Job ID = 6529466 SRX = SRX287681 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:57 19200904 reads; of these: 19200904 (100.00%) were unpaired; of these: 1306496 (6.80%) aligned 0 times 13670304 (71.20%) aligned exactly 1 time 4224104 (22.00%) aligned >1 times 93.20% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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 8 files... [bam_rmdupse_core] 1807861 / 17894408 = 0.1010 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 02:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.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 02:17:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:21: 1000000 INFO @ Tue, 30 Jun 2020 02:17:27: 2000000 INFO @ Tue, 30 Jun 2020 02:17:34: 3000000 INFO @ Tue, 30 Jun 2020 02:17:40: 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 02:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.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 02:17:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:47: 5000000 INFO @ Tue, 30 Jun 2020 02:17:52: 1000000 INFO @ Tue, 30 Jun 2020 02:17:55: 6000000 INFO @ Tue, 30 Jun 2020 02:18:00: 2000000 INFO @ Tue, 30 Jun 2020 02:18:02: 7000000 INFO @ Tue, 30 Jun 2020 02:18:07: 3000000 INFO @ Tue, 30 Jun 2020 02:18:09: 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 02:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.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 02:18:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:14: 4000000 INFO @ Tue, 30 Jun 2020 02:18:17: 9000000 INFO @ Tue, 30 Jun 2020 02:18:22: 5000000 INFO @ Tue, 30 Jun 2020 02:18:22: 1000000 INFO @ Tue, 30 Jun 2020 02:18:24: 10000000 INFO @ Tue, 30 Jun 2020 02:18:29: 2000000 INFO @ Tue, 30 Jun 2020 02:18:29: 6000000 INFO @ Tue, 30 Jun 2020 02:18:32: 11000000 INFO @ Tue, 30 Jun 2020 02:18:37: 3000000 INFO @ Tue, 30 Jun 2020 02:18:37: 7000000 INFO @ Tue, 30 Jun 2020 02:18:39: 12000000 INFO @ Tue, 30 Jun 2020 02:18:44: 4000000 INFO @ Tue, 30 Jun 2020 02:18:45: 8000000 INFO @ Tue, 30 Jun 2020 02:18:47: 13000000 INFO @ Tue, 30 Jun 2020 02:18:52: 5000000 INFO @ Tue, 30 Jun 2020 02:18:52: 9000000 INFO @ Tue, 30 Jun 2020 02:18:55: 14000000 INFO @ Tue, 30 Jun 2020 02:19:00: 6000000 INFO @ Tue, 30 Jun 2020 02:19:00: 10000000 INFO @ Tue, 30 Jun 2020 02:19:02: 15000000 INFO @ Tue, 30 Jun 2020 02:19:08: 7000000 INFO @ Tue, 30 Jun 2020 02:19:09: 11000000 INFO @ Tue, 30 Jun 2020 02:19:11: 16000000 INFO @ Tue, 30 Jun 2020 02:19:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:11: #1 total tags in treatment: 16086547 INFO @ Tue, 30 Jun 2020 02:19:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:11: #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 02:19:12: #1 tags after filtering in treatment: 16086546 INFO @ Tue, 30 Jun 2020 02:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:13: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:19:13: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:13: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:19:13: #2 alternative fragment length(s) may be 3,36,39,537 bps INFO @ Tue, 30 Jun 2020 02:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05_model.r WARNING @ Tue, 30 Jun 2020 02:19:13: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:13: #2 You may need to consider one of the other alternative d(s): 3,36,39,537 WARNING @ Tue, 30 Jun 2020 02:19:13: #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 02:19:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:16: 8000000 INFO @ Tue, 30 Jun 2020 02:19:16: 12000000 INFO @ Tue, 30 Jun 2020 02:19:23: 9000000 INFO @ Tue, 30 Jun 2020 02:19:24: 13000000 INFO @ Tue, 30 Jun 2020 02:19:31: 10000000 INFO @ Tue, 30 Jun 2020 02:19:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:39: 11000000 INFO @ Tue, 30 Jun 2020 02:19:40: 15000000 INFO @ Tue, 30 Jun 2020 02:19:47: 12000000 INFO @ Tue, 30 Jun 2020 02:19:48: 16000000 INFO @ Tue, 30 Jun 2020 02:19:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:48: #1 total tags in treatment: 16086547 INFO @ Tue, 30 Jun 2020 02:19:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:48: #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 02:19:49: #1 tags after filtering in treatment: 16086546 INFO @ Tue, 30 Jun 2020 02:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:50: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:19:50: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:50: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:19:50: #2 alternative fragment length(s) may be 3,36,39,537 bps INFO @ Tue, 30 Jun 2020 02:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10_model.r WARNING @ Tue, 30 Jun 2020 02:19:50: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:50: #2 You may need to consider one of the other alternative d(s): 3,36,39,537 WARNING @ Tue, 30 Jun 2020 02:19:50: #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 02:19:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:54: 13000000 INFO @ Tue, 30 Jun 2020 02:20:01: 14000000 INFO @ Tue, 30 Jun 2020 02:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.05_summits.bed INFO @ Tue, 30 Jun 2020 02:20:05: Done! pass1 - making usageList (526 chroms): 2 millis pass2 - checking and writing primary data (2216 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:08: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:15: 16000000 INFO @ Tue, 30 Jun 2020 02:20:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:16: #1 total tags in treatment: 16086547 INFO @ Tue, 30 Jun 2020 02:20:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:16: #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 02:20:17: #1 tags after filtering in treatment: 16086546 INFO @ Tue, 30 Jun 2020 02:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:18: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:20:18: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:18: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:20:18: #2 alternative fragment length(s) may be 3,36,39,537 bps INFO @ Tue, 30 Jun 2020 02:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20_model.r WARNING @ Tue, 30 Jun 2020 02:20:18: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:18: #2 You may need to consider one of the other alternative d(s): 3,36,39,537 WARNING @ Tue, 30 Jun 2020 02:20:18: #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 02:20:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.10_summits.bed INFO @ Tue, 30 Jun 2020 02:20:42: Done! pass1 - making usageList (449 chroms): 2 millis pass2 - checking and writing primary data (1572 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287681/SRX287681.20_summits.bed INFO @ Tue, 30 Jun 2020 02:21:08: Done! pass1 - making usageList (223 chroms): 0 millis pass2 - checking and writing primary data (458 records, 4 fields): 10 millis CompletedMACS2peakCalling