Job ID = 16438966 SRX = SRX15206506 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:54 20340984 reads; of these: 20340984 (100.00%) were unpaired; of these: 938440 (4.61%) aligned 0 times 15093866 (74.20%) aligned exactly 1 time 4308678 (21.18%) aligned >1 times 95.39% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 9229118 / 19402544 = 0.4757 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 14:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.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 14:29:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:29:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:29:12: 1000000 INFO @ Tue, 02 Aug 2022 14:29:20: 2000000 INFO @ Tue, 02 Aug 2022 14:29:27: 3000000 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 14:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.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 14:29:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:29:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:29:34: 4000000 INFO @ Tue, 02 Aug 2022 14:29:42: 5000000 INFO @ Tue, 02 Aug 2022 14:29:43: 1000000 INFO @ Tue, 02 Aug 2022 14:29:49: 6000000 INFO @ Tue, 02 Aug 2022 14:29:52: 2000000 INFO @ Tue, 02 Aug 2022 14:29:57: 7000000 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 14:30:02: 3000000 INFO @ Tue, 02 Aug 2022 14:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.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 14:30:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:30:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:30:05: 8000000 INFO @ Tue, 02 Aug 2022 14:30:12: 4000000 INFO @ Tue, 02 Aug 2022 14:30:13: 9000000 INFO @ Tue, 02 Aug 2022 14:30:13: 1000000 INFO @ Tue, 02 Aug 2022 14:30:21: 10000000 INFO @ Tue, 02 Aug 2022 14:30:22: 5000000 INFO @ Tue, 02 Aug 2022 14:30:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:30:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:30:22: #1 total tags in treatment: 10173426 INFO @ Tue, 02 Aug 2022 14:30:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:22: #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 14:30:23: #1 tags after filtering in treatment: 10173321 INFO @ Tue, 02 Aug 2022 14:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:23: #2 number of paired peaks: 1395 INFO @ Tue, 02 Aug 2022 14:30:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:24: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:24: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 14:30:24: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 14:30:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05_model.r INFO @ Tue, 02 Aug 2022 14:30:24: 2000000 WARNING @ Tue, 02 Aug 2022 14:30:24: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:30:24: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 14:30:24: #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 14:30:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:30:32: 6000000 INFO @ Tue, 02 Aug 2022 14:30:34: 3000000 INFO @ Tue, 02 Aug 2022 14:30:42: 7000000 INFO @ Tue, 02 Aug 2022 14:30:44: 4000000 INFO @ Tue, 02 Aug 2022 14:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:30:53: 8000000 INFO @ Tue, 02 Aug 2022 14:30:54: 5000000 INFO @ Tue, 02 Aug 2022 14:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.05_summits.bed INFO @ Tue, 02 Aug 2022 14:30:57: Done! pass1 - making usageList (602 chroms): 2 millis pass2 - checking and writing primary data (3068 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:31:03: 9000000 INFO @ Tue, 02 Aug 2022 14:31:04: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:31:13: 10000000 INFO @ Tue, 02 Aug 2022 14:31:14: 7000000 INFO @ Tue, 02 Aug 2022 14:31:15: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:31:15: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:31:15: #1 total tags in treatment: 10173426 INFO @ Tue, 02 Aug 2022 14:31:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:31:15: #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 14:31:16: #1 tags after filtering in treatment: 10173321 INFO @ Tue, 02 Aug 2022 14:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:31:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:31:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:31:16: #2 number of paired peaks: 1395 INFO @ Tue, 02 Aug 2022 14:31:16: start model_add_line... INFO @ Tue, 02 Aug 2022 14:31:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:31:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:31:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:31:17: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 14:31:17: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 14:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10_model.r WARNING @ Tue, 02 Aug 2022 14:31:17: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:31:17: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 14:31:17: #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 14:31:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:31:24: 8000000 INFO @ Tue, 02 Aug 2022 14:31:33: 9000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:31:43: 10000000 INFO @ Tue, 02 Aug 2022 14:31:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:31:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:31:44: #1 total tags in treatment: 10173426 INFO @ Tue, 02 Aug 2022 14:31:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:31:44: #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 14:31:45: #1 tags after filtering in treatment: 10173321 INFO @ Tue, 02 Aug 2022 14:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:31:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:31:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:31:46: #2 number of paired peaks: 1395 INFO @ Tue, 02 Aug 2022 14:31:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:31:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:31:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:31:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:31:46: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 14:31:46: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 14:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20_model.r WARNING @ Tue, 02 Aug 2022 14:31:46: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:31:46: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 14:31:46: #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 14:31:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.10_summits.bed INFO @ Tue, 02 Aug 2022 14:31:50: Done! pass1 - making usageList (456 chroms): 2 millis pass2 - checking and writing primary data (1562 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:32:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206506/SRX15206506.20_summits.bed INFO @ Tue, 02 Aug 2022 14:32:19: Done! pass1 - making usageList (268 chroms): 1 millis pass2 - checking and writing primary data (664 records, 4 fields): 57 millis CompletedMACS2peakCalling