Job ID = 16438114 SRX = SRX12261343 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: 00:09:14 22504665 reads; of these: 22504665 (100.00%) were unpaired; of these: 944610 (4.20%) aligned 0 times 14202453 (63.11%) aligned exactly 1 time 7357602 (32.69%) aligned >1 times 95.80% overall alignment rate Time searching: 00:09:14 Overall time: 00:09:14 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 12 files... [bam_rmdupse_core] 8147933 / 21560055 = 0.3779 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 13:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.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 13:53:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:53:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:53:47: 1000000 INFO @ Tue, 02 Aug 2022 13:53:53: 2000000 INFO @ Tue, 02 Aug 2022 13:53:58: 3000000 INFO @ Tue, 02 Aug 2022 13:54:04: 4000000 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 13:54:10: 5000000 INFO @ Tue, 02 Aug 2022 13:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.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 13:54:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:54:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:54:17: 6000000 INFO @ Tue, 02 Aug 2022 13:54:18: 1000000 INFO @ Tue, 02 Aug 2022 13:54:24: 7000000 INFO @ Tue, 02 Aug 2022 13:54:26: 2000000 INFO @ Tue, 02 Aug 2022 13:54:31: 8000000 INFO @ Tue, 02 Aug 2022 13:54:34: 3000000 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 13:54:38: 9000000 INFO @ Tue, 02 Aug 2022 13:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.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 13:54:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:54:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:54:41: 4000000 INFO @ Tue, 02 Aug 2022 13:54:45: 10000000 INFO @ Tue, 02 Aug 2022 13:54:48: 1000000 INFO @ Tue, 02 Aug 2022 13:54:49: 5000000 INFO @ Tue, 02 Aug 2022 13:54:53: 11000000 INFO @ Tue, 02 Aug 2022 13:54:56: 2000000 INFO @ Tue, 02 Aug 2022 13:54:57: 6000000 INFO @ Tue, 02 Aug 2022 13:55:00: 12000000 INFO @ Tue, 02 Aug 2022 13:55:04: 3000000 INFO @ Tue, 02 Aug 2022 13:55:05: 7000000 INFO @ Tue, 02 Aug 2022 13:55:08: 13000000 INFO @ Tue, 02 Aug 2022 13:55:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:55:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:55:11: #1 total tags in treatment: 13412122 INFO @ Tue, 02 Aug 2022 13:55:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:55:11: #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 13:55:11: #1 tags after filtering in treatment: 13412117 INFO @ Tue, 02 Aug 2022 13:55:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:55:11: #1 finished! INFO @ Tue, 02 Aug 2022 13:55:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:55:12: 4000000 INFO @ Tue, 02 Aug 2022 13:55:12: #2 number of paired peaks: 835 WARNING @ Tue, 02 Aug 2022 13:55:12: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 02 Aug 2022 13:55:12: start model_add_line... INFO @ Tue, 02 Aug 2022 13:55:12: start X-correlation... INFO @ Tue, 02 Aug 2022 13:55:12: end of X-cor INFO @ Tue, 02 Aug 2022 13:55:12: #2 finished! INFO @ Tue, 02 Aug 2022 13:55:12: #2 predicted fragment length is 65 bps INFO @ Tue, 02 Aug 2022 13:55:12: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 02 Aug 2022 13:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05_model.r WARNING @ Tue, 02 Aug 2022 13:55:12: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:55:12: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 02 Aug 2022 13:55:12: #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 13:55:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:55:13: 8000000 INFO @ Tue, 02 Aug 2022 13:55:20: 5000000 INFO @ Tue, 02 Aug 2022 13:55:20: 9000000 INFO @ Tue, 02 Aug 2022 13:55:27: 6000000 INFO @ Tue, 02 Aug 2022 13:55:28: 10000000 INFO @ Tue, 02 Aug 2022 13:55:35: 7000000 INFO @ Tue, 02 Aug 2022 13:55:36: 11000000 INFO @ Tue, 02 Aug 2022 13:55:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:55:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:55:44: 12000000 INFO @ Tue, 02 Aug 2022 13:55:49: 9000000 INFO @ Tue, 02 Aug 2022 13:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.05_summits.bed INFO @ Tue, 02 Aug 2022 13:55:51: Done! INFO @ Tue, 02 Aug 2022 13:55:52: 13000000 pass1 - making usageList (687 chroms): 1 millis pass2 - checking and writing primary data (2213 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:55:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:55:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:55:55: #1 total tags in treatment: 13412122 INFO @ Tue, 02 Aug 2022 13:55:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:55:55: #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 13:55:55: #1 tags after filtering in treatment: 13412117 INFO @ Tue, 02 Aug 2022 13:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:55:55: #1 finished! INFO @ Tue, 02 Aug 2022 13:55:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:55:56: #2 number of paired peaks: 835 WARNING @ Tue, 02 Aug 2022 13:55:56: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 02 Aug 2022 13:55:56: start model_add_line... INFO @ Tue, 02 Aug 2022 13:55:56: start X-correlation... INFO @ Tue, 02 Aug 2022 13:55:57: end of X-cor INFO @ Tue, 02 Aug 2022 13:55:57: #2 finished! INFO @ Tue, 02 Aug 2022 13:55:57: #2 predicted fragment length is 65 bps INFO @ Tue, 02 Aug 2022 13:55:57: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 02 Aug 2022 13:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10_model.r WARNING @ Tue, 02 Aug 2022 13:55:57: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:55:57: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 02 Aug 2022 13:55:57: #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 13:55:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:55:57: 10000000 INFO @ Tue, 02 Aug 2022 13:56:04: 11000000 INFO @ Tue, 02 Aug 2022 13:56:11: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:56:18: 13000000 INFO @ Tue, 02 Aug 2022 13:56:21: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:56:21: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:56:21: #1 total tags in treatment: 13412122 INFO @ Tue, 02 Aug 2022 13:56:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:56:21: #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 13:56:21: #1 tags after filtering in treatment: 13412117 INFO @ Tue, 02 Aug 2022 13:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:56:21: #1 finished! INFO @ Tue, 02 Aug 2022 13:56:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:56:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:56:22: #2 number of paired peaks: 835 WARNING @ Tue, 02 Aug 2022 13:56:22: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 02 Aug 2022 13:56:22: start model_add_line... INFO @ Tue, 02 Aug 2022 13:56:22: start X-correlation... INFO @ Tue, 02 Aug 2022 13:56:22: end of X-cor INFO @ Tue, 02 Aug 2022 13:56:22: #2 finished! INFO @ Tue, 02 Aug 2022 13:56:22: #2 predicted fragment length is 65 bps INFO @ Tue, 02 Aug 2022 13:56:22: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 02 Aug 2022 13:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20_model.r WARNING @ Tue, 02 Aug 2022 13:56:22: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:56:22: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 02 Aug 2022 13:56:22: #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 13:56:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.10_summits.bed INFO @ Tue, 02 Aug 2022 13:56:35: Done! pass1 - making usageList (577 chroms): 2 millis pass2 - checking and writing primary data (1638 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:56:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261343/SRX12261343.20_summits.bed INFO @ Tue, 02 Aug 2022 13:57:01: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 33 millis CompletedMACS2peakCalling