Job ID = 16436270 SRX = SRX15369013 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: 00:07:05 17388117 reads; of these: 17388117 (100.00%) were unpaired; of these: 964171 (5.54%) aligned 0 times 11506021 (66.17%) aligned exactly 1 time 4917925 (28.28%) aligned >1 times 94.46% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 8 files... [bam_rmdupse_core] 13684696 / 16423946 = 0.8332 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.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, 02 Aug 2022 11:27:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:27:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:27:07: 1000000 INFO @ Tue, 02 Aug 2022 11:27:13: 2000000 INFO @ Tue, 02 Aug 2022 11:27:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:27:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:27:18: #1 total tags in treatment: 2739250 INFO @ Tue, 02 Aug 2022 11:27:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:27:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:27:18: #1 tags after filtering in treatment: 2739128 INFO @ Tue, 02 Aug 2022 11:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:27:18: #1 finished! INFO @ Tue, 02 Aug 2022 11:27:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:27:18: #2 number of paired peaks: 3718 INFO @ Tue, 02 Aug 2022 11:27:18: start model_add_line... INFO @ Tue, 02 Aug 2022 11:27:19: start X-correlation... INFO @ Tue, 02 Aug 2022 11:27:19: end of X-cor INFO @ Tue, 02 Aug 2022 11:27:19: #2 finished! INFO @ Tue, 02 Aug 2022 11:27:19: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 11:27:19: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 11:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05_model.r WARNING @ Tue, 02 Aug 2022 11:27:19: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:27:19: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 11:27:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:27:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:27:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.05_summits.bed INFO @ Tue, 02 Aug 2022 11:27:28: Done! pass1 - making usageList (674 chroms): 2 millis pass2 - checking and writing primary data (2222 records, 4 fields): 32 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.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, 02 Aug 2022 11:27:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:27:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:27:36: 1000000 INFO @ Tue, 02 Aug 2022 11:27:43: 2000000 INFO @ Tue, 02 Aug 2022 11:27:47: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:27:47: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:27:47: #1 total tags in treatment: 2739250 INFO @ Tue, 02 Aug 2022 11:27:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:27:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:27:47: #1 tags after filtering in treatment: 2739128 INFO @ Tue, 02 Aug 2022 11:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:27:47: #1 finished! INFO @ Tue, 02 Aug 2022 11:27:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:27:48: #2 number of paired peaks: 3718 INFO @ Tue, 02 Aug 2022 11:27:48: start model_add_line... INFO @ Tue, 02 Aug 2022 11:27:48: start X-correlation... INFO @ Tue, 02 Aug 2022 11:27:48: end of X-cor INFO @ Tue, 02 Aug 2022 11:27:48: #2 finished! INFO @ Tue, 02 Aug 2022 11:27:48: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 11:27:48: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 11:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10_model.r WARNING @ Tue, 02 Aug 2022 11:27:48: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:27:48: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 11:27:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:27:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:27:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.10_summits.bed INFO @ Tue, 02 Aug 2022 11:27:57: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (1446 records, 4 fields): 37 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.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, 02 Aug 2022 11:28:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:28:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:28:07: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:28:13: 2000000 INFO @ Tue, 02 Aug 2022 11:28:17: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:28:17: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:28:17: #1 total tags in treatment: 2739250 INFO @ Tue, 02 Aug 2022 11:28:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:28:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:28:18: #1 tags after filtering in treatment: 2739128 INFO @ Tue, 02 Aug 2022 11:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:28:18: #1 finished! INFO @ Tue, 02 Aug 2022 11:28:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:28:18: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:28:18: #2 number of paired peaks: 3718 INFO @ Tue, 02 Aug 2022 11:28:18: start model_add_line... INFO @ Tue, 02 Aug 2022 11:28:18: start X-correlation... INFO @ Tue, 02 Aug 2022 11:28:18: end of X-cor INFO @ Tue, 02 Aug 2022 11:28:18: #2 finished! INFO @ Tue, 02 Aug 2022 11:28:18: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 11:28:18: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 11:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20_model.r WARNING @ Tue, 02 Aug 2022 11:28:18: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:28:18: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 11:28:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:28:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:28:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369013/SRX15369013.20_summits.bed INFO @ Tue, 02 Aug 2022 11:28:28: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 30 millis CompletedMACS2peakCalling