Job ID = 6529442 SRX = SRX2831138 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: 00:06:45 29172280 reads; of these: 29172280 (100.00%) were unpaired; of these: 3134835 (10.75%) aligned 0 times 20052110 (68.74%) aligned exactly 1 time 5985335 (20.52%) aligned >1 times 89.25% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 3611113 / 26037445 = 0.1387 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 02:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.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 02:34:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:07: 1000000 INFO @ Tue, 30 Jun 2020 02:34:14: 2000000 INFO @ Tue, 30 Jun 2020 02:34:21: 3000000 INFO @ Tue, 30 Jun 2020 02:34:28: 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 02:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.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 02:34:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:35: 5000000 INFO @ Tue, 30 Jun 2020 02:34:38: 1000000 INFO @ Tue, 30 Jun 2020 02:34:42: 6000000 INFO @ Tue, 30 Jun 2020 02:34:46: 2000000 INFO @ Tue, 30 Jun 2020 02:34:50: 7000000 INFO @ Tue, 30 Jun 2020 02:34:53: 3000000 INFO @ Tue, 30 Jun 2020 02:34:57: 8000000 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 02:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.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 02:35:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:01: 4000000 INFO @ Tue, 30 Jun 2020 02:35:05: 9000000 INFO @ Tue, 30 Jun 2020 02:35:08: 1000000 INFO @ Tue, 30 Jun 2020 02:35:08: 5000000 INFO @ Tue, 30 Jun 2020 02:35:12: 10000000 INFO @ Tue, 30 Jun 2020 02:35:16: 6000000 INFO @ Tue, 30 Jun 2020 02:35:16: 2000000 INFO @ Tue, 30 Jun 2020 02:35:19: 11000000 INFO @ Tue, 30 Jun 2020 02:35:23: 7000000 INFO @ Tue, 30 Jun 2020 02:35:23: 3000000 INFO @ Tue, 30 Jun 2020 02:35:26: 12000000 INFO @ Tue, 30 Jun 2020 02:35:30: 8000000 INFO @ Tue, 30 Jun 2020 02:35:31: 4000000 INFO @ Tue, 30 Jun 2020 02:35:34: 13000000 INFO @ Tue, 30 Jun 2020 02:35:38: 9000000 INFO @ Tue, 30 Jun 2020 02:35:39: 5000000 INFO @ Tue, 30 Jun 2020 02:35:42: 14000000 INFO @ Tue, 30 Jun 2020 02:35:45: 10000000 INFO @ Tue, 30 Jun 2020 02:35:46: 6000000 INFO @ Tue, 30 Jun 2020 02:35:49: 15000000 INFO @ Tue, 30 Jun 2020 02:35:52: 11000000 INFO @ Tue, 30 Jun 2020 02:35:54: 7000000 INFO @ Tue, 30 Jun 2020 02:35:57: 16000000 INFO @ Tue, 30 Jun 2020 02:35:59: 12000000 INFO @ Tue, 30 Jun 2020 02:36:01: 8000000 INFO @ Tue, 30 Jun 2020 02:36:04: 17000000 INFO @ Tue, 30 Jun 2020 02:36:07: 13000000 INFO @ Tue, 30 Jun 2020 02:36:09: 9000000 INFO @ Tue, 30 Jun 2020 02:36:12: 18000000 INFO @ Tue, 30 Jun 2020 02:36:14: 14000000 INFO @ Tue, 30 Jun 2020 02:36:16: 10000000 INFO @ Tue, 30 Jun 2020 02:36:20: 19000000 INFO @ Tue, 30 Jun 2020 02:36:22: 15000000 INFO @ Tue, 30 Jun 2020 02:36:23: 11000000 INFO @ Tue, 30 Jun 2020 02:36:28: 20000000 INFO @ Tue, 30 Jun 2020 02:36:29: 16000000 INFO @ Tue, 30 Jun 2020 02:36:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:36:35: 21000000 INFO @ Tue, 30 Jun 2020 02:36:37: 17000000 INFO @ Tue, 30 Jun 2020 02:36:38: 13000000 INFO @ Tue, 30 Jun 2020 02:36:43: 22000000 INFO @ Tue, 30 Jun 2020 02:36:44: 18000000 INFO @ Tue, 30 Jun 2020 02:36:46: 14000000 INFO @ Tue, 30 Jun 2020 02:36:46: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:36:46: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:36:46: #1 total tags in treatment: 22426332 INFO @ Tue, 30 Jun 2020 02:36:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:46: #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 02:36:47: #1 tags after filtering in treatment: 22426256 INFO @ Tue, 30 Jun 2020 02:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:48: #2 number of paired peaks: 675 WARNING @ Tue, 30 Jun 2020 02:36:48: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:48: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:36:48: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 30 Jun 2020 02:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05_model.r WARNING @ Tue, 30 Jun 2020 02:36:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:36:48: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 30 Jun 2020 02:36:48: #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 02:36:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:36:52: 19000000 INFO @ Tue, 30 Jun 2020 02:36:53: 15000000 INFO @ Tue, 30 Jun 2020 02:37:00: 20000000 INFO @ Tue, 30 Jun 2020 02:37:01: 16000000 INFO @ Tue, 30 Jun 2020 02:37:07: 21000000 INFO @ Tue, 30 Jun 2020 02:37:09: 17000000 INFO @ Tue, 30 Jun 2020 02:37:15: 22000000 INFO @ Tue, 30 Jun 2020 02:37:16: 18000000 INFO @ Tue, 30 Jun 2020 02:37:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:18: #1 total tags in treatment: 22426332 INFO @ Tue, 30 Jun 2020 02:37:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:18: #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 02:37:19: #1 tags after filtering in treatment: 22426256 INFO @ Tue, 30 Jun 2020 02:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:20: #2 number of paired peaks: 675 WARNING @ Tue, 30 Jun 2020 02:37:20: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:20: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:37:20: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 30 Jun 2020 02:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10_model.r WARNING @ Tue, 30 Jun 2020 02:37:20: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:20: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 30 Jun 2020 02:37:20: #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 02:37:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:37:24: 19000000 INFO @ Tue, 30 Jun 2020 02:37:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:31: 20000000 INFO @ Tue, 30 Jun 2020 02:37:38: 21000000 INFO @ Tue, 30 Jun 2020 02:37:45: 22000000 INFO @ Tue, 30 Jun 2020 02:37:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:48: #1 total tags in treatment: 22426332 INFO @ Tue, 30 Jun 2020 02:37:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:48: #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 02:37:48: #1 tags after filtering in treatment: 22426256 INFO @ Tue, 30 Jun 2020 02:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.05_summits.bed INFO @ Tue, 30 Jun 2020 02:37:49: Done! pass1 - making usageList (559 chroms): 1 millis pass2 - checking and writing primary data (6921 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:37:50: #2 number of paired peaks: 675 WARNING @ Tue, 30 Jun 2020 02:37:50: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:50: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:37:50: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 30 Jun 2020 02:37:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20_model.r WARNING @ Tue, 30 Jun 2020 02:37:50: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:50: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 30 Jun 2020 02:37:50: #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 02:37:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.10_summits.bed INFO @ Tue, 30 Jun 2020 02:38:20: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (2220 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831138/SRX2831138.20_summits.bed INFO @ Tue, 30 Jun 2020 02:38:50: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 8 millis CompletedMACS2peakCalling