Job ID = 14171049 SRX = SRX7320036 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: 00:11:03 39133827 reads; of these: 39133827 (100.00%) were unpaired; of these: 2276954 (5.82%) aligned 0 times 28813601 (73.63%) aligned exactly 1 time 8043272 (20.55%) aligned >1 times 94.18% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 7216260 / 36856873 = 0.1958 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 09:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.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 09:35:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:35:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:35:16: 1000000 INFO @ Sat, 11 Dec 2021 09:35:25: 2000000 INFO @ Sat, 11 Dec 2021 09:35:33: 3000000 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 09:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.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 09:35:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:35:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:35:42: 4000000 INFO @ Sat, 11 Dec 2021 09:35:45: 1000000 INFO @ Sat, 11 Dec 2021 09:35:50: 5000000 INFO @ Sat, 11 Dec 2021 09:35:53: 2000000 INFO @ Sat, 11 Dec 2021 09:35:58: 6000000 INFO @ Sat, 11 Dec 2021 09:36:02: 3000000 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 09:36:06: 7000000 INFO @ Sat, 11 Dec 2021 09:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.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 09:36:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:36:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:36:10: 4000000 INFO @ Sat, 11 Dec 2021 09:36:14: 8000000 INFO @ Sat, 11 Dec 2021 09:36:17: 1000000 INFO @ Sat, 11 Dec 2021 09:36:18: 5000000 INFO @ Sat, 11 Dec 2021 09:36:23: 9000000 INFO @ Sat, 11 Dec 2021 09:36:25: 2000000 INFO @ Sat, 11 Dec 2021 09:36:26: 6000000 INFO @ Sat, 11 Dec 2021 09:36:31: 10000000 INFO @ Sat, 11 Dec 2021 09:36:34: 3000000 INFO @ Sat, 11 Dec 2021 09:36:35: 7000000 INFO @ Sat, 11 Dec 2021 09:36:39: 11000000 INFO @ Sat, 11 Dec 2021 09:36:42: 4000000 INFO @ Sat, 11 Dec 2021 09:36:43: 8000000 INFO @ Sat, 11 Dec 2021 09:36:48: 12000000 INFO @ Sat, 11 Dec 2021 09:36:51: 9000000 INFO @ Sat, 11 Dec 2021 09:36:51: 5000000 INFO @ Sat, 11 Dec 2021 09:36:57: 13000000 INFO @ Sat, 11 Dec 2021 09:36:59: 10000000 INFO @ Sat, 11 Dec 2021 09:37:00: 6000000 INFO @ Sat, 11 Dec 2021 09:37:05: 14000000 INFO @ Sat, 11 Dec 2021 09:37:06: 11000000 INFO @ Sat, 11 Dec 2021 09:37:09: 7000000 INFO @ Sat, 11 Dec 2021 09:37:14: 15000000 INFO @ Sat, 11 Dec 2021 09:37:14: 12000000 INFO @ Sat, 11 Dec 2021 09:37:18: 8000000 INFO @ Sat, 11 Dec 2021 09:37:23: 13000000 INFO @ Sat, 11 Dec 2021 09:37:23: 16000000 INFO @ Sat, 11 Dec 2021 09:37:27: 9000000 INFO @ Sat, 11 Dec 2021 09:37:31: 14000000 INFO @ Sat, 11 Dec 2021 09:37:32: 17000000 INFO @ Sat, 11 Dec 2021 09:37:36: 10000000 INFO @ Sat, 11 Dec 2021 09:37:39: 15000000 INFO @ Sat, 11 Dec 2021 09:37:42: 18000000 INFO @ Sat, 11 Dec 2021 09:37:45: 11000000 INFO @ Sat, 11 Dec 2021 09:37:47: 16000000 INFO @ Sat, 11 Dec 2021 09:37:51: 19000000 INFO @ Sat, 11 Dec 2021 09:37:55: 12000000 INFO @ Sat, 11 Dec 2021 09:37:55: 17000000 INFO @ Sat, 11 Dec 2021 09:38:00: 20000000 INFO @ Sat, 11 Dec 2021 09:38:03: 18000000 INFO @ Sat, 11 Dec 2021 09:38:04: 13000000 INFO @ Sat, 11 Dec 2021 09:38:09: 21000000 INFO @ Sat, 11 Dec 2021 09:38:12: 19000000 INFO @ Sat, 11 Dec 2021 09:38:13: 14000000 INFO @ Sat, 11 Dec 2021 09:38:19: 22000000 INFO @ Sat, 11 Dec 2021 09:38:20: 20000000 INFO @ Sat, 11 Dec 2021 09:38:22: 15000000 INFO @ Sat, 11 Dec 2021 09:38:28: 23000000 INFO @ Sat, 11 Dec 2021 09:38:29: 21000000 INFO @ Sat, 11 Dec 2021 09:38:32: 16000000 INFO @ Sat, 11 Dec 2021 09:38:37: 24000000 INFO @ Sat, 11 Dec 2021 09:38:38: 22000000 INFO @ Sat, 11 Dec 2021 09:38:41: 17000000 INFO @ Sat, 11 Dec 2021 09:38:46: 23000000 INFO @ Sat, 11 Dec 2021 09:38:48: 25000000 INFO @ Sat, 11 Dec 2021 09:38:50: 18000000 INFO @ Sat, 11 Dec 2021 09:38:55: 24000000 INFO @ Sat, 11 Dec 2021 09:38:57: 26000000 INFO @ Sat, 11 Dec 2021 09:39:00: 19000000 INFO @ Sat, 11 Dec 2021 09:39:04: 25000000 INFO @ Sat, 11 Dec 2021 09:39:06: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:39:09: 20000000 INFO @ Sat, 11 Dec 2021 09:39:13: 26000000 INFO @ Sat, 11 Dec 2021 09:39:16: 28000000 INFO @ Sat, 11 Dec 2021 09:39:19: 21000000 INFO @ Sat, 11 Dec 2021 09:39:21: 27000000 INFO @ Sat, 11 Dec 2021 09:39:25: 29000000 INFO @ Sat, 11 Dec 2021 09:39:28: 22000000 INFO @ Sat, 11 Dec 2021 09:39:30: 28000000 INFO @ Sat, 11 Dec 2021 09:39:31: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:39:31: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:39:31: #1 total tags in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:39:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:31: #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 09:39:32: #1 tags after filtering in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:39:32: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:34: #2 number of paired peaks: 116 WARNING @ Sat, 11 Dec 2021 09:39:34: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 11 Dec 2021 09:39:34: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:34: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:34: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:34: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:34: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:39:34: #2 alternative fragment length(s) may be 1,48,497,502,524,528,550,580,583 bps INFO @ Sat, 11 Dec 2021 09:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05_model.r WARNING @ Sat, 11 Dec 2021 09:39:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:39:34: #2 You may need to consider one of the other alternative d(s): 1,48,497,502,524,528,550,580,583 WARNING @ Sat, 11 Dec 2021 09:39:34: #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 09:39:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:39:38: 23000000 INFO @ Sat, 11 Dec 2021 09:39:38: 29000000 INFO @ Sat, 11 Dec 2021 09:39:44: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:39:44: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:39:44: #1 total tags in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:39:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:44: #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 09:39:45: #1 tags after filtering in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:39:45: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:47: 24000000 INFO @ Sat, 11 Dec 2021 09:39:47: #2 number of paired peaks: 116 WARNING @ Sat, 11 Dec 2021 09:39:47: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 11 Dec 2021 09:39:47: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:47: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:47: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:47: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:47: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:39:47: #2 alternative fragment length(s) may be 1,48,497,502,524,528,550,580,583 bps INFO @ Sat, 11 Dec 2021 09:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10_model.r WARNING @ Sat, 11 Dec 2021 09:39:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:39:47: #2 You may need to consider one of the other alternative d(s): 1,48,497,502,524,528,550,580,583 WARNING @ Sat, 11 Dec 2021 09:39:47: #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 09:39:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:39:56: 25000000 INFO @ Sat, 11 Dec 2021 09:40:05: 26000000 INFO @ Sat, 11 Dec 2021 09:40:13: 27000000 INFO @ Sat, 11 Dec 2021 09:40:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:40:22: 28000000 INFO @ Sat, 11 Dec 2021 09:40:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:40:31: 29000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:40:37: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:40:37: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:40:37: #1 total tags in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:40:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:40:37: #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 09:40:38: #1 tags after filtering in treatment: 29640613 INFO @ Sat, 11 Dec 2021 09:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:40:38: #1 finished! INFO @ Sat, 11 Dec 2021 09:40:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:40:40: #2 number of paired peaks: 116 WARNING @ Sat, 11 Dec 2021 09:40:40: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 11 Dec 2021 09:40:40: start model_add_line... INFO @ Sat, 11 Dec 2021 09:40:40: start X-correlation... INFO @ Sat, 11 Dec 2021 09:40:40: end of X-cor INFO @ Sat, 11 Dec 2021 09:40:40: #2 finished! INFO @ Sat, 11 Dec 2021 09:40:40: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:40:40: #2 alternative fragment length(s) may be 1,48,497,502,524,528,550,580,583 bps INFO @ Sat, 11 Dec 2021 09:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20_model.r WARNING @ Sat, 11 Dec 2021 09:40:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:40:40: #2 You may need to consider one of the other alternative d(s): 1,48,497,502,524,528,550,580,583 WARNING @ Sat, 11 Dec 2021 09:40:40: #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 09:40:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.05_summits.bed INFO @ Sat, 11 Dec 2021 09:40:40: Done! pass1 - making usageList (0 chroms): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.10_summits.bed INFO @ Sat, 11 Dec 2021 09:40:53: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:41:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320036/SRX7320036.20_summits.bed INFO @ Sat, 11 Dec 2021 09:41:45: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling