Job ID = 6529304 SRX = SRX1490781 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: 00:03:39 14259690 reads; of these: 14259690 (100.00%) were unpaired; of these: 951638 (6.67%) aligned 0 times 10450836 (73.29%) aligned exactly 1 time 2857216 (20.04%) aligned >1 times 93.33% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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 8 files... [bam_rmdupse_core] 1156829 / 13308052 = 0.0869 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 01:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.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 01:50:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:50:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:50:23: 1000000 INFO @ Tue, 30 Jun 2020 01:50:29: 2000000 INFO @ Tue, 30 Jun 2020 01:50:35: 3000000 INFO @ Tue, 30 Jun 2020 01:50:41: 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 01:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.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 01:50:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:50:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:50:47: 5000000 INFO @ Tue, 30 Jun 2020 01:50:54: 6000000 INFO @ Tue, 30 Jun 2020 01:50:54: 1000000 INFO @ Tue, 30 Jun 2020 01:51:01: 7000000 INFO @ Tue, 30 Jun 2020 01:51:02: 2000000 INFO @ Tue, 30 Jun 2020 01:51:08: 8000000 INFO @ Tue, 30 Jun 2020 01:51:10: 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 01:51:15: 9000000 INFO @ Tue, 30 Jun 2020 01:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.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 01:51:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:51:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:51:18: 4000000 INFO @ Tue, 30 Jun 2020 01:51:23: 10000000 INFO @ Tue, 30 Jun 2020 01:51:25: 1000000 INFO @ Tue, 30 Jun 2020 01:51:26: 5000000 INFO @ Tue, 30 Jun 2020 01:51:31: 11000000 INFO @ Tue, 30 Jun 2020 01:51:33: 2000000 INFO @ Tue, 30 Jun 2020 01:51:33: 6000000 INFO @ Tue, 30 Jun 2020 01:51:38: 12000000 INFO @ Tue, 30 Jun 2020 01:51:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:51:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:51:40: #1 total tags in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:51:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:51:40: #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 01:51:40: #1 tags after filtering in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:51:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:51:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:51:40: 3000000 INFO @ Tue, 30 Jun 2020 01:51:41: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 01:51:41: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 01:51:41: start model_add_line... INFO @ Tue, 30 Jun 2020 01:51:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:51:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:51:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:51:41: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 01:51:41: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 01:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05_model.r WARNING @ Tue, 30 Jun 2020 01:51:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:51:41: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 30 Jun 2020 01:51:41: #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 01:51:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:51:41: 7000000 INFO @ Tue, 30 Jun 2020 01:51:48: 4000000 INFO @ Tue, 30 Jun 2020 01:51:49: 8000000 INFO @ Tue, 30 Jun 2020 01:51:55: 5000000 INFO @ Tue, 30 Jun 2020 01:51:57: 9000000 INFO @ Tue, 30 Jun 2020 01:52:03: 6000000 INFO @ Tue, 30 Jun 2020 01:52:05: 10000000 INFO @ Tue, 30 Jun 2020 01:52:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:52:10: 7000000 INFO @ Tue, 30 Jun 2020 01:52:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:52:18: 8000000 INFO @ Tue, 30 Jun 2020 01:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.05_summits.bed INFO @ Tue, 30 Jun 2020 01:52:19: Done! pass1 - making usageList (183 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:52:21: 12000000 INFO @ Tue, 30 Jun 2020 01:52:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:52:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:52:22: #1 total tags in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:52:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:52:22: #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 01:52:22: #1 tags after filtering in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:52:22: #1 finished! INFO @ Tue, 30 Jun 2020 01:52:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:52:23: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 01:52:23: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 01:52:23: start model_add_line... INFO @ Tue, 30 Jun 2020 01:52:23: start X-correlation... INFO @ Tue, 30 Jun 2020 01:52:23: end of X-cor INFO @ Tue, 30 Jun 2020 01:52:23: #2 finished! INFO @ Tue, 30 Jun 2020 01:52:23: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 01:52:23: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 01:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10_model.r WARNING @ Tue, 30 Jun 2020 01:52:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:52:23: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 30 Jun 2020 01:52:23: #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 01:52:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:52:26: 9000000 INFO @ Tue, 30 Jun 2020 01:52:33: 10000000 INFO @ Tue, 30 Jun 2020 01:52:40: 11000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:52:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:52:48: 12000000 INFO @ Tue, 30 Jun 2020 01:52:49: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:52:49: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:52:49: #1 total tags in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:52:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:52:49: #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 01:52:49: #1 tags after filtering in treatment: 12151223 INFO @ Tue, 30 Jun 2020 01:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:52:49: #1 finished! INFO @ Tue, 30 Jun 2020 01:52:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:52:50: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 01:52:50: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 01:52:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:52:50: start X-correlation... INFO @ Tue, 30 Jun 2020 01:52:50: end of X-cor INFO @ Tue, 30 Jun 2020 01:52:50: #2 finished! INFO @ Tue, 30 Jun 2020 01:52:50: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 01:52:50: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 01:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20_model.r WARNING @ Tue, 30 Jun 2020 01:52:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:52:50: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 30 Jun 2020 01:52:50: #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 01:52:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:52:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.10_summits.bed INFO @ Tue, 30 Jun 2020 01:53:00: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490781/SRX1490781.20_summits.bed INFO @ Tue, 30 Jun 2020 01:53:27: Done! pass1 - making usageList (108 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 4 millis CompletedMACS2peakCalling