Job ID = 14172848 SRX = SRX7434121 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: 00:09:00 23681151 reads; of these: 23681151 (100.00%) were unpaired; of these: 3227399 (13.63%) aligned 0 times 15529500 (65.58%) aligned exactly 1 time 4924252 (20.79%) aligned >1 times 86.37% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 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] 3651449 / 20453752 = 0.1785 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 17:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.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 17:23:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:23:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:23:53: 1000000 INFO @ Sat, 11 Dec 2021 17:24:01: 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 17:24:11: 3000000 INFO @ Sat, 11 Dec 2021 17:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.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 17:24:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:24:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:24:22: 4000000 INFO @ Sat, 11 Dec 2021 17:24:25: 1000000 INFO @ Sat, 11 Dec 2021 17:24:37: 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 17:24:42: 2000000 INFO @ Sat, 11 Dec 2021 17:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.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 17:24:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:24:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:24:55: 6000000 INFO @ Sat, 11 Dec 2021 17:25:00: 3000000 INFO @ Sat, 11 Dec 2021 17:25:01: 1000000 INFO @ Sat, 11 Dec 2021 17:25:12: 7000000 INFO @ Sat, 11 Dec 2021 17:25:18: 4000000 INFO @ Sat, 11 Dec 2021 17:25:19: 2000000 INFO @ Sat, 11 Dec 2021 17:25:26: 8000000 INFO @ Sat, 11 Dec 2021 17:25:34: 5000000 INFO @ Sat, 11 Dec 2021 17:25:36: 3000000 INFO @ Sat, 11 Dec 2021 17:25:41: 9000000 INFO @ Sat, 11 Dec 2021 17:25:47: 6000000 INFO @ Sat, 11 Dec 2021 17:25:50: 4000000 INFO @ Sat, 11 Dec 2021 17:25:53: 10000000 INFO @ Sat, 11 Dec 2021 17:25:57: 7000000 INFO @ Sat, 11 Dec 2021 17:26:01: 5000000 INFO @ Sat, 11 Dec 2021 17:26:04: 11000000 INFO @ Sat, 11 Dec 2021 17:26:07: 8000000 INFO @ Sat, 11 Dec 2021 17:26:11: 6000000 INFO @ Sat, 11 Dec 2021 17:26:14: 12000000 INFO @ Sat, 11 Dec 2021 17:26:17: 9000000 INFO @ Sat, 11 Dec 2021 17:26:22: 7000000 INFO @ Sat, 11 Dec 2021 17:26:24: 13000000 INFO @ Sat, 11 Dec 2021 17:26:26: 10000000 INFO @ Sat, 11 Dec 2021 17:26:32: 8000000 INFO @ Sat, 11 Dec 2021 17:26:35: 14000000 INFO @ Sat, 11 Dec 2021 17:26:35: 11000000 INFO @ Sat, 11 Dec 2021 17:26:42: 9000000 INFO @ Sat, 11 Dec 2021 17:26:44: 12000000 INFO @ Sat, 11 Dec 2021 17:26:45: 15000000 INFO @ Sat, 11 Dec 2021 17:26:52: 10000000 INFO @ Sat, 11 Dec 2021 17:26:53: 13000000 INFO @ Sat, 11 Dec 2021 17:26:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:27:01: 11000000 INFO @ Sat, 11 Dec 2021 17:27:02: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:27:02: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:27:02: #1 total tags in treatment: 16802303 INFO @ Sat, 11 Dec 2021 17:27:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:27:02: #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 17:27:02: 14000000 INFO @ Sat, 11 Dec 2021 17:27:03: #1 tags after filtering in treatment: 16802218 INFO @ Sat, 11 Dec 2021 17:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:27:03: #1 finished! INFO @ Sat, 11 Dec 2021 17:27:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:27:05: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 17:27:05: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 17:27:05: start model_add_line... INFO @ Sat, 11 Dec 2021 17:27:05: start X-correlation... INFO @ Sat, 11 Dec 2021 17:27:05: end of X-cor INFO @ Sat, 11 Dec 2021 17:27:05: #2 finished! INFO @ Sat, 11 Dec 2021 17:27:05: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 17:27:05: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 17:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05_model.r WARNING @ Sat, 11 Dec 2021 17:27:05: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:27:05: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 17:27:05: #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 17:27:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:27:10: 12000000 INFO @ Sat, 11 Dec 2021 17:27:12: 15000000 INFO @ Sat, 11 Dec 2021 17:27:19: 13000000 INFO @ Sat, 11 Dec 2021 17:27:21: 16000000 INFO @ Sat, 11 Dec 2021 17:27:28: 14000000 INFO @ Sat, 11 Dec 2021 17:27:28: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:27:28: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:27:28: #1 total tags in treatment: 16802303 INFO @ Sat, 11 Dec 2021 17:27:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:27:28: #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 17:27:29: #1 tags after filtering in treatment: 16802218 INFO @ Sat, 11 Dec 2021 17:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:27:29: #1 finished! INFO @ Sat, 11 Dec 2021 17:27:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:27:31: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 17:27:31: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 17:27:31: start model_add_line... INFO @ Sat, 11 Dec 2021 17:27:31: start X-correlation... INFO @ Sat, 11 Dec 2021 17:27:31: end of X-cor INFO @ Sat, 11 Dec 2021 17:27:31: #2 finished! INFO @ Sat, 11 Dec 2021 17:27:31: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 17:27:31: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 17:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10_model.r WARNING @ Sat, 11 Dec 2021 17:27:31: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:27:31: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 17:27:31: #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 17:27:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:27:37: 15000000 INFO @ Sat, 11 Dec 2021 17:27:46: 16000000 INFO @ Sat, 11 Dec 2021 17:27:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:27:54: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:27:54: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:27:54: #1 total tags in treatment: 16802303 INFO @ Sat, 11 Dec 2021 17:27:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:27:54: #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 17:27:54: #1 tags after filtering in treatment: 16802218 INFO @ Sat, 11 Dec 2021 17:27:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:27:54: #1 finished! INFO @ Sat, 11 Dec 2021 17:27:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:27:56: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 17:27:56: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 17:27:56: start model_add_line... INFO @ Sat, 11 Dec 2021 17:27:56: start X-correlation... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:27:56: end of X-cor INFO @ Sat, 11 Dec 2021 17:27:56: #2 finished! INFO @ Sat, 11 Dec 2021 17:27:56: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 17:27:56: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 17:27:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20_model.r WARNING @ Sat, 11 Dec 2021 17:27:56: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:27:56: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 17:27:56: #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 17:27:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:27:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.05_summits.bed INFO @ Sat, 11 Dec 2021 17:28:17: Done! pass1 - making usageList (671 chroms): 4 millis pass2 - checking and writing primary data (3500 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:28:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.10_summits.bed INFO @ Sat, 11 Dec 2021 17:28:43: Done! INFO @ Sat, 11 Dec 2021 17:28:44: #3 Call peaks for each chromosome... pass1 - making usageList (540 chroms): 2 millis pass2 - checking and writing primary data (1906 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:29:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:29:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:29:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434121/SRX7434121.20_summits.bed INFO @ Sat, 11 Dec 2021 17:29:08: Done! pass1 - making usageList (232 chroms): 2 millis pass2 - checking and writing primary data (468 records, 4 fields): 14 millis CompletedMACS2peakCalling