Job ID = 14167387 SRX = SRX8574256 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: 00:08:30 35403260 reads; of these: 35403260 (100.00%) were unpaired; of these: 3156343 (8.92%) aligned 0 times 24031882 (67.88%) aligned exactly 1 time 8215035 (23.20%) aligned >1 times 91.08% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 8293754 / 32246917 = 0.2572 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 @ Fri, 10 Dec 2021 12:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.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 @ Fri, 10 Dec 2021 12:19:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:19:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:19:51: 1000000 INFO @ Fri, 10 Dec 2021 12:19:56: 2000000 INFO @ Fri, 10 Dec 2021 12:20:00: 3000000 INFO @ Fri, 10 Dec 2021 12:20:04: 4000000 INFO @ Fri, 10 Dec 2021 12:20:09: 5000000 INFO @ Fri, 10 Dec 2021 12:20:13: 6000000 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 @ Fri, 10 Dec 2021 12:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.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 @ Fri, 10 Dec 2021 12:20:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:20:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:20:17: 7000000 INFO @ Fri, 10 Dec 2021 12:20:21: 1000000 INFO @ Fri, 10 Dec 2021 12:20:22: 8000000 INFO @ Fri, 10 Dec 2021 12:20:26: 2000000 INFO @ Fri, 10 Dec 2021 12:20:26: 9000000 INFO @ Fri, 10 Dec 2021 12:20:30: 3000000 INFO @ Fri, 10 Dec 2021 12:20:31: 10000000 INFO @ Fri, 10 Dec 2021 12:20:35: 4000000 INFO @ Fri, 10 Dec 2021 12:20:35: 11000000 INFO @ Fri, 10 Dec 2021 12:20:39: 5000000 INFO @ Fri, 10 Dec 2021 12:20:39: 12000000 INFO @ Fri, 10 Dec 2021 12:20:44: 6000000 INFO @ Fri, 10 Dec 2021 12:20:44: 13000000 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 @ Fri, 10 Dec 2021 12:20:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.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 @ Fri, 10 Dec 2021 12:20:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:20:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:20:48: 7000000 INFO @ Fri, 10 Dec 2021 12:20:48: 14000000 INFO @ Fri, 10 Dec 2021 12:20:52: 1000000 INFO @ Fri, 10 Dec 2021 12:20:53: 8000000 INFO @ Fri, 10 Dec 2021 12:20:53: 15000000 INFO @ Fri, 10 Dec 2021 12:20:57: 9000000 INFO @ Fri, 10 Dec 2021 12:20:57: 2000000 INFO @ Fri, 10 Dec 2021 12:20:57: 16000000 INFO @ Fri, 10 Dec 2021 12:21:02: 10000000 INFO @ Fri, 10 Dec 2021 12:21:02: 17000000 INFO @ Fri, 10 Dec 2021 12:21:02: 3000000 INFO @ Fri, 10 Dec 2021 12:21:06: 11000000 INFO @ Fri, 10 Dec 2021 12:21:06: 18000000 INFO @ Fri, 10 Dec 2021 12:21:07: 4000000 INFO @ Fri, 10 Dec 2021 12:21:11: 12000000 INFO @ Fri, 10 Dec 2021 12:21:11: 19000000 INFO @ Fri, 10 Dec 2021 12:21:12: 5000000 INFO @ Fri, 10 Dec 2021 12:21:15: 13000000 INFO @ Fri, 10 Dec 2021 12:21:16: 20000000 INFO @ Fri, 10 Dec 2021 12:21:18: 6000000 INFO @ Fri, 10 Dec 2021 12:21:19: 14000000 INFO @ Fri, 10 Dec 2021 12:21:20: 21000000 INFO @ Fri, 10 Dec 2021 12:21:23: 7000000 INFO @ Fri, 10 Dec 2021 12:21:24: 15000000 INFO @ Fri, 10 Dec 2021 12:21:25: 22000000 INFO @ Fri, 10 Dec 2021 12:21:28: 8000000 INFO @ Fri, 10 Dec 2021 12:21:28: 16000000 INFO @ Fri, 10 Dec 2021 12:21:29: 23000000 INFO @ Fri, 10 Dec 2021 12:21:33: 9000000 INFO @ Fri, 10 Dec 2021 12:21:33: 17000000 INFO @ Fri, 10 Dec 2021 12:21:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:21:34: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:21:34: #1 total tags in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:21:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:21:35: #1 tags after filtering in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:21:35: #1 finished! INFO @ Fri, 10 Dec 2021 12:21:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:21:36: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:21:36: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:21:36: start model_add_line... INFO @ Fri, 10 Dec 2021 12:21:36: start X-correlation... INFO @ Fri, 10 Dec 2021 12:21:36: end of X-cor INFO @ Fri, 10 Dec 2021 12:21:36: #2 finished! INFO @ Fri, 10 Dec 2021 12:21:36: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:21:36: #2 alternative fragment length(s) may be 1,22,41,590 bps INFO @ Fri, 10 Dec 2021 12:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05_model.r WARNING @ Fri, 10 Dec 2021 12:21:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:21:36: #2 You may need to consider one of the other alternative d(s): 1,22,41,590 WARNING @ Fri, 10 Dec 2021 12:21:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:21:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:21:37: 18000000 INFO @ Fri, 10 Dec 2021 12:21:38: 10000000 INFO @ Fri, 10 Dec 2021 12:21:42: 19000000 INFO @ Fri, 10 Dec 2021 12:21:43: 11000000 INFO @ Fri, 10 Dec 2021 12:21:47: 20000000 INFO @ Fri, 10 Dec 2021 12:21:48: 12000000 INFO @ Fri, 10 Dec 2021 12:21:51: 21000000 INFO @ Fri, 10 Dec 2021 12:21:53: 13000000 INFO @ Fri, 10 Dec 2021 12:21:56: 22000000 INFO @ Fri, 10 Dec 2021 12:21:58: 14000000 INFO @ Fri, 10 Dec 2021 12:22:00: 23000000 INFO @ Fri, 10 Dec 2021 12:22:04: 15000000 INFO @ Fri, 10 Dec 2021 12:22:05: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:22:05: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:22:05: #1 total tags in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:22:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:22:06: #1 tags after filtering in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:22:06: #1 finished! INFO @ Fri, 10 Dec 2021 12:22:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:22:07: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:22:07: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:22:07: start model_add_line... INFO @ Fri, 10 Dec 2021 12:22:07: start X-correlation... INFO @ Fri, 10 Dec 2021 12:22:07: end of X-cor INFO @ Fri, 10 Dec 2021 12:22:07: #2 finished! INFO @ Fri, 10 Dec 2021 12:22:07: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:22:07: #2 alternative fragment length(s) may be 1,22,41,590 bps INFO @ Fri, 10 Dec 2021 12:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10_model.r WARNING @ Fri, 10 Dec 2021 12:22:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:22:07: #2 You may need to consider one of the other alternative d(s): 1,22,41,590 WARNING @ Fri, 10 Dec 2021 12:22:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:22:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:22:09: 16000000 INFO @ Fri, 10 Dec 2021 12:22:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:14: 17000000 INFO @ Fri, 10 Dec 2021 12:22:19: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:22:24: 19000000 INFO @ Fri, 10 Dec 2021 12:22:29: 20000000 INFO @ Fri, 10 Dec 2021 12:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.05_summits.bed INFO @ Fri, 10 Dec 2021 12:22:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:22:34: 21000000 INFO @ Fri, 10 Dec 2021 12:22:39: 22000000 INFO @ Fri, 10 Dec 2021 12:22:44: 23000000 INFO @ Fri, 10 Dec 2021 12:22:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:22:49: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:22:49: #1 total tags in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:22:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:22:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:22:50: #1 tags after filtering in treatment: 23953163 INFO @ Fri, 10 Dec 2021 12:22:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:22:50: #1 finished! INFO @ Fri, 10 Dec 2021 12:22:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:22:51: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:22:51: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:22:51: start model_add_line... INFO @ Fri, 10 Dec 2021 12:22:52: start X-correlation... INFO @ Fri, 10 Dec 2021 12:22:52: end of X-cor INFO @ Fri, 10 Dec 2021 12:22:52: #2 finished! INFO @ Fri, 10 Dec 2021 12:22:52: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:22:52: #2 alternative fragment length(s) may be 1,22,41,590 bps INFO @ Fri, 10 Dec 2021 12:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20_model.r WARNING @ Fri, 10 Dec 2021 12:22:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:22:52: #2 You may need to consider one of the other alternative d(s): 1,22,41,590 WARNING @ Fri, 10 Dec 2021 12:22:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:22:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.10_summits.bed INFO @ Fri, 10 Dec 2021 12:23:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:23:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574256/SRX8574256.20_summits.bed INFO @ Fri, 10 Dec 2021 12:23:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling