Job ID = 6529252 SRX = SRX1115692 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: 00:05:09 24221131 reads; of these: 24221131 (100.00%) were unpaired; of these: 1542672 (6.37%) aligned 0 times 17487661 (72.20%) aligned exactly 1 time 5190798 (21.43%) aligned >1 times 93.63% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 2801256 / 22678459 = 0.1235 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 01:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.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 01:35:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:35:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:04: 1000000 INFO @ Tue, 30 Jun 2020 01:36:10: 2000000 INFO @ Tue, 30 Jun 2020 01:36:15: 3000000 INFO @ Tue, 30 Jun 2020 01:36:21: 4000000 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 01:36:27: 5000000 INFO @ Tue, 30 Jun 2020 01:36:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.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 01:36:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:33: 6000000 INFO @ Tue, 30 Jun 2020 01:36:33: 1000000 INFO @ Tue, 30 Jun 2020 01:36:38: 2000000 INFO @ Tue, 30 Jun 2020 01:36:39: 7000000 INFO @ Tue, 30 Jun 2020 01:36:43: 3000000 INFO @ Tue, 30 Jun 2020 01:36:45: 8000000 INFO @ Tue, 30 Jun 2020 01:36:48: 4000000 INFO @ Tue, 30 Jun 2020 01:36:51: 9000000 INFO @ Tue, 30 Jun 2020 01:36:53: 5000000 BedGraph に変換中... INFO @ Tue, 30 Jun 2020 01:36:57: 10000000 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 01:36:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.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 01:36:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:58: 6000000 INFO @ Tue, 30 Jun 2020 01:37:02: 11000000 INFO @ Tue, 30 Jun 2020 01:37:03: 1000000 INFO @ Tue, 30 Jun 2020 01:37:03: 7000000 INFO @ Tue, 30 Jun 2020 01:37:08: 2000000 INFO @ Tue, 30 Jun 2020 01:37:08: 8000000 INFO @ Tue, 30 Jun 2020 01:37:09: 12000000 INFO @ Tue, 30 Jun 2020 01:37:13: 3000000 INFO @ Tue, 30 Jun 2020 01:37:13: 9000000 INFO @ Tue, 30 Jun 2020 01:37:14: 13000000 INFO @ Tue, 30 Jun 2020 01:37:18: 4000000 INFO @ Tue, 30 Jun 2020 01:37:18: 10000000 INFO @ Tue, 30 Jun 2020 01:37:20: 14000000 INFO @ Tue, 30 Jun 2020 01:37:23: 5000000 INFO @ Tue, 30 Jun 2020 01:37:23: 11000000 INFO @ Tue, 30 Jun 2020 01:37:26: 15000000 INFO @ Tue, 30 Jun 2020 01:37:28: 6000000 INFO @ Tue, 30 Jun 2020 01:37:29: 12000000 INFO @ Tue, 30 Jun 2020 01:37:32: 16000000 INFO @ Tue, 30 Jun 2020 01:37:33: 7000000 INFO @ Tue, 30 Jun 2020 01:37:34: 13000000 INFO @ Tue, 30 Jun 2020 01:37:38: 8000000 INFO @ Tue, 30 Jun 2020 01:37:39: 14000000 INFO @ Tue, 30 Jun 2020 01:37:39: 17000000 INFO @ Tue, 30 Jun 2020 01:37:44: 9000000 INFO @ Tue, 30 Jun 2020 01:37:44: 15000000 INFO @ Tue, 30 Jun 2020 01:37:45: 18000000 INFO @ Tue, 30 Jun 2020 01:37:49: 10000000 INFO @ Tue, 30 Jun 2020 01:37:49: 16000000 INFO @ Tue, 30 Jun 2020 01:37:51: 19000000 INFO @ Tue, 30 Jun 2020 01:37:54: 11000000 INFO @ Tue, 30 Jun 2020 01:37:54: 17000000 INFO @ Tue, 30 Jun 2020 01:37:57: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:37:57: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:37:57: #1 total tags in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:37:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:37:57: #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 01:37:58: #1 tags after filtering in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:37:58: #1 finished! INFO @ Tue, 30 Jun 2020 01:37:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:37:59: 12000000 INFO @ Tue, 30 Jun 2020 01:37:59: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 01:37:59: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 01:37:59: start model_add_line... INFO @ Tue, 30 Jun 2020 01:37:59: start X-correlation... INFO @ Tue, 30 Jun 2020 01:37:59: end of X-cor INFO @ Tue, 30 Jun 2020 01:37:59: #2 finished! INFO @ Tue, 30 Jun 2020 01:37:59: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:37:59: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 01:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05_model.r WARNING @ Tue, 30 Jun 2020 01:37:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:37:59: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 01:37:59: #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 01:37:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:38:00: 18000000 INFO @ Tue, 30 Jun 2020 01:38:04: 13000000 INFO @ Tue, 30 Jun 2020 01:38:05: 19000000 INFO @ Tue, 30 Jun 2020 01:38:09: 14000000 INFO @ Tue, 30 Jun 2020 01:38:09: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:38:09: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:38:09: #1 total tags in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:38:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:38:09: #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 01:38:10: #1 tags after filtering in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:38:10: #1 finished! INFO @ Tue, 30 Jun 2020 01:38:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:38:11: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 01:38:11: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 01:38:11: start model_add_line... INFO @ Tue, 30 Jun 2020 01:38:11: start X-correlation... INFO @ Tue, 30 Jun 2020 01:38:11: end of X-cor INFO @ Tue, 30 Jun 2020 01:38:11: #2 finished! INFO @ Tue, 30 Jun 2020 01:38:11: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:38:11: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 01:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10_model.r WARNING @ Tue, 30 Jun 2020 01:38:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:38:11: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 01:38:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:38:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:38:14: 15000000 INFO @ Tue, 30 Jun 2020 01:38:18: 16000000 INFO @ Tue, 30 Jun 2020 01:38:24: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:38:29: 18000000 INFO @ Tue, 30 Jun 2020 01:38:34: 19000000 INFO @ Tue, 30 Jun 2020 01:38:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:38:38: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:38:38: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:38:38: #1 total tags in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:38:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:38:38: #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 01:38:39: #1 tags after filtering in treatment: 19877203 INFO @ Tue, 30 Jun 2020 01:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:38:39: #1 finished! INFO @ Tue, 30 Jun 2020 01:38:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:38:40: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 01:38:40: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 01:38:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:38:40: start X-correlation... INFO @ Tue, 30 Jun 2020 01:38:40: end of X-cor INFO @ Tue, 30 Jun 2020 01:38:40: #2 finished! INFO @ Tue, 30 Jun 2020 01:38:40: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:38:40: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 01:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20_model.r WARNING @ Tue, 30 Jun 2020 01:38:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:38:40: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 01:38:40: #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 01:38:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:38:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.05_summits.bed INFO @ Tue, 30 Jun 2020 01:38:53: Done! pass1 - making usageList (544 chroms): 1 millis pass2 - checking and writing primary data (1882 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.10_summits.bed INFO @ Tue, 30 Jun 2020 01:39:04: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:39:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115692/SRX1115692.20_summits.bed INFO @ Tue, 30 Jun 2020 01:39:32: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 6 millis CompletedMACS2peakCalling