Job ID = 6455727 SRX = SRX288024 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:10:51 prefetch.2.10.7: 1) Downloading 'SRR870213'... 2020-06-21T10:10:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:18 prefetch.2.10.7: 1) 'SRR870213' was downloaded successfully Read 18433026 spots for SRR870213/SRR870213.sra Written 18433026 spots for SRR870213/SRR870213.sra 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: 00:05:12 18433026 reads; of these: 18433026 (100.00%) were unpaired; of these: 2487192 (13.49%) aligned 0 times 11542858 (62.62%) aligned exactly 1 time 4402976 (23.89%) aligned >1 times 86.51% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 3255291 / 15945834 = 0.2041 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 @ Sun, 21 Jun 2020 19:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.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 @ Sun, 21 Jun 2020 19:24:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:38: 1000000 INFO @ Sun, 21 Jun 2020 19:24:44: 2000000 INFO @ Sun, 21 Jun 2020 19:24:50: 3000000 INFO @ Sun, 21 Jun 2020 19:24:56: 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 @ Sun, 21 Jun 2020 19:25:02: 5000000 INFO @ Sun, 21 Jun 2020 19:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.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 @ Sun, 21 Jun 2020 19:25:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:08: 1000000 INFO @ Sun, 21 Jun 2020 19:25:08: 6000000 INFO @ Sun, 21 Jun 2020 19:25:15: 2000000 INFO @ Sun, 21 Jun 2020 19:25:15: 7000000 INFO @ Sun, 21 Jun 2020 19:25:21: 3000000 INFO @ Sun, 21 Jun 2020 19:25:21: 8000000 INFO @ Sun, 21 Jun 2020 19:25:27: 4000000 INFO @ Sun, 21 Jun 2020 19:25:27: 9000000 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 @ Sun, 21 Jun 2020 19:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.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 @ Sun, 21 Jun 2020 19:25:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:33: 5000000 INFO @ Sun, 21 Jun 2020 19:25:34: 10000000 INFO @ Sun, 21 Jun 2020 19:25:39: 1000000 INFO @ Sun, 21 Jun 2020 19:25:39: 6000000 INFO @ Sun, 21 Jun 2020 19:25:41: 11000000 INFO @ Sun, 21 Jun 2020 19:25:45: 7000000 INFO @ Sun, 21 Jun 2020 19:25:45: 2000000 INFO @ Sun, 21 Jun 2020 19:25:47: 12000000 INFO @ Sun, 21 Jun 2020 19:25:51: 8000000 INFO @ Sun, 21 Jun 2020 19:25:51: 3000000 INFO @ Sun, 21 Jun 2020 19:25:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:52: #1 total tags in treatment: 12690543 INFO @ Sun, 21 Jun 2020 19:25:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:25:52: #1 tags after filtering in treatment: 12690536 INFO @ Sun, 21 Jun 2020 19:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:53: #2 number of paired peaks: 234 WARNING @ Sun, 21 Jun 2020 19:25:53: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:53: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:25:53: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 21 Jun 2020 19:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05_model.r WARNING @ Sun, 21 Jun 2020 19:25:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:53: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 21 Jun 2020 19:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:25:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:57: 9000000 INFO @ Sun, 21 Jun 2020 19:25:57: 4000000 INFO @ Sun, 21 Jun 2020 19:26:03: 10000000 INFO @ Sun, 21 Jun 2020 19:26:03: 5000000 INFO @ Sun, 21 Jun 2020 19:26:09: 6000000 INFO @ Sun, 21 Jun 2020 19:26:09: 11000000 INFO @ Sun, 21 Jun 2020 19:26:15: 7000000 INFO @ Sun, 21 Jun 2020 19:26:15: 12000000 INFO @ Sun, 21 Jun 2020 19:26:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:20: #1 total tags in treatment: 12690543 INFO @ Sun, 21 Jun 2020 19:26:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:26:20: #1 tags after filtering in treatment: 12690536 INFO @ Sun, 21 Jun 2020 19:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:21: 8000000 INFO @ Sun, 21 Jun 2020 19:26:21: #2 number of paired peaks: 234 WARNING @ Sun, 21 Jun 2020 19:26:21: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:21: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:26:21: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 21 Jun 2020 19:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10_model.r WARNING @ Sun, 21 Jun 2020 19:26:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:21: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 21 Jun 2020 19:26:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:26:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:26: 9000000 INFO @ Sun, 21 Jun 2020 19:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:32: Done! INFO @ Sun, 21 Jun 2020 19:26:32: 10000000 pass1 - making usageList (549 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:38: 11000000 INFO @ Sun, 21 Jun 2020 19:26:43: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:47: #1 total tags in treatment: 12690543 INFO @ Sun, 21 Jun 2020 19:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:26:48: #1 tags after filtering in treatment: 12690536 INFO @ Sun, 21 Jun 2020 19:26:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:49: #2 number of paired peaks: 234 WARNING @ Sun, 21 Jun 2020 19:26:49: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:49: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:26:49: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 21 Jun 2020 19:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20_model.r WARNING @ Sun, 21 Jun 2020 19:26:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:49: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 21 Jun 2020 19:26:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:26:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.10_summits.bed INFO @ Sun, 21 Jun 2020 19:27:00: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288024/SRX288024.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:28: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 5 millis CompletedMACS2peakCalling