Job ID = 6529623 SRX = SRX3511962 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: 00:02:30 4676767 reads; of these: 4676767 (100.00%) were unpaired; of these: 439906 (9.41%) aligned 0 times 3017702 (64.53%) aligned exactly 1 time 1219159 (26.07%) aligned >1 times 90.59% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 426477 / 4236861 = 0.1007 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 02:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.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 02:14:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:58: 1000000 INFO @ Tue, 30 Jun 2020 02:15:05: 2000000 INFO @ Tue, 30 Jun 2020 02:15:11: 3000000 INFO @ Tue, 30 Jun 2020 02:15:17: #1 tag size is determined as 99 bps INFO @ Tue, 30 Jun 2020 02:15:17: #1 tag size = 99 INFO @ Tue, 30 Jun 2020 02:15:17: #1 total tags in treatment: 3810384 INFO @ Tue, 30 Jun 2020 02:15:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:17: #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 02:15:17: #1 tags after filtering in treatment: 3810374 INFO @ Tue, 30 Jun 2020 02:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 02:15:18: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:18: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:18: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:18: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #3 Pre-compute pvalue-qvalue table... 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 02:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.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 02:15:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:28: 1000000 INFO @ Tue, 30 Jun 2020 02:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.05_summits.bed INFO @ Tue, 30 Jun 2020 02:15:31: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:15:34: 2000000 INFO @ Tue, 30 Jun 2020 02:15:41: 3000000 INFO @ Tue, 30 Jun 2020 02:15:47: #1 tag size is determined as 99 bps INFO @ Tue, 30 Jun 2020 02:15:47: #1 tag size = 99 INFO @ Tue, 30 Jun 2020 02:15:47: #1 total tags in treatment: 3810384 INFO @ Tue, 30 Jun 2020 02:15:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:47: #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 02:15:47: #1 tags after filtering in treatment: 3810374 INFO @ Tue, 30 Jun 2020 02:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 02:15:47: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:47: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:47: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:47: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 30 Jun 2020 02:15:47: #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 02:15:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #3 Pre-compute pvalue-qvalue table... 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 02:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.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 02:15:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:58: 1000000 INFO @ Tue, 30 Jun 2020 02:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:00: Done! pass1 - making usageList (288 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:05: 2000000 INFO @ Tue, 30 Jun 2020 02:16:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:16:18: #1 tag size is determined as 99 bps INFO @ Tue, 30 Jun 2020 02:16:18: #1 tag size = 99 INFO @ Tue, 30 Jun 2020 02:16:18: #1 total tags in treatment: 3810384 INFO @ Tue, 30 Jun 2020 02:16:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:18: #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 02:16:18: #1 tags after filtering in treatment: 3810374 INFO @ Tue, 30 Jun 2020 02:16:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:19: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 02:16:19: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:19: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 02:16:19: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 02:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:19: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:19: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 30 Jun 2020 02:16:19: #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 02:16:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511962/SRX3511962.20_summits.bed INFO @ Tue, 30 Jun 2020 02:16:32: Done! pass1 - making usageList (126 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 5 millis CompletedMACS2peakCalling