Job ID = 6529349 SRX = SRX2011087 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: 00:06:42 15911453 reads; of these: 15911453 (100.00%) were unpaired; of these: 1002629 (6.30%) aligned 0 times 12309093 (77.36%) aligned exactly 1 time 2599731 (16.34%) aligned >1 times 93.70% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 923546 / 14908824 = 0.0619 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 02:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.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 02:18:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:04: 1000000 INFO @ Tue, 30 Jun 2020 02:19:11: 2000000 INFO @ Tue, 30 Jun 2020 02:19:18: 3000000 INFO @ Tue, 30 Jun 2020 02:19:25: 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 02:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.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 02:19:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:32: 5000000 INFO @ Tue, 30 Jun 2020 02:19:35: 1000000 INFO @ Tue, 30 Jun 2020 02:19:41: 6000000 INFO @ Tue, 30 Jun 2020 02:19:43: 2000000 INFO @ Tue, 30 Jun 2020 02:19:49: 7000000 INFO @ Tue, 30 Jun 2020 02:19:51: 3000000 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 02:19:57: 8000000 INFO @ Tue, 30 Jun 2020 02:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.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 02:19:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:59: 4000000 INFO @ Tue, 30 Jun 2020 02:20:05: 9000000 INFO @ Tue, 30 Jun 2020 02:20:05: 1000000 INFO @ Tue, 30 Jun 2020 02:20:07: 5000000 INFO @ Tue, 30 Jun 2020 02:20:13: 10000000 INFO @ Tue, 30 Jun 2020 02:20:14: 2000000 INFO @ Tue, 30 Jun 2020 02:20:16: 6000000 INFO @ Tue, 30 Jun 2020 02:20:22: 3000000 INFO @ Tue, 30 Jun 2020 02:20:23: 11000000 INFO @ Tue, 30 Jun 2020 02:20:24: 7000000 INFO @ Tue, 30 Jun 2020 02:20:31: 4000000 INFO @ Tue, 30 Jun 2020 02:20:32: 12000000 INFO @ Tue, 30 Jun 2020 02:20:33: 8000000 INFO @ Tue, 30 Jun 2020 02:20:40: 5000000 INFO @ Tue, 30 Jun 2020 02:20:40: 13000000 INFO @ Tue, 30 Jun 2020 02:20:42: 9000000 INFO @ Tue, 30 Jun 2020 02:20:48: 6000000 INFO @ Tue, 30 Jun 2020 02:20:49: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:20:49: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:20:49: #1 total tags in treatment: 13985278 INFO @ Tue, 30 Jun 2020 02:20:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:49: #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 02:20:50: #1 tags after filtering in treatment: 13985237 INFO @ Tue, 30 Jun 2020 02:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:50: 10000000 INFO @ Tue, 30 Jun 2020 02:20:51: #2 number of paired peaks: 177 WARNING @ Tue, 30 Jun 2020 02:20:51: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:51: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 02:20:51: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 30 Jun 2020 02:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05_model.r WARNING @ Tue, 30 Jun 2020 02:20:51: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:51: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 30 Jun 2020 02:20:51: #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 02:20:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:57: 7000000 INFO @ Tue, 30 Jun 2020 02:20:59: 11000000 INFO @ Tue, 30 Jun 2020 02:21:05: 8000000 INFO @ Tue, 30 Jun 2020 02:21:07: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:21:14: 9000000 INFO @ Tue, 30 Jun 2020 02:21:16: 13000000 INFO @ Tue, 30 Jun 2020 02:21:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:22: 10000000 INFO @ Tue, 30 Jun 2020 02:21:24: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:21:24: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:21:24: #1 total tags in treatment: 13985278 INFO @ Tue, 30 Jun 2020 02:21:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:24: #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 02:21:25: #1 tags after filtering in treatment: 13985237 INFO @ Tue, 30 Jun 2020 02:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:26: #2 number of paired peaks: 177 WARNING @ Tue, 30 Jun 2020 02:21:26: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:26: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 02:21:26: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 30 Jun 2020 02:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10_model.r WARNING @ Tue, 30 Jun 2020 02:21:26: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:26: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 30 Jun 2020 02:21:26: #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 02:21:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:30: 11000000 INFO @ Tue, 30 Jun 2020 02:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:30: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (1232 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:37: 12000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:21:44: 13000000 INFO @ Tue, 30 Jun 2020 02:21:51: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:21:51: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:21:51: #1 total tags in treatment: 13985278 INFO @ Tue, 30 Jun 2020 02:21:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:51: #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 02:21:52: #1 tags after filtering in treatment: 13985237 INFO @ Tue, 30 Jun 2020 02:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:52: #2 number of paired peaks: 177 WARNING @ Tue, 30 Jun 2020 02:21:52: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:53: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 02:21:53: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 30 Jun 2020 02:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:53: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:53: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Tue, 30 Jun 2020 02:21:53: #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 02:21:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.10_summits.bed INFO @ Tue, 30 Jun 2020 02:22:05: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011087/SRX2011087.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:32: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 5 millis CompletedMACS2peakCalling