Job ID = 6529845 SRX = SRX5241027 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: 00:10:04 21898618 reads; of these: 21898618 (100.00%) were unpaired; of these: 1166659 (5.33%) aligned 0 times 14967831 (68.35%) aligned exactly 1 time 5764128 (26.32%) aligned >1 times 94.67% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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] 3046823 / 20731959 = 0.1470 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 03:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.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 03:09:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:48: 1000000 INFO @ Tue, 30 Jun 2020 03:09:56: 2000000 INFO @ Tue, 30 Jun 2020 03:10:04: 3000000 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 03:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.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 03:10:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:11: 4000000 INFO @ Tue, 30 Jun 2020 03:10:17: 1000000 INFO @ Tue, 30 Jun 2020 03:10:18: 5000000 INFO @ Tue, 30 Jun 2020 03:10:25: 2000000 INFO @ Tue, 30 Jun 2020 03:10:25: 6000000 INFO @ Tue, 30 Jun 2020 03:10:33: 3000000 INFO @ Tue, 30 Jun 2020 03:10:35: 7000000 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 03:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.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 03:10:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:41: 4000000 INFO @ Tue, 30 Jun 2020 03:10:43: 8000000 INFO @ Tue, 30 Jun 2020 03:10:49: 5000000 INFO @ Tue, 30 Jun 2020 03:10:49: 1000000 INFO @ Tue, 30 Jun 2020 03:10:51: 9000000 INFO @ Tue, 30 Jun 2020 03:10:57: 6000000 INFO @ Tue, 30 Jun 2020 03:10:58: 2000000 INFO @ Tue, 30 Jun 2020 03:10:59: 10000000 INFO @ Tue, 30 Jun 2020 03:11:05: 7000000 INFO @ Tue, 30 Jun 2020 03:11:07: 11000000 INFO @ Tue, 30 Jun 2020 03:11:07: 3000000 INFO @ Tue, 30 Jun 2020 03:11:14: 8000000 INFO @ Tue, 30 Jun 2020 03:11:15: 12000000 INFO @ Tue, 30 Jun 2020 03:11:16: 4000000 INFO @ Tue, 30 Jun 2020 03:11:22: 9000000 INFO @ Tue, 30 Jun 2020 03:11:23: 13000000 INFO @ Tue, 30 Jun 2020 03:11:25: 5000000 INFO @ Tue, 30 Jun 2020 03:11:31: 10000000 INFO @ Tue, 30 Jun 2020 03:11:31: 14000000 INFO @ Tue, 30 Jun 2020 03:11:34: 6000000 INFO @ Tue, 30 Jun 2020 03:11:39: 11000000 INFO @ Tue, 30 Jun 2020 03:11:40: 15000000 INFO @ Tue, 30 Jun 2020 03:11:43: 7000000 INFO @ Tue, 30 Jun 2020 03:11:47: 12000000 INFO @ Tue, 30 Jun 2020 03:11:49: 16000000 INFO @ Tue, 30 Jun 2020 03:11:53: 8000000 INFO @ Tue, 30 Jun 2020 03:11:56: 13000000 INFO @ Tue, 30 Jun 2020 03:11:57: 17000000 INFO @ Tue, 30 Jun 2020 03:12:02: 9000000 INFO @ Tue, 30 Jun 2020 03:12:04: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:12:04: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:12:04: #1 total tags in treatment: 17685136 INFO @ Tue, 30 Jun 2020 03:12:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:04: #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 03:12:04: 14000000 INFO @ Tue, 30 Jun 2020 03:12:04: #1 tags after filtering in treatment: 17685029 INFO @ Tue, 30 Jun 2020 03:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:04: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:06: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:12:06: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:06: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:06: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:06: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 03:12:06: #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 03:12:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:11: 10000000 INFO @ Tue, 30 Jun 2020 03:12:13: 15000000 INFO @ Tue, 30 Jun 2020 03:12:20: 11000000 INFO @ Tue, 30 Jun 2020 03:12:21: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:29: 12000000 INFO @ Tue, 30 Jun 2020 03:12:30: 17000000 INFO @ Tue, 30 Jun 2020 03:12:36: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:12:36: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:12:36: #1 total tags in treatment: 17685136 INFO @ Tue, 30 Jun 2020 03:12:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:36: #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 03:12:36: #1 tags after filtering in treatment: 17685029 INFO @ Tue, 30 Jun 2020 03:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:36: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:38: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:12:38: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:38: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:38: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:38: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:38: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:38: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 03:12:38: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 03:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:38: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:38: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 03:12:38: #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 03:12:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:38: 13000000 INFO @ Tue, 30 Jun 2020 03:12:47: 14000000 INFO @ Tue, 30 Jun 2020 03:12:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:55: 15000000 INFO @ Tue, 30 Jun 2020 03:13:03: 16000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.05_summits.bed INFO @ Tue, 30 Jun 2020 03:13:09: Done! pass1 - making usageList (670 chroms): 2 millis pass2 - checking and writing primary data (7714 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:11: 17000000 INFO @ Tue, 30 Jun 2020 03:13:17: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:13:17: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:13:17: #1 total tags in treatment: 17685136 INFO @ Tue, 30 Jun 2020 03:13:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:17: #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 03:13:17: #1 tags after filtering in treatment: 17685029 INFO @ Tue, 30 Jun 2020 03:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:19: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:13:19: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:19: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:19: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:19: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 03:13:19: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 03:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:19: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:19: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 03:13:19: #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 03:13:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:39: Done! pass1 - making usageList (531 chroms): 2 millis pass2 - checking and writing primary data (2433 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241027/SRX5241027.20_summits.bed INFO @ Tue, 30 Jun 2020 03:14:19: Done! pass1 - making usageList (372 chroms): 1 millis pass2 - checking and writing primary data (1000 records, 4 fields): 16 millis CompletedMACS2peakCalling