Job ID = 6530026 SRX = SRX645134 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: 00:20:45 61600257 reads; of these: 61600257 (100.00%) were unpaired; of these: 36842857 (59.81%) aligned 0 times 18268040 (29.66%) aligned exactly 1 time 6489360 (10.53%) aligned >1 times 40.19% overall alignment rate Time searching: 00:20:45 Overall time: 00:20:45 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] 3154594 / 24757400 = 0.1274 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 03:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.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 03:40:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:46: 1000000 INFO @ Tue, 30 Jun 2020 03:40:54: 2000000 INFO @ Tue, 30 Jun 2020 03:41:02: 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 03:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.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 03:41:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:41:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:41:10: 4000000 INFO @ Tue, 30 Jun 2020 03:41:16: 1000000 INFO @ Tue, 30 Jun 2020 03:41:18: 5000000 INFO @ Tue, 30 Jun 2020 03:41:24: 2000000 INFO @ Tue, 30 Jun 2020 03:41:25: 6000000 INFO @ Tue, 30 Jun 2020 03:41:32: 3000000 INFO @ Tue, 30 Jun 2020 03:41:33: 7000000 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 03:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.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 03:41:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:41:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:41:40: 4000000 INFO @ Tue, 30 Jun 2020 03:41:41: 8000000 INFO @ Tue, 30 Jun 2020 03:41:47: 1000000 INFO @ Tue, 30 Jun 2020 03:41:48: 5000000 INFO @ Tue, 30 Jun 2020 03:41:50: 9000000 INFO @ Tue, 30 Jun 2020 03:41:55: 2000000 INFO @ Tue, 30 Jun 2020 03:41:57: 6000000 INFO @ Tue, 30 Jun 2020 03:41:58: 10000000 INFO @ Tue, 30 Jun 2020 03:42:04: 3000000 INFO @ Tue, 30 Jun 2020 03:42:05: 7000000 INFO @ Tue, 30 Jun 2020 03:42:06: 11000000 INFO @ Tue, 30 Jun 2020 03:42:13: 4000000 INFO @ Tue, 30 Jun 2020 03:42:13: 8000000 INFO @ Tue, 30 Jun 2020 03:42:14: 12000000 INFO @ Tue, 30 Jun 2020 03:42:22: 9000000 INFO @ Tue, 30 Jun 2020 03:42:22: 5000000 INFO @ Tue, 30 Jun 2020 03:42:23: 13000000 INFO @ Tue, 30 Jun 2020 03:42:30: 10000000 INFO @ Tue, 30 Jun 2020 03:42:30: 6000000 INFO @ Tue, 30 Jun 2020 03:42:32: 14000000 INFO @ Tue, 30 Jun 2020 03:42:38: 11000000 INFO @ Tue, 30 Jun 2020 03:42:39: 7000000 INFO @ Tue, 30 Jun 2020 03:42:41: 15000000 INFO @ Tue, 30 Jun 2020 03:42:47: 12000000 INFO @ Tue, 30 Jun 2020 03:42:49: 8000000 INFO @ Tue, 30 Jun 2020 03:42:50: 16000000 INFO @ Tue, 30 Jun 2020 03:42:55: 13000000 INFO @ Tue, 30 Jun 2020 03:42:58: 9000000 INFO @ Tue, 30 Jun 2020 03:42:59: 17000000 INFO @ Tue, 30 Jun 2020 03:43:03: 14000000 INFO @ Tue, 30 Jun 2020 03:43:08: 10000000 INFO @ Tue, 30 Jun 2020 03:43:09: 18000000 INFO @ Tue, 30 Jun 2020 03:43:12: 15000000 INFO @ Tue, 30 Jun 2020 03:43:17: 11000000 INFO @ Tue, 30 Jun 2020 03:43:18: 19000000 INFO @ Tue, 30 Jun 2020 03:43:20: 16000000 INFO @ Tue, 30 Jun 2020 03:43:27: 20000000 INFO @ Tue, 30 Jun 2020 03:43:27: 12000000 INFO @ Tue, 30 Jun 2020 03:43:29: 17000000 INFO @ Tue, 30 Jun 2020 03:43:36: 21000000 INFO @ Tue, 30 Jun 2020 03:43:36: 13000000 INFO @ Tue, 30 Jun 2020 03:43:37: 18000000 INFO @ Tue, 30 Jun 2020 03:43:42: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:43:42: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:43:42: #1 total tags in treatment: 21602806 INFO @ Tue, 30 Jun 2020 03:43:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:43:42: #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 03:43:42: #1 tags after filtering in treatment: 21602801 INFO @ Tue, 30 Jun 2020 03:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:43:42: #1 finished! INFO @ Tue, 30 Jun 2020 03:43:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:43:44: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 03:43:44: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 03:43:44: start model_add_line... INFO @ Tue, 30 Jun 2020 03:43:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:43:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:43:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:43:44: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:43:44: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 30 Jun 2020 03:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05_model.r WARNING @ Tue, 30 Jun 2020 03:43:44: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:43:44: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 30 Jun 2020 03:43:44: #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 03:43:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:43:45: 19000000 INFO @ Tue, 30 Jun 2020 03:43:46: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:43:54: 20000000 INFO @ Tue, 30 Jun 2020 03:43:56: 15000000 INFO @ Tue, 30 Jun 2020 03:44:02: 21000000 INFO @ Tue, 30 Jun 2020 03:44:06: 16000000 INFO @ Tue, 30 Jun 2020 03:44:08: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:44:08: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:44:08: #1 total tags in treatment: 21602806 INFO @ Tue, 30 Jun 2020 03:44:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:08: #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 03:44:08: #1 tags after filtering in treatment: 21602801 INFO @ Tue, 30 Jun 2020 03:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:08: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:09: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 03:44:09: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:09: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:10: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:10: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:10: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:10: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:44:10: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 30 Jun 2020 03:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10_model.r WARNING @ Tue, 30 Jun 2020 03:44:10: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:10: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 30 Jun 2020 03:44:10: #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 03:44:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:14: 17000000 INFO @ Tue, 30 Jun 2020 03:44:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:23: 18000000 INFO @ Tue, 30 Jun 2020 03:44:31: 19000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:44:39: 20000000 INFO @ Tue, 30 Jun 2020 03:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.05_summits.bed INFO @ Tue, 30 Jun 2020 03:44:43: Done! pass1 - making usageList (824 chroms): 1 millis pass2 - checking and writing primary data (3587 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:44:47: 21000000 INFO @ Tue, 30 Jun 2020 03:44:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:52: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:44:52: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:44:52: #1 total tags in treatment: 21602806 INFO @ Tue, 30 Jun 2020 03:44:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:52: #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 03:44:53: #1 tags after filtering in treatment: 21602801 INFO @ Tue, 30 Jun 2020 03:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:53: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:54: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 03:44:54: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:54: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:54: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:54: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:54: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:54: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:44:54: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 30 Jun 2020 03:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20_model.r WARNING @ Tue, 30 Jun 2020 03:44:54: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:54: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 30 Jun 2020 03:44:54: #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 03:44:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.10_summits.bed INFO @ Tue, 30 Jun 2020 03:45:06: Done! pass1 - making usageList (713 chroms): 1 millis pass2 - checking and writing primary data (2235 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:45:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645134/SRX645134.20_summits.bed INFO @ Tue, 30 Jun 2020 03:45:56: Done! pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (1302 records, 4 fields): 14 millis CompletedMACS2peakCalling