Job ID = 6529175 SRX = SRX026868 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: 00:05:55 23509855 reads; of these: 23509855 (100.00%) were unpaired; of these: 823068 (3.50%) aligned 0 times 15167941 (64.52%) aligned exactly 1 time 7518846 (31.98%) aligned >1 times 96.50% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 7102828 / 22686787 = 0.3131 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 01:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.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 01:45:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:15: 1000000 INFO @ Tue, 30 Jun 2020 01:45:20: 2000000 INFO @ Tue, 30 Jun 2020 01:45:25: 3000000 INFO @ Tue, 30 Jun 2020 01:45:30: 4000000 INFO @ Tue, 30 Jun 2020 01:45:35: 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 01:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.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 01:45:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:40: 6000000 INFO @ Tue, 30 Jun 2020 01:45:45: 7000000 INFO @ Tue, 30 Jun 2020 01:45:45: 1000000 INFO @ Tue, 30 Jun 2020 01:45:51: 8000000 INFO @ Tue, 30 Jun 2020 01:45:52: 2000000 INFO @ Tue, 30 Jun 2020 01:45:56: 9000000 INFO @ Tue, 30 Jun 2020 01:45:58: 3000000 INFO @ Tue, 30 Jun 2020 01:46:01: 10000000 INFO @ Tue, 30 Jun 2020 01:46:04: 4000000 INFO @ Tue, 30 Jun 2020 01:46:06: 11000000 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 01:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.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 01:46:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:10: 5000000 INFO @ Tue, 30 Jun 2020 01:46:12: 12000000 INFO @ Tue, 30 Jun 2020 01:46:15: 1000000 INFO @ Tue, 30 Jun 2020 01:46:16: 6000000 INFO @ Tue, 30 Jun 2020 01:46:18: 13000000 INFO @ Tue, 30 Jun 2020 01:46:21: 2000000 INFO @ Tue, 30 Jun 2020 01:46:22: 7000000 INFO @ Tue, 30 Jun 2020 01:46:24: 14000000 INFO @ Tue, 30 Jun 2020 01:46:28: 3000000 INFO @ Tue, 30 Jun 2020 01:46:28: 8000000 INFO @ Tue, 30 Jun 2020 01:46:30: 15000000 INFO @ Tue, 30 Jun 2020 01:46:33: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:46:33: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:46:33: #1 total tags in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:46:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:33: #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 01:46:34: 4000000 INFO @ Tue, 30 Jun 2020 01:46:34: #1 tags after filtering in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:34: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:35: 9000000 INFO @ Tue, 30 Jun 2020 01:46:35: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 01:46:35: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:35: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:46:35: #2 alternative fragment length(s) may be 2,26 bps INFO @ Tue, 30 Jun 2020 01:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05_model.r WARNING @ Tue, 30 Jun 2020 01:46:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:46:35: #2 You may need to consider one of the other alternative d(s): 2,26 WARNING @ Tue, 30 Jun 2020 01:46:35: #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 01:46:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:40: 5000000 INFO @ Tue, 30 Jun 2020 01:46:41: 10000000 INFO @ Tue, 30 Jun 2020 01:46:46: 6000000 INFO @ Tue, 30 Jun 2020 01:46:47: 11000000 INFO @ Tue, 30 Jun 2020 01:46:52: 7000000 INFO @ Tue, 30 Jun 2020 01:46:53: 12000000 INFO @ Tue, 30 Jun 2020 01:46:58: 8000000 INFO @ Tue, 30 Jun 2020 01:47:00: 13000000 INFO @ Tue, 30 Jun 2020 01:47:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:04: 9000000 INFO @ Tue, 30 Jun 2020 01:47:06: 14000000 INFO @ Tue, 30 Jun 2020 01:47:10: 10000000 INFO @ Tue, 30 Jun 2020 01:47:12: 15000000 INFO @ Tue, 30 Jun 2020 01:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.05_summits.bed INFO @ Tue, 30 Jun 2020 01:47:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:47:16: 11000000 INFO @ Tue, 30 Jun 2020 01:47:16: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:47:16: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:47:16: #1 total tags in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:47:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:16: #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 01:47:17: #1 tags after filtering in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:18: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 01:47:18: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:18: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:47:18: #2 alternative fragment length(s) may be 2,26 bps INFO @ Tue, 30 Jun 2020 01:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10_model.r WARNING @ Tue, 30 Jun 2020 01:47:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:18: #2 You may need to consider one of the other alternative d(s): 2,26 WARNING @ Tue, 30 Jun 2020 01:47:18: #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 01:47:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:22: 12000000 INFO @ Tue, 30 Jun 2020 01:47:29: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:47:34: 14000000 INFO @ Tue, 30 Jun 2020 01:47:41: 15000000 INFO @ Tue, 30 Jun 2020 01:47:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:45: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:47:45: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:47:45: #1 total tags in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:47:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:45: #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 01:47:46: #1 tags after filtering in treatment: 15583959 INFO @ Tue, 30 Jun 2020 01:47:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:46: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:47: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 01:47:47: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:47: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:47:47: #2 alternative fragment length(s) may be 2,26 bps INFO @ Tue, 30 Jun 2020 01:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20_model.r WARNING @ Tue, 30 Jun 2020 01:47:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:47: #2 You may need to consider one of the other alternative d(s): 2,26 WARNING @ Tue, 30 Jun 2020 01:47:47: #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 01:47:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:48:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026868/SRX026868.20_summits.bed INFO @ Tue, 30 Jun 2020 01:48:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling