARNING @ Tue, 30 Jun 2020 02:52:21: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:21: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:52:21: #2 alternative fragment length(s) may be 2,50,534,556,565,571 bps INFO @ Tue, 30 Jun 2020 02:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:21: #2 You may need to consider one of the other alternative d(s): 2,50,534,556,565,571 WARNING @ Tue, 30 Jun 2020 02:52:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:52:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:22: 14000000 INFO @ Tue, 30 Jun 2020 02:52:24: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:52:28: 15000000 INFO @ Tue, 30 Jun 2020 02:52:30: 20000000 INFO @ Tue, 30 Jun 2020 02:52:35: 16000000 INFO @ Tue, 30 Jun 2020 02:52:36: 21000000 INFO @ Tue, 30 Jun 2020 02:52:41: 17000000 INFO @ Tue, 30 Jun 2020 02:52:43: 22000000 INFO @ Tue, 30 Jun 2020 02:52:47: 18000000 INFO @ Tue, 30 Jun 2020 02:52:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:52:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:52:48: #1 total tags in treatment: 22703080 INFO @ Tue, 30 Jun 2020 02:52:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:52:48: #1 tags after filtering in treatment: 22703034 INFO @ Tue, 30 Jun 2020 02:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:50: #2 number of paired peaks: 676 WARNING @ Tue, 30 Jun 2020 02:52:50: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:50: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:52:50: #2 alternative fragment length(s) may be 2,50,534,556,565,571 bps INFO @ Tue, 30 Jun 2020 02:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10_model.r WARNING @ Tue, 30 Jun 2020 02:52:50: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:50: #2 You may need to consider one of the other alternative d(s): 2,50,534,556,565,571 WARNING @ Tue, 30 Jun 2020 02:52:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:52:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:54: 19000000 INFO @ Tue, 30 Jun 2020 02:53:00: 20000000 INFO @ Tue, 30 Jun 2020 02:53:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:06: 21000000 INFO @ Tue, 30 Jun 2020 02:53:12: 22000000 INFO @ Tue, 30 Jun 2020 02:53:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:17: #1 total tags in treatment: 22703080 INFO @ Tue, 30 Jun 2020 02:53:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:53:17: #1 tags after filtering in treatment: 22703034 INFO @ Tue, 30 Jun 2020 02:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:19: #2 number of paired peaks: 676 WARNING @ Tue, 30 Jun 2020 02:53:19: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:19: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:53:19: #2 alternative fragment length(s) may be 2,50,534,556,565,571 bps INFO @ Tue, 30 Jun 2020 02:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:19: #2 You may need to consider one of the other alternative d(s): 2,50,534,556,565,571 WARNING @ Tue, 30 Jun 2020 02:53:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:53:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:20: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (3426 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:49: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (2010 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404020/SRX3404020.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:17: Done! pass1 - making usageList (271 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 8 millis CompletedMACS2peakCalling