Job ID = 6530086 SRX = SRX7672887 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: 00:06:20 25012710 reads; of these: 25012710 (100.00%) were unpaired; of these: 3287222 (13.14%) aligned 0 times 15731863 (62.90%) aligned exactly 1 time 5993625 (23.96%) aligned >1 times 86.86% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 2904641 / 21725488 = 0.1337 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 03:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.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 03:42:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:42:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:42:06: 1000000 INFO @ Tue, 30 Jun 2020 03:42:11: 2000000 INFO @ Tue, 30 Jun 2020 03:42:16: 3000000 INFO @ Tue, 30 Jun 2020 03:42:21: 4000000 INFO @ Tue, 30 Jun 2020 03:42:26: 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 03:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.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 03:42:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:42:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:42:32: 6000000 INFO @ Tue, 30 Jun 2020 03:42:37: 1000000 INFO @ Tue, 30 Jun 2020 03:42:37: 7000000 INFO @ Tue, 30 Jun 2020 03:42:43: 8000000 INFO @ Tue, 30 Jun 2020 03:42:44: 2000000 INFO @ Tue, 30 Jun 2020 03:42:49: 9000000 INFO @ Tue, 30 Jun 2020 03:42:50: 3000000 INFO @ Tue, 30 Jun 2020 03:42:54: 10000000 INFO @ Tue, 30 Jun 2020 03:42:57: 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 03:43:00: 11000000 INFO @ Tue, 30 Jun 2020 03:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.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 03:43:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:43:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:43:03: 5000000 INFO @ Tue, 30 Jun 2020 03:43:06: 12000000 INFO @ Tue, 30 Jun 2020 03:43:08: 1000000 INFO @ Tue, 30 Jun 2020 03:43:10: 6000000 INFO @ Tue, 30 Jun 2020 03:43:11: 13000000 INFO @ Tue, 30 Jun 2020 03:43:15: 2000000 INFO @ Tue, 30 Jun 2020 03:43:17: 14000000 INFO @ Tue, 30 Jun 2020 03:43:17: 7000000 INFO @ Tue, 30 Jun 2020 03:43:22: 3000000 INFO @ Tue, 30 Jun 2020 03:43:23: 15000000 INFO @ Tue, 30 Jun 2020 03:43:24: 8000000 INFO @ Tue, 30 Jun 2020 03:43:28: 4000000 INFO @ Tue, 30 Jun 2020 03:43:29: 16000000 INFO @ Tue, 30 Jun 2020 03:43:31: 9000000 INFO @ Tue, 30 Jun 2020 03:43:34: 17000000 INFO @ Tue, 30 Jun 2020 03:43:35: 5000000 INFO @ Tue, 30 Jun 2020 03:43:37: 10000000 INFO @ Tue, 30 Jun 2020 03:43:40: 18000000 INFO @ Tue, 30 Jun 2020 03:43:42: 6000000 INFO @ Tue, 30 Jun 2020 03:43:44: 11000000 INFO @ Tue, 30 Jun 2020 03:43:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:43:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:43:45: #1 total tags in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:43:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:43:45: #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 03:43:46: #1 tags after filtering in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:43:46: #1 finished! INFO @ Tue, 30 Jun 2020 03:43:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:43:47: #2 number of paired peaks: 288 WARNING @ Tue, 30 Jun 2020 03:43:47: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 30 Jun 2020 03:43:47: start model_add_line... INFO @ Tue, 30 Jun 2020 03:43:47: start X-correlation... INFO @ Tue, 30 Jun 2020 03:43:47: end of X-cor INFO @ Tue, 30 Jun 2020 03:43:47: #2 finished! INFO @ Tue, 30 Jun 2020 03:43:47: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:43:47: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 30 Jun 2020 03:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05_model.r WARNING @ Tue, 30 Jun 2020 03:43:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:43:47: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 30 Jun 2020 03:43:47: #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 03:43:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:43:48: 7000000 INFO @ Tue, 30 Jun 2020 03:43:50: 12000000 INFO @ Tue, 30 Jun 2020 03:43:55: 8000000 INFO @ Tue, 30 Jun 2020 03:43:57: 13000000 INFO @ Tue, 30 Jun 2020 03:44:01: 9000000 INFO @ Tue, 30 Jun 2020 03:44:03: 14000000 INFO @ Tue, 30 Jun 2020 03:44:08: 10000000 INFO @ Tue, 30 Jun 2020 03:44:10: 15000000 INFO @ Tue, 30 Jun 2020 03:44:14: 11000000 INFO @ Tue, 30 Jun 2020 03:44:16: 16000000 INFO @ Tue, 30 Jun 2020 03:44:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:21: 12000000 INFO @ Tue, 30 Jun 2020 03:44:23: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:44:27: 13000000 INFO @ Tue, 30 Jun 2020 03:44:29: 18000000 INFO @ Tue, 30 Jun 2020 03:44:34: 14000000 INFO @ Tue, 30 Jun 2020 03:44:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:44:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:44:35: #1 total tags in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:44:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:35: #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 03:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.05_summits.bed INFO @ Tue, 30 Jun 2020 03:44:35: Done! pass1 - making usageList (655 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:44:36: #1 tags after filtering in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:36: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:37: #2 number of paired peaks: 288 WARNING @ Tue, 30 Jun 2020 03:44:37: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:37: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:44:37: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 30 Jun 2020 03:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10_model.r WARNING @ Tue, 30 Jun 2020 03:44:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:37: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 30 Jun 2020 03:44:37: #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 03:44:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:40: 15000000 INFO @ Tue, 30 Jun 2020 03:44:47: 16000000 INFO @ Tue, 30 Jun 2020 03:44:53: 17000000 INFO @ Tue, 30 Jun 2020 03:44:59: 18000000 INFO @ Tue, 30 Jun 2020 03:45:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:45:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:45:05: #1 total tags in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:45:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:45:05: #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 03:45:05: #1 tags after filtering in treatment: 18820847 INFO @ Tue, 30 Jun 2020 03:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:45:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:45:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:45:06: #2 number of paired peaks: 288 WARNING @ Tue, 30 Jun 2020 03:45:06: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 30 Jun 2020 03:45:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:45:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:45:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:45:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:45:06: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:45:06: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 30 Jun 2020 03:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20_model.r WARNING @ Tue, 30 Jun 2020 03:45:06: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:45:06: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 30 Jun 2020 03:45:06: #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 03:45:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:45:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:45:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.10_summits.bed INFO @ Tue, 30 Jun 2020 03:45:27: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (1894 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672887/SRX7672887.20_summits.bed INFO @ Tue, 30 Jun 2020 03:45:56: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 9 millis CompletedMACS2peakCalling