Job ID = 6627439 SRX = SRX8521298 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: 00:12:02 59511368 reads; of these: 59511368 (100.00%) were unpaired; of these: 49616793 (83.37%) aligned 0 times 7259687 (12.20%) aligned exactly 1 time 2634888 (4.43%) aligned >1 times 16.63% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 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] 1896763 / 9894575 = 0.1917 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 11:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.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 11:51:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:51:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:51:12: 1000000 INFO @ Tue, 14 Jul 2020 11:51:20: 2000000 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 11:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.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 11:51:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:51:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:51:29: 3000000 INFO @ Tue, 14 Jul 2020 11:51:37: 4000000 INFO @ Tue, 14 Jul 2020 11:51:39: 1000000 INFO @ Tue, 14 Jul 2020 11:51:46: 5000000 INFO @ Tue, 14 Jul 2020 11:51:48: 2000000 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 11:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.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 11:51:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:51:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:51:55: 6000000 INFO @ Tue, 14 Jul 2020 11:51:57: 3000000 INFO @ Tue, 14 Jul 2020 11:52:04: 1000000 INFO @ Tue, 14 Jul 2020 11:52:05: 7000000 INFO @ Tue, 14 Jul 2020 11:52:06: 4000000 INFO @ Tue, 14 Jul 2020 11:52:13: 2000000 INFO @ Tue, 14 Jul 2020 11:52:15: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:52:15: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:52:15: #1 total tags in treatment: 7997812 INFO @ Tue, 14 Jul 2020 11:52:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:52:15: #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 11:52:15: #1 tags after filtering in treatment: 7997650 INFO @ Tue, 14 Jul 2020 11:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:52:15: #1 finished! INFO @ Tue, 14 Jul 2020 11:52:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:52:16: 5000000 INFO @ Tue, 14 Jul 2020 11:52:16: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 11:52:16: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 11:52:16: start model_add_line... INFO @ Tue, 14 Jul 2020 11:52:16: start X-correlation... INFO @ Tue, 14 Jul 2020 11:52:16: end of X-cor INFO @ Tue, 14 Jul 2020 11:52:16: #2 finished! INFO @ Tue, 14 Jul 2020 11:52:16: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:52:16: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 11:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05_model.r WARNING @ Tue, 14 Jul 2020 11:52:16: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:52:16: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 11:52:16: #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 11:52:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:52:21: 3000000 INFO @ Tue, 14 Jul 2020 11:52:24: 6000000 INFO @ Tue, 14 Jul 2020 11:52:30: 4000000 INFO @ Tue, 14 Jul 2020 11:52:34: 7000000 INFO @ Tue, 14 Jul 2020 11:52:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:52:38: 5000000 INFO @ Tue, 14 Jul 2020 11:52:43: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:52:43: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:52:43: #1 total tags in treatment: 7997812 INFO @ Tue, 14 Jul 2020 11:52:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:52:43: #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 11:52:43: #1 tags after filtering in treatment: 7997650 INFO @ Tue, 14 Jul 2020 11:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:52:43: #1 finished! INFO @ Tue, 14 Jul 2020 11:52:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:52:44: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 11:52:44: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 11:52:44: start model_add_line... INFO @ Tue, 14 Jul 2020 11:52:44: start X-correlation... INFO @ Tue, 14 Jul 2020 11:52:44: end of X-cor INFO @ Tue, 14 Jul 2020 11:52:44: #2 finished! INFO @ Tue, 14 Jul 2020 11:52:44: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:52:44: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 11:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10_model.r WARNING @ Tue, 14 Jul 2020 11:52:44: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:52:44: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 11:52:44: #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 11:52:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.05_summits.bed INFO @ Tue, 14 Jul 2020 11:52:46: Done! INFO @ Tue, 14 Jul 2020 11:52:47: 6000000 pass1 - making usageList (246 chroms): 33 millis pass2 - checking and writing primary data (1725 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:52:58: 7000000 INFO @ Tue, 14 Jul 2020 11:53:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:53:09: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:53:09: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:53:09: #1 total tags in treatment: 7997812 INFO @ Tue, 14 Jul 2020 11:53:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:53:09: #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 11:53:10: #1 tags after filtering in treatment: 7997650 INFO @ Tue, 14 Jul 2020 11:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:53:10: #1 finished! INFO @ Tue, 14 Jul 2020 11:53:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:53:11: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 11:53:11: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 11:53:11: start model_add_line... INFO @ Tue, 14 Jul 2020 11:53:11: start X-correlation... INFO @ Tue, 14 Jul 2020 11:53:11: end of X-cor INFO @ Tue, 14 Jul 2020 11:53:11: #2 finished! INFO @ Tue, 14 Jul 2020 11:53:11: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:53:11: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 11:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20_model.r WARNING @ Tue, 14 Jul 2020 11:53:11: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:53:11: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 11:53:11: #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 11:53:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.10_summits.bed INFO @ Tue, 14 Jul 2020 11:53:14: Done! pass1 - making usageList (154 chroms): 33 millis pass2 - checking and writing primary data (581 records, 4 fields): 67 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:53:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521298/SRX8521298.20_summits.bed INFO @ Tue, 14 Jul 2020 11:53:42: Done! pass1 - making usageList (92 chroms): 33 millis pass2 - checking and writing primary data (184 records, 4 fields): 47 millis CompletedMACS2peakCalling