Job ID = 6529554 SRX = SRX3159479 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: 00:07:20 31503810 reads; of these: 31503810 (100.00%) were unpaired; of these: 4385166 (13.92%) aligned 0 times 19412094 (61.62%) aligned exactly 1 time 7706550 (24.46%) aligned >1 times 86.08% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 8291209 / 27118644 = 0.3057 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, 30 Jun 2020 02:31:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.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, 30 Jun 2020 02:31:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:37: 1000000 INFO @ Tue, 30 Jun 2020 02:31:45: 2000000 INFO @ Tue, 30 Jun 2020 02:31:52: 3000000 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, 30 Jun 2020 02:31:59: 4000000 INFO @ Tue, 30 Jun 2020 02:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.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, 30 Jun 2020 02:32:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:08: 5000000 INFO @ Tue, 30 Jun 2020 02:32:09: 1000000 INFO @ Tue, 30 Jun 2020 02:32:16: 6000000 INFO @ Tue, 30 Jun 2020 02:32:17: 2000000 INFO @ Tue, 30 Jun 2020 02:32:24: 7000000 INFO @ Tue, 30 Jun 2020 02:32:26: 3000000 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, 30 Jun 2020 02:32:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.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, 30 Jun 2020 02:32:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:32: 8000000 INFO @ Tue, 30 Jun 2020 02:32:35: 4000000 INFO @ Tue, 30 Jun 2020 02:32:39: 1000000 INFO @ Tue, 30 Jun 2020 02:32:41: 9000000 INFO @ Tue, 30 Jun 2020 02:32:44: 5000000 INFO @ Tue, 30 Jun 2020 02:32:48: 2000000 INFO @ Tue, 30 Jun 2020 02:32:50: 10000000 INFO @ Tue, 30 Jun 2020 02:32:53: 6000000 INFO @ Tue, 30 Jun 2020 02:32:56: 3000000 INFO @ Tue, 30 Jun 2020 02:32:59: 11000000 INFO @ Tue, 30 Jun 2020 02:33:02: 7000000 INFO @ Tue, 30 Jun 2020 02:33:05: 4000000 INFO @ Tue, 30 Jun 2020 02:33:07: 12000000 INFO @ Tue, 30 Jun 2020 02:33:10: 8000000 INFO @ Tue, 30 Jun 2020 02:33:14: 5000000 INFO @ Tue, 30 Jun 2020 02:33:16: 13000000 INFO @ Tue, 30 Jun 2020 02:33:19: 9000000 INFO @ Tue, 30 Jun 2020 02:33:22: 6000000 INFO @ Tue, 30 Jun 2020 02:33:25: 14000000 INFO @ Tue, 30 Jun 2020 02:33:28: 10000000 INFO @ Tue, 30 Jun 2020 02:33:31: 7000000 INFO @ Tue, 30 Jun 2020 02:33:34: 15000000 INFO @ Tue, 30 Jun 2020 02:33:38: 11000000 INFO @ Tue, 30 Jun 2020 02:33:40: 8000000 INFO @ Tue, 30 Jun 2020 02:33:43: 16000000 INFO @ Tue, 30 Jun 2020 02:33:47: 12000000 INFO @ Tue, 30 Jun 2020 02:33:48: 9000000 INFO @ Tue, 30 Jun 2020 02:33:52: 17000000 INFO @ Tue, 30 Jun 2020 02:33:57: 13000000 INFO @ Tue, 30 Jun 2020 02:33:57: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:34:01: 18000000 INFO @ Tue, 30 Jun 2020 02:34:06: 11000000 INFO @ Tue, 30 Jun 2020 02:34:06: 14000000 INFO @ Tue, 30 Jun 2020 02:34:08: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:34:08: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:34:08: #1 total tags in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:34:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:09: #1 tags after filtering in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:34:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:10: #2 number of paired peaks: 856 WARNING @ Tue, 30 Jun 2020 02:34:10: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:10: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:34:10: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05_model.r WARNING @ Tue, 30 Jun 2020 02:34:10: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:10: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:34:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:14: 12000000 INFO @ Tue, 30 Jun 2020 02:34:15: 15000000 INFO @ Tue, 30 Jun 2020 02:34:23: 13000000 INFO @ Tue, 30 Jun 2020 02:34:24: 16000000 INFO @ Tue, 30 Jun 2020 02:34:31: 14000000 INFO @ Tue, 30 Jun 2020 02:34:33: 17000000 INFO @ Tue, 30 Jun 2020 02:34:40: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:34:42: 18000000 INFO @ Tue, 30 Jun 2020 02:34:48: 16000000 INFO @ Tue, 30 Jun 2020 02:34:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:49: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:34:49: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:34:49: #1 total tags in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:34:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:49: #1 tags after filtering in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:51: #2 number of paired peaks: 856 WARNING @ Tue, 30 Jun 2020 02:34:51: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:51: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:34:51: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10_model.r WARNING @ Tue, 30 Jun 2020 02:34:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:51: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:34:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:56: 17000000 INFO @ Tue, 30 Jun 2020 02:35:04: 18000000 INFO @ Tue, 30 Jun 2020 02:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.05_summits.bed INFO @ Tue, 30 Jun 2020 02:35:06: Done! pass1 - making usageList (720 chroms): 2 millis pass2 - checking and writing primary data (5078 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:10: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:35:10: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:35:10: #1 total tags in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:35:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:35:11: #1 tags after filtering in treatment: 18827435 INFO @ Tue, 30 Jun 2020 02:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:11: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:12: #2 number of paired peaks: 856 WARNING @ Tue, 30 Jun 2020 02:35:12: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:12: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:35:12: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20_model.r WARNING @ Tue, 30 Jun 2020 02:35:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:12: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:35:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:35:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.10_summits.bed INFO @ Tue, 30 Jun 2020 02:35:47: Done! pass1 - making usageList (617 chroms): 1 millis pass2 - checking and writing primary data (3284 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159479/SRX3159479.20_summits.bed INFO @ Tue, 30 Jun 2020 02:36:08: Done! pass1 - making usageList (467 chroms): 2 millis pass2 - checking and writing primary data (1863 records, 4 fields): 17 millis CompletedMACS2peakCalling