Job ID = 6627669 SRX = SRX8521388 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: 00:06:20 50773540 reads; of these: 50773540 (100.00%) were unpaired; of these: 47071583 (92.71%) aligned 0 times 2727331 (5.37%) aligned exactly 1 time 974626 (1.92%) aligned >1 times 7.29% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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_rmdupse_core] 465124 / 3701957 = 0.1256 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, 14 Jul 2020 12:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.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, 14 Jul 2020 12:37:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:37:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:37:53: 1000000 INFO @ Tue, 14 Jul 2020 12:37:59: 2000000 INFO @ Tue, 14 Jul 2020 12:38:05: 3000000 INFO @ Tue, 14 Jul 2020 12:38:06: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:38:06: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:38:06: #1 total tags in treatment: 3236833 INFO @ Tue, 14 Jul 2020 12:38:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:38:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:38:07: #1 tags after filtering in treatment: 3236556 INFO @ Tue, 14 Jul 2020 12:38:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:38:07: #1 finished! INFO @ Tue, 14 Jul 2020 12:38:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:38:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:38:07: #2 number of paired peaks: 919 WARNING @ Tue, 14 Jul 2020 12:38:07: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Tue, 14 Jul 2020 12:38:07: start model_add_line... INFO @ Tue, 14 Jul 2020 12:38:07: start X-correlation... INFO @ Tue, 14 Jul 2020 12:38:07: end of X-cor INFO @ Tue, 14 Jul 2020 12:38:07: #2 finished! INFO @ Tue, 14 Jul 2020 12:38:07: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 12:38:07: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 12:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05_model.r WARNING @ Tue, 14 Jul 2020 12:38:07: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:38:07: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 12:38:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:38:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:38:14: #3 Call peaks for each chromosome... 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, 14 Jul 2020 12:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.05_summits.bed INFO @ Tue, 14 Jul 2020 12:38:18: Done! INFO @ Tue, 14 Jul 2020 12:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.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, 14 Jul 2020 12:38:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:38:18: #1 read treatment tags... pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:38:23: 1000000 INFO @ Tue, 14 Jul 2020 12:38:29: 2000000 INFO @ Tue, 14 Jul 2020 12:38:35: 3000000 INFO @ Tue, 14 Jul 2020 12:38:36: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:38:36: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:38:36: #1 total tags in treatment: 3236833 INFO @ Tue, 14 Jul 2020 12:38:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:38:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:38:36: #1 tags after filtering in treatment: 3236556 INFO @ Tue, 14 Jul 2020 12:38:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:38:36: #1 finished! INFO @ Tue, 14 Jul 2020 12:38:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:38:36: #2 number of paired peaks: 919 WARNING @ Tue, 14 Jul 2020 12:38:36: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Tue, 14 Jul 2020 12:38:36: start model_add_line... INFO @ Tue, 14 Jul 2020 12:38:37: start X-correlation... INFO @ Tue, 14 Jul 2020 12:38:37: end of X-cor INFO @ Tue, 14 Jul 2020 12:38:37: #2 finished! INFO @ Tue, 14 Jul 2020 12:38:37: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 12:38:37: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 12:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10_model.r WARNING @ Tue, 14 Jul 2020 12:38:37: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:38:37: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 12:38:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:38:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:38:44: #3 Call peaks for each chromosome... 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, 14 Jul 2020 12:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.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, 14 Jul 2020 12:38:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:38:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.10_summits.bed INFO @ Tue, 14 Jul 2020 12:38:47: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:38:53: 1000000 INFO @ Tue, 14 Jul 2020 12:38:58: 2000000 INFO @ Tue, 14 Jul 2020 12:39:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:39:05: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:39:05: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:39:05: #1 total tags in treatment: 3236833 INFO @ Tue, 14 Jul 2020 12:39:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:39:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:39:05: #1 tags after filtering in treatment: 3236556 INFO @ Tue, 14 Jul 2020 12:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:39:05: #1 finished! INFO @ Tue, 14 Jul 2020 12:39:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:39:06: #2 number of paired peaks: 919 WARNING @ Tue, 14 Jul 2020 12:39:06: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Tue, 14 Jul 2020 12:39:06: start model_add_line... INFO @ Tue, 14 Jul 2020 12:39:06: start X-correlation... INFO @ Tue, 14 Jul 2020 12:39:06: end of X-cor INFO @ Tue, 14 Jul 2020 12:39:06: #2 finished! INFO @ Tue, 14 Jul 2020 12:39:06: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 12:39:06: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 12:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20_model.r WARNING @ Tue, 14 Jul 2020 12:39:06: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:39:06: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 12:39:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:39:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:39:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:39:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521388/SRX8521388.20_summits.bed INFO @ Tue, 14 Jul 2020 12:39:17: Done! pass1 - making usageList (67 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 4 millis CompletedMACS2peakCalling