Job ID = 6529340 SRX = SRX191916 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: 00:09:57 37267715 reads; of these: 37267715 (100.00%) were unpaired; of these: 1215719 (3.26%) aligned 0 times 24804967 (66.56%) aligned exactly 1 time 11247029 (30.18%) aligned >1 times 96.74% overall alignment rate Time searching: 00:09:57 Overall time: 00:09:57 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] 8371081 / 36051996 = 0.2322 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 02:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.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 02:08:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:25: 1000000 INFO @ Tue, 30 Jun 2020 02:08:30: 2000000 INFO @ Tue, 30 Jun 2020 02:08:36: 3000000 INFO @ Tue, 30 Jun 2020 02:08:41: 4000000 INFO @ Tue, 30 Jun 2020 02:08:47: 5000000 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 02:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.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 02:08:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:53: 6000000 INFO @ Tue, 30 Jun 2020 02:08:56: 1000000 INFO @ Tue, 30 Jun 2020 02:08:59: 7000000 INFO @ Tue, 30 Jun 2020 02:09:02: 2000000 INFO @ Tue, 30 Jun 2020 02:09:05: 8000000 INFO @ Tue, 30 Jun 2020 02:09:09: 3000000 INFO @ Tue, 30 Jun 2020 02:09:12: 9000000 INFO @ Tue, 30 Jun 2020 02:09:15: 4000000 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 02:09:18: 10000000 INFO @ Tue, 30 Jun 2020 02:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.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 02:09:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:21: 5000000 INFO @ Tue, 30 Jun 2020 02:09:24: 11000000 INFO @ Tue, 30 Jun 2020 02:09:25: 1000000 INFO @ Tue, 30 Jun 2020 02:09:28: 6000000 INFO @ Tue, 30 Jun 2020 02:09:30: 12000000 INFO @ Tue, 30 Jun 2020 02:09:32: 2000000 INFO @ Tue, 30 Jun 2020 02:09:34: 7000000 INFO @ Tue, 30 Jun 2020 02:09:36: 13000000 INFO @ Tue, 30 Jun 2020 02:09:38: 3000000 INFO @ Tue, 30 Jun 2020 02:09:40: 8000000 INFO @ Tue, 30 Jun 2020 02:09:43: 14000000 INFO @ Tue, 30 Jun 2020 02:09:45: 4000000 INFO @ Tue, 30 Jun 2020 02:09:47: 9000000 INFO @ Tue, 30 Jun 2020 02:09:49: 15000000 INFO @ Tue, 30 Jun 2020 02:09:51: 5000000 INFO @ Tue, 30 Jun 2020 02:09:53: 10000000 INFO @ Tue, 30 Jun 2020 02:09:55: 16000000 INFO @ Tue, 30 Jun 2020 02:09:57: 6000000 INFO @ Tue, 30 Jun 2020 02:09:59: 11000000 INFO @ Tue, 30 Jun 2020 02:10:01: 17000000 INFO @ Tue, 30 Jun 2020 02:10:04: 7000000 INFO @ Tue, 30 Jun 2020 02:10:05: 12000000 INFO @ Tue, 30 Jun 2020 02:10:08: 18000000 INFO @ Tue, 30 Jun 2020 02:10:10: 8000000 INFO @ Tue, 30 Jun 2020 02:10:12: 13000000 INFO @ Tue, 30 Jun 2020 02:10:14: 19000000 INFO @ Tue, 30 Jun 2020 02:10:17: 9000000 INFO @ Tue, 30 Jun 2020 02:10:18: 14000000 INFO @ Tue, 30 Jun 2020 02:10:21: 20000000 INFO @ Tue, 30 Jun 2020 02:10:23: 10000000 INFO @ Tue, 30 Jun 2020 02:10:24: 15000000 INFO @ Tue, 30 Jun 2020 02:10:27: 21000000 INFO @ Tue, 30 Jun 2020 02:10:30: 11000000 INFO @ Tue, 30 Jun 2020 02:10:31: 16000000 INFO @ Tue, 30 Jun 2020 02:10:34: 22000000 INFO @ Tue, 30 Jun 2020 02:10:36: 12000000 INFO @ Tue, 30 Jun 2020 02:10:37: 17000000 INFO @ Tue, 30 Jun 2020 02:10:40: 23000000 INFO @ Tue, 30 Jun 2020 02:10:43: 13000000 INFO @ Tue, 30 Jun 2020 02:10:44: 18000000 INFO @ Tue, 30 Jun 2020 02:10:47: 24000000 INFO @ Tue, 30 Jun 2020 02:10:49: 14000000 INFO @ Tue, 30 Jun 2020 02:10:50: 19000000 INFO @ Tue, 30 Jun 2020 02:10:54: 25000000 INFO @ Tue, 30 Jun 2020 02:10:56: 15000000 INFO @ Tue, 30 Jun 2020 02:10:57: 20000000 INFO @ Tue, 30 Jun 2020 02:11:00: 26000000 INFO @ Tue, 30 Jun 2020 02:11:02: 16000000 INFO @ Tue, 30 Jun 2020 02:11:03: 21000000 INFO @ Tue, 30 Jun 2020 02:11:07: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:11:09: 17000000 INFO @ Tue, 30 Jun 2020 02:11:10: 22000000 INFO @ Tue, 30 Jun 2020 02:11:12: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:11:12: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:11:12: #1 total tags in treatment: 27680915 INFO @ Tue, 30 Jun 2020 02:11:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:11:12: #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 02:11:13: #1 tags after filtering in treatment: 27680871 INFO @ Tue, 30 Jun 2020 02:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:11:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:11:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:11:14: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:11:14: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:11:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:11:15: start X-correlation... INFO @ Tue, 30 Jun 2020 02:11:15: end of X-cor INFO @ Tue, 30 Jun 2020 02:11:15: #2 finished! INFO @ Tue, 30 Jun 2020 02:11:15: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:11:15: #2 alternative fragment length(s) may be 2,35,60,505,537,576 bps INFO @ Tue, 30 Jun 2020 02:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05_model.r WARNING @ Tue, 30 Jun 2020 02:11:15: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:11:15: #2 You may need to consider one of the other alternative d(s): 2,35,60,505,537,576 WARNING @ Tue, 30 Jun 2020 02:11:15: #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 02:11:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:11:16: 18000000 INFO @ Tue, 30 Jun 2020 02:11:16: 23000000 INFO @ Tue, 30 Jun 2020 02:11:22: 19000000 INFO @ Tue, 30 Jun 2020 02:11:23: 24000000 INFO @ Tue, 30 Jun 2020 02:11:29: 20000000 INFO @ Tue, 30 Jun 2020 02:11:30: 25000000 INFO @ Tue, 30 Jun 2020 02:11:35: 21000000 INFO @ Tue, 30 Jun 2020 02:11:37: 26000000 INFO @ Tue, 30 Jun 2020 02:11:42: 22000000 INFO @ Tue, 30 Jun 2020 02:11:43: 27000000 INFO @ Tue, 30 Jun 2020 02:11:48: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:11:48: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:11:48: #1 total tags in treatment: 27680915 INFO @ Tue, 30 Jun 2020 02:11:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:11:48: #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 02:11:49: 23000000 INFO @ Tue, 30 Jun 2020 02:11:49: #1 tags after filtering in treatment: 27680871 INFO @ Tue, 30 Jun 2020 02:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:11:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:11:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:11:51: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:11:51: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:11:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:11:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:11:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:11:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:11:51: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:11:51: #2 alternative fragment length(s) may be 2,35,60,505,537,576 bps INFO @ Tue, 30 Jun 2020 02:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10_model.r WARNING @ Tue, 30 Jun 2020 02:11:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:11:51: #2 You may need to consider one of the other alternative d(s): 2,35,60,505,537,576 WARNING @ Tue, 30 Jun 2020 02:11:51: #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 02:11:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:11:55: 24000000 INFO @ Tue, 30 Jun 2020 02:12:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:12:01: 25000000 INFO @ Tue, 30 Jun 2020 02:12:07: 26000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:12:13: 27000000 INFO @ Tue, 30 Jun 2020 02:12:17: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:12:17: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:12:17: #1 total tags in treatment: 27680915 INFO @ Tue, 30 Jun 2020 02:12:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:17: #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 02:12:18: #1 tags after filtering in treatment: 27680871 INFO @ Tue, 30 Jun 2020 02:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:20: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:12:20: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:20: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:12:20: #2 alternative fragment length(s) may be 2,35,60,505,537,576 bps INFO @ Tue, 30 Jun 2020 02:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20_model.r WARNING @ Tue, 30 Jun 2020 02:12:20: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:12:20: #2 You may need to consider one of the other alternative d(s): 2,35,60,505,537,576 WARNING @ Tue, 30 Jun 2020 02:12:20: #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 02:12:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.05_summits.bed INFO @ Tue, 30 Jun 2020 02:12:23: Done! pass1 - making usageList (483 chroms): 1 millis pass2 - checking and writing primary data (2718 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:12:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:04: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:13:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191916/SRX191916.20_summits.bed INFO @ Tue, 30 Jun 2020 02:13:32: Done! pass1 - making usageList (121 chroms): 0 millis pass2 - checking and writing primary data (324 records, 4 fields): 7 millis CompletedMACS2peakCalling