Job ID = 6454562 SRX = SRX2321785 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:19 prefetch.2.10.7: 1) Downloading 'SRR4841811'... 2020-06-21T09:00:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:01 prefetch.2.10.7: 1) 'SRR4841811' was downloaded successfully Read 30759933 spots for SRR4841811/SRR4841811.sra Written 30759933 spots for SRR4841811/SRR4841811.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: 00:06:28 30759933 reads; of these: 30759933 (100.00%) were unpaired; of these: 1997141 (6.49%) aligned 0 times 22675809 (73.72%) aligned exactly 1 time 6086983 (19.79%) aligned >1 times 93.51% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 5550693 / 28762792 = 0.1930 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 18:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.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 18:19:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:37: 1000000 INFO @ Sun, 21 Jun 2020 18:19:43: 2000000 INFO @ Sun, 21 Jun 2020 18:19:49: 3000000 INFO @ Sun, 21 Jun 2020 18:19:55: 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 18:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.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 18:20:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:02: 5000000 INFO @ Sun, 21 Jun 2020 18:20:07: 1000000 INFO @ Sun, 21 Jun 2020 18:20:08: 6000000 INFO @ Sun, 21 Jun 2020 18:20:13: 2000000 INFO @ Sun, 21 Jun 2020 18:20:15: 7000000 INFO @ Sun, 21 Jun 2020 18:20:20: 3000000 INFO @ Sun, 21 Jun 2020 18:20:22: 8000000 INFO @ Sun, 21 Jun 2020 18:20:26: 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 @ Sun, 21 Jun 2020 18:20:29: 9000000 INFO @ Sun, 21 Jun 2020 18:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.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 18:20:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:33: 5000000 INFO @ Sun, 21 Jun 2020 18:20:36: 10000000 INFO @ Sun, 21 Jun 2020 18:20:38: 1000000 INFO @ Sun, 21 Jun 2020 18:20:39: 6000000 INFO @ Sun, 21 Jun 2020 18:20:42: 11000000 INFO @ Sun, 21 Jun 2020 18:20:45: 2000000 INFO @ Sun, 21 Jun 2020 18:20:46: 7000000 INFO @ Sun, 21 Jun 2020 18:20:49: 12000000 INFO @ Sun, 21 Jun 2020 18:20:51: 3000000 INFO @ Sun, 21 Jun 2020 18:20:52: 8000000 INFO @ Sun, 21 Jun 2020 18:20:56: 13000000 INFO @ Sun, 21 Jun 2020 18:20:58: 4000000 INFO @ Sun, 21 Jun 2020 18:20:59: 9000000 INFO @ Sun, 21 Jun 2020 18:21:04: 14000000 INFO @ Sun, 21 Jun 2020 18:21:05: 5000000 INFO @ Sun, 21 Jun 2020 18:21:05: 10000000 INFO @ Sun, 21 Jun 2020 18:21:11: 15000000 INFO @ Sun, 21 Jun 2020 18:21:11: 11000000 INFO @ Sun, 21 Jun 2020 18:21:12: 6000000 INFO @ Sun, 21 Jun 2020 18:21:18: 16000000 INFO @ Sun, 21 Jun 2020 18:21:18: 12000000 INFO @ Sun, 21 Jun 2020 18:21:18: 7000000 INFO @ Sun, 21 Jun 2020 18:21:24: 17000000 INFO @ Sun, 21 Jun 2020 18:21:25: 13000000 INFO @ Sun, 21 Jun 2020 18:21:25: 8000000 INFO @ Sun, 21 Jun 2020 18:21:32: 18000000 INFO @ Sun, 21 Jun 2020 18:21:32: 14000000 INFO @ Sun, 21 Jun 2020 18:21:32: 9000000 INFO @ Sun, 21 Jun 2020 18:21:39: 10000000 INFO @ Sun, 21 Jun 2020 18:21:39: 15000000 INFO @ Sun, 21 Jun 2020 18:21:39: 19000000 INFO @ Sun, 21 Jun 2020 18:21:46: 11000000 INFO @ Sun, 21 Jun 2020 18:21:46: 16000000 INFO @ Sun, 21 Jun 2020 18:21:46: 20000000 INFO @ Sun, 21 Jun 2020 18:21:53: 17000000 INFO @ Sun, 21 Jun 2020 18:21:53: 12000000 INFO @ Sun, 21 Jun 2020 18:21:54: 21000000 INFO @ Sun, 21 Jun 2020 18:21:59: 18000000 INFO @ Sun, 21 Jun 2020 18:22:00: 13000000 INFO @ Sun, 21 Jun 2020 18:22:01: 22000000 INFO @ Sun, 21 Jun 2020 18:22:06: 19000000 INFO @ Sun, 21 Jun 2020 18:22:07: 14000000 INFO @ Sun, 21 Jun 2020 18:22:08: 23000000 INFO @ Sun, 21 Jun 2020 18:22:10: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:22:10: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:22:10: #1 total tags in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:22:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:10: #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 18:22:11: #1 tags after filtering in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:12: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 18:22:12: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:22:12: #2 alternative fragment length(s) may be 2,11,591 bps INFO @ Sun, 21 Jun 2020 18:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05_model.r WARNING @ Sun, 21 Jun 2020 18:22:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:12: #2 You may need to consider one of the other alternative d(s): 2,11,591 WARNING @ Sun, 21 Jun 2020 18:22:12: #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 18:22:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:13: 20000000 INFO @ Sun, 21 Jun 2020 18:22:13: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:22:19: 21000000 INFO @ Sun, 21 Jun 2020 18:22:20: 16000000 INFO @ Sun, 21 Jun 2020 18:22:26: 22000000 INFO @ Sun, 21 Jun 2020 18:22:27: 17000000 INFO @ Sun, 21 Jun 2020 18:22:33: 23000000 INFO @ Sun, 21 Jun 2020 18:22:34: 18000000 INFO @ Sun, 21 Jun 2020 18:22:34: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:22:34: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:22:34: #1 total tags in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:22:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:34: #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 18:22:35: #1 tags after filtering in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:37: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 18:22:37: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:37: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:22:37: #2 alternative fragment length(s) may be 2,11,591 bps INFO @ Sun, 21 Jun 2020 18:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10_model.r WARNING @ Sun, 21 Jun 2020 18:22:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:37: #2 You may need to consider one of the other alternative d(s): 2,11,591 WARNING @ Sun, 21 Jun 2020 18:22:37: #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 18:22:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:41: 19000000 INFO @ Sun, 21 Jun 2020 18:22:48: 20000000 INFO @ Sun, 21 Jun 2020 18:22:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:54: 21000000 INFO @ Sun, 21 Jun 2020 18:23:01: 22000000 INFO @ Sun, 21 Jun 2020 18:23:08: 23000000 INFO @ Sun, 21 Jun 2020 18:23:09: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:23:09: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:23:09: #1 total tags in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:23:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:09: #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 18:23:10: #1 tags after filtering in treatment: 23212099 INFO @ Sun, 21 Jun 2020 18:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:11: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 18:23:11: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:23:12: #2 alternative fragment length(s) may be 2,11,591 bps INFO @ Sun, 21 Jun 2020 18:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20_model.r WARNING @ Sun, 21 Jun 2020 18:23:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:12: #2 You may need to consider one of the other alternative d(s): 2,11,591 WARNING @ Sun, 21 Jun 2020 18:23:12: #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 18:23:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:15: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:40: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321785/SRX2321785.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling