Job ID = 6627458 SRX = SRX8521326 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: 00:06:48 40130767 reads; of these: 40130767 (100.00%) were unpaired; of these: 33134817 (82.57%) aligned 0 times 4843486 (12.07%) aligned exactly 1 time 2152464 (5.36%) aligned >1 times 17.43% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 1240783 / 6995950 = 0.1774 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 11:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.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 11:45:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:45:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:45:38: 1000000 INFO @ Tue, 14 Jul 2020 11:45:43: 2000000 INFO @ Tue, 14 Jul 2020 11:45:49: 3000000 INFO @ Tue, 14 Jul 2020 11:45:54: 4000000 INFO @ Tue, 14 Jul 2020 11:45:59: 5000000 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 11:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.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 11:46:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:46:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:46:03: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:46:03: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:46:03: #1 total tags in treatment: 5755167 INFO @ Tue, 14 Jul 2020 11:46:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:46:03: #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 11:46:03: #1 tags after filtering in treatment: 5755000 INFO @ Tue, 14 Jul 2020 11:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:46:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:46:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:46:04: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 11:46:04: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 11:46:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:46:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:46:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:46:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:46:04: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:46:04: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 11:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05_model.r WARNING @ Tue, 14 Jul 2020 11:46:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:46:04: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 11:46:04: #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 11:46:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:46:08: 1000000 INFO @ Tue, 14 Jul 2020 11:46:13: 2000000 INFO @ Tue, 14 Jul 2020 11:46:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:46:19: 3000000 INFO @ Tue, 14 Jul 2020 11:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.05_summits.bed INFO @ Tue, 14 Jul 2020 11:46:22: Done! pass1 - making usageList (253 chroms): 0 millis pass2 - checking and writing primary data (657 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:46:24: 4000000 INFO @ Tue, 14 Jul 2020 11:46:29: 5000000 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 11:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.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 11:46:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:46:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:46:33: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:46:33: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:46:33: #1 total tags in treatment: 5755167 INFO @ Tue, 14 Jul 2020 11:46:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:46:33: #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 11:46:34: #1 tags after filtering in treatment: 5755000 INFO @ Tue, 14 Jul 2020 11:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:46:34: #1 finished! INFO @ Tue, 14 Jul 2020 11:46:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:46:34: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 11:46:34: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 11:46:34: start model_add_line... INFO @ Tue, 14 Jul 2020 11:46:34: start X-correlation... INFO @ Tue, 14 Jul 2020 11:46:34: end of X-cor INFO @ Tue, 14 Jul 2020 11:46:34: #2 finished! INFO @ Tue, 14 Jul 2020 11:46:34: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:46:34: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 11:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10_model.r WARNING @ Tue, 14 Jul 2020 11:46:34: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:46:34: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 11:46:34: #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 11:46:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:46:40: 1000000 INFO @ Tue, 14 Jul 2020 11:46:46: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:46:47: 2000000 INFO @ Tue, 14 Jul 2020 11:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.10_summits.bed INFO @ Tue, 14 Jul 2020 11:46:53: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:46:54: 3000000 INFO @ Tue, 14 Jul 2020 11:47:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:47:07: 5000000 INFO @ Tue, 14 Jul 2020 11:47:12: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:47:12: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:47:12: #1 total tags in treatment: 5755167 INFO @ Tue, 14 Jul 2020 11:47:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:47:12: #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 11:47:13: #1 tags after filtering in treatment: 5755000 INFO @ Tue, 14 Jul 2020 11:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:47:13: #1 finished! INFO @ Tue, 14 Jul 2020 11:47:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:47:13: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 11:47:13: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 11:47:13: start model_add_line... INFO @ Tue, 14 Jul 2020 11:47:13: start X-correlation... INFO @ Tue, 14 Jul 2020 11:47:13: end of X-cor INFO @ Tue, 14 Jul 2020 11:47:13: #2 finished! INFO @ Tue, 14 Jul 2020 11:47:13: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:47:13: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 11:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20_model.r WARNING @ Tue, 14 Jul 2020 11:47:13: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:47:13: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 11:47:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:47:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:47:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:47:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521326/SRX8521326.20_summits.bed INFO @ Tue, 14 Jul 2020 11:47:33: Done! pass1 - making usageList (83 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 4 millis CompletedMACS2peakCalling