Job ID = 14172601 SRX = SRX10089761 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: 00:14:36 32853039 reads; of these: 32853039 (100.00%) were unpaired; of these: 974824 (2.97%) aligned 0 times 23829819 (72.53%) aligned exactly 1 time 8048396 (24.50%) aligned >1 times 97.03% overall alignment rate Time searching: 00:14:36 Overall time: 00:14:36 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 16 files... [bam_rmdupse_core] 5325622 / 31878215 = 0.1671 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.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, 11 Dec 2021 16:31:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:31:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:31:51: 1000000 INFO @ Sat, 11 Dec 2021 16:32:01: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:32:11: 3000000 INFO @ Sat, 11 Dec 2021 16:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.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, 11 Dec 2021 16:32:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:32:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:32:22: 1000000 INFO @ Sat, 11 Dec 2021 16:32:22: 4000000 INFO @ Sat, 11 Dec 2021 16:32:32: 2000000 INFO @ Sat, 11 Dec 2021 16:32:33: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:32:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.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, 11 Dec 2021 16:32:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:32:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:32:43: 3000000 INFO @ Sat, 11 Dec 2021 16:32:44: 6000000 INFO @ Sat, 11 Dec 2021 16:32:51: 1000000 INFO @ Sat, 11 Dec 2021 16:32:54: 4000000 INFO @ Sat, 11 Dec 2021 16:32:56: 7000000 INFO @ Sat, 11 Dec 2021 16:33:00: 2000000 INFO @ Sat, 11 Dec 2021 16:33:04: 5000000 INFO @ Sat, 11 Dec 2021 16:33:07: 8000000 INFO @ Sat, 11 Dec 2021 16:33:09: 3000000 INFO @ Sat, 11 Dec 2021 16:33:15: 6000000 INFO @ Sat, 11 Dec 2021 16:33:18: 4000000 INFO @ Sat, 11 Dec 2021 16:33:18: 9000000 INFO @ Sat, 11 Dec 2021 16:33:25: 7000000 INFO @ Sat, 11 Dec 2021 16:33:26: 5000000 INFO @ Sat, 11 Dec 2021 16:33:29: 10000000 INFO @ Sat, 11 Dec 2021 16:33:35: 6000000 INFO @ Sat, 11 Dec 2021 16:33:36: 8000000 INFO @ Sat, 11 Dec 2021 16:33:41: 11000000 INFO @ Sat, 11 Dec 2021 16:33:43: 7000000 INFO @ Sat, 11 Dec 2021 16:33:46: 9000000 INFO @ Sat, 11 Dec 2021 16:33:52: 8000000 INFO @ Sat, 11 Dec 2021 16:33:52: 12000000 INFO @ Sat, 11 Dec 2021 16:33:56: 10000000 INFO @ Sat, 11 Dec 2021 16:34:00: 9000000 INFO @ Sat, 11 Dec 2021 16:34:03: 13000000 INFO @ Sat, 11 Dec 2021 16:34:07: 11000000 INFO @ Sat, 11 Dec 2021 16:34:09: 10000000 INFO @ Sat, 11 Dec 2021 16:34:14: 14000000 INFO @ Sat, 11 Dec 2021 16:34:18: 11000000 INFO @ Sat, 11 Dec 2021 16:34:19: 12000000 INFO @ Sat, 11 Dec 2021 16:34:26: 15000000 INFO @ Sat, 11 Dec 2021 16:34:28: 12000000 INFO @ Sat, 11 Dec 2021 16:34:31: 13000000 INFO @ Sat, 11 Dec 2021 16:34:38: 13000000 INFO @ Sat, 11 Dec 2021 16:34:38: 16000000 INFO @ Sat, 11 Dec 2021 16:34:43: 14000000 INFO @ Sat, 11 Dec 2021 16:34:47: 14000000 INFO @ Sat, 11 Dec 2021 16:34:48: 17000000 INFO @ Sat, 11 Dec 2021 16:34:54: 15000000 INFO @ Sat, 11 Dec 2021 16:34:56: 15000000 INFO @ Sat, 11 Dec 2021 16:35:00: 18000000 INFO @ Sat, 11 Dec 2021 16:35:06: 16000000 INFO @ Sat, 11 Dec 2021 16:35:06: 16000000 INFO @ Sat, 11 Dec 2021 16:35:11: 19000000 INFO @ Sat, 11 Dec 2021 16:35:16: 17000000 INFO @ Sat, 11 Dec 2021 16:35:16: 17000000 INFO @ Sat, 11 Dec 2021 16:35:22: 20000000 INFO @ Sat, 11 Dec 2021 16:35:25: 18000000 INFO @ Sat, 11 Dec 2021 16:35:28: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:35:34: 19000000 INFO @ Sat, 11 Dec 2021 16:35:34: 21000000 INFO @ Sat, 11 Dec 2021 16:35:39: 19000000 INFO @ Sat, 11 Dec 2021 16:35:44: 20000000 INFO @ Sat, 11 Dec 2021 16:35:47: 22000000 INFO @ Sat, 11 Dec 2021 16:35:51: 20000000 INFO @ Sat, 11 Dec 2021 16:35:53: 21000000 INFO @ Sat, 11 Dec 2021 16:35:58: 23000000 INFO @ Sat, 11 Dec 2021 16:36:02: 21000000 INFO @ Sat, 11 Dec 2021 16:36:03: 22000000 INFO @ Sat, 11 Dec 2021 16:36:10: 24000000 INFO @ Sat, 11 Dec 2021 16:36:12: 23000000 INFO @ Sat, 11 Dec 2021 16:36:14: 22000000 INFO @ Sat, 11 Dec 2021 16:36:21: 25000000 INFO @ Sat, 11 Dec 2021 16:36:22: 24000000 INFO @ Sat, 11 Dec 2021 16:36:25: 23000000 INFO @ Sat, 11 Dec 2021 16:36:31: 25000000 INFO @ Sat, 11 Dec 2021 16:36:32: 26000000 INFO @ Sat, 11 Dec 2021 16:36:36: 24000000 INFO @ Sat, 11 Dec 2021 16:36:39: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 16:36:39: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 16:36:39: #1 total tags in treatment: 26552593 INFO @ Sat, 11 Dec 2021 16:36:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:36:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:36:40: 26000000 INFO @ Sat, 11 Dec 2021 16:36:40: #1 tags after filtering in treatment: 26552592 INFO @ Sat, 11 Dec 2021 16:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:36:40: #1 finished! INFO @ Sat, 11 Dec 2021 16:36:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:36:42: #2 number of paired peaks: 226 WARNING @ Sat, 11 Dec 2021 16:36:42: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sat, 11 Dec 2021 16:36:42: start model_add_line... INFO @ Sat, 11 Dec 2021 16:36:42: start X-correlation... INFO @ Sat, 11 Dec 2021 16:36:43: end of X-cor INFO @ Sat, 11 Dec 2021 16:36:43: #2 finished! INFO @ Sat, 11 Dec 2021 16:36:43: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 16:36:43: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 16:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05_model.r WARNING @ Sat, 11 Dec 2021 16:36:43: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:36:43: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 16:36:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:36:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:36:45: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 16:36:45: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 16:36:45: #1 total tags in treatment: 26552593 INFO @ Sat, 11 Dec 2021 16:36:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:36:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:36:46: #1 tags after filtering in treatment: 26552592 INFO @ Sat, 11 Dec 2021 16:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:36:46: #1 finished! INFO @ Sat, 11 Dec 2021 16:36:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:36:46: 25000000 INFO @ Sat, 11 Dec 2021 16:36:48: #2 number of paired peaks: 226 WARNING @ Sat, 11 Dec 2021 16:36:48: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sat, 11 Dec 2021 16:36:48: start model_add_line... INFO @ Sat, 11 Dec 2021 16:36:48: start X-correlation... INFO @ Sat, 11 Dec 2021 16:36:48: end of X-cor INFO @ Sat, 11 Dec 2021 16:36:48: #2 finished! INFO @ Sat, 11 Dec 2021 16:36:48: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 16:36:48: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 16:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20_model.r WARNING @ Sat, 11 Dec 2021 16:36:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:36:48: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 16:36:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:36:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:36:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:36:56: 26000000 INFO @ Sat, 11 Dec 2021 16:37:02: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 16:37:02: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 16:37:02: #1 total tags in treatment: 26552593 INFO @ Sat, 11 Dec 2021 16:37:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:37:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:37:03: #1 tags after filtering in treatment: 26552592 INFO @ Sat, 11 Dec 2021 16:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:37:03: #1 finished! INFO @ Sat, 11 Dec 2021 16:37:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:37:05: #2 number of paired peaks: 226 WARNING @ Sat, 11 Dec 2021 16:37:05: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sat, 11 Dec 2021 16:37:05: start model_add_line... INFO @ Sat, 11 Dec 2021 16:37:05: start X-correlation... INFO @ Sat, 11 Dec 2021 16:37:05: end of X-cor INFO @ Sat, 11 Dec 2021 16:37:05: #2 finished! INFO @ Sat, 11 Dec 2021 16:37:05: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 16:37:05: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 16:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10_model.r WARNING @ Sat, 11 Dec 2021 16:37:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:37:05: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 16:37:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:37:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:37:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:37:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:38:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.05_summits.bed INFO @ Sat, 11 Dec 2021 16:38:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.20_summits.bed INFO @ Sat, 11 Dec 2021 16:38:14: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:38:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089761/SRX10089761.10_summits.bed INFO @ Sat, 11 Dec 2021 16:38:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling